GMODWeb: a web framework for the generic model organism database

ABSTRACT: The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of Model Organism Database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from http://turnkey.sourceforge.net

Framework and tool for rapid assessment of stream susceptibility to hydromodification

ABSTRACT: Changes in streamflow and sediment loading associated with urban development have the potential to exacerbate channel erosion, and result in impacts to wetland, riparian, and stream habitats, as well as infrastructure and property losses. The typical ''one-size-fits-all'' management prescription of flow control with retention or detention basins has not been wholly effective, pointing to a need for improved management strategies and tools for mitigating the impacts of ''hydromodification.'' We present an approach for developing screeninglevel tools for assessing channel susceptibility to hydromodification, and describe a novel tool for rapid, fieldbased assessments of the relative susceptibility of stream segments. The tool is based on the results of extensive field surveys, which indicate that susceptibility is the driver of channel response, not the magnitude of urbanization. A combination of relatively simple, but quantitative, field indicators are used as input parameters for a set of decision trees that follow a logical progression in assigning categorical susceptibility ratings to the channel segment being assessed. The susceptibility rating informs the level of data collection, modeling, and ultimate mitigation efforts that can be expected for a particular stream segment type. The screening approach represents a critical first step toward tailoring hydromodification management strategies and mitigation measures to different stream types and geomorphic settings

Essential Role for endogenous siRNAs during meiosis in mouse oocytes.

The RNase III enzyme DICER generates both microRNAs (miRNAs) and endogenous short interfering RNAs (endo-siRNAs). Both small RNA species silence gene expression post-transcriptionally in association with the ARGONAUTE (AGO) family of proteins. In mammals, there are four AGO proteins (AGO1-4), of which only AGO2 possesses endonucleolytic activity. siRNAs trigger endonucleolytic cleavage of target mRNAs, mediated by AGO2, whereas miRNAs cause translational repression and mRNA decay through association with any of the four AGO proteins. Dicer deletion in mouse oocytes leads to female infertility due to defects during meiosis I. Because mouse oocytes express both miRNAs and endo-siRNAs, this phenotype could be due to the absence of either class of small RNA, or both. However, we and others demonstrated that miRNA function is suppressed in mouse oocytes, which suggested that endo-siRNAs, not miRNAs, are essential for female meiosis. To determine if this was the case we generated mice that express a catalytically inactive knock-in allele of Ago2 (Ago2ADH) exclusively in oocytes and thereby disrupted the function of siRNAs. Oogenesis and hormonal response are normal in Ago2ADH oocytes, but meiotic maturation is impaired, with severe defects in spindle formation and chromosome alignment that lead to meiotic catastrophe. The transcriptome of these oocytes is widely perturbed and shows a highly significant correlation with the transcriptome of Dicer null and Ago2 null oocytes. Expression of the mouse transcript (MT), the most abundant transposable element in mouse oocytes, is increased. This study reveals that endo-siRNAs are essential during meiosis I in mouse females, demonstrating a role for endo-siRNAs in mammals.This research was supported by the National Institutes of Health Grants HD022681 (to RMS), and R37 GM062534-14 (to GJH), National Human Genome Research Institute 5T32HG000046-13 (to FL) and by a kind gift from Kathryn W. Davis. GJH is an investigator of the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.This is the final version of the article. It first appeared from PLoS via http://dx.doi.org/10.1371/journal.pgen.100501

LDL-cholesterol lowering and clinical outcomes in hypercholesterolemic subjects with and without a familial hypercholesterolemia phenotype: Analysis from the secondary prevention 4S trial

Background and aims: Trial evidence for the benefits of cholesterol-lowering is limited for familial hypercho lesterolemia (FH) patients, since they have not been the focus of large outcome trials. We assess statin use in coronary artery disease (CAD) subjects with low-density lipoprotein cholesterol (LDL-C) ≥4.9 mmol/L with or without an FH phenotype. Methods: The 4S trial randomized hypercholesterolemic CAD patients to simvastatin or placebo. We first strat ified participants into baseline LDL-C <4.9 and ≥ 4.9 mmol/L; next, based on the DLCN criteria for FH, the latter group was stratified into four subgroups by presence of none, one or both of “premature CAD” and “family history of CAD”. Participants having both are defined as having an FH phenotype. Results: 2267 and 2164 participants had LDL-C <4.9 and ≥ 4.9 mmol/L, respectively. Mortality endpoints and major coronary events (MCE) were significantly reduced with simvastatin versus placebo in both groups over 5.4 years, but the latter derived greater absolute risk reductions (ARR) (4.1–4.3% for mortality endpoints, versus 2.5–2.8%). LDL-C reductions were similar among the 4 subgroups with levels ≥4.9 mmol/L. Participants with FH phenotype (n = 152) appeared to derive greater relative benefits with simvastatin than the other three subgroups (all-cause death: 84% relative risk reduction, p = 0.046; MCE: 55% reduction, p = 0.0297); statistical interaction was non significant. Participants with FH phenotype derived greater ARR than any other group with simvastatin versus placebo (all-cause mortality: 6.6% ARR; MCE 13.2%; versus 3.8% and 8.3%, respectively, among participants with LDL-C ≥4.9 mmol/L but without features suggestive of FH). Conclusions: The FH phenotype appeared to be associated with greater clinical benefits from a given magnitude of LDL-C reduction as compared to individuals without FH phenotype

Gas phase characterization of the noncovalent quaternary structure of Cholera toxin and the Cholera toxin B subunit pentamer

Cholera toxin (CTx) is an AB5 cytotonic protein that has medical relevance in cholera and as a novel mucosal adjuvant. Here, we report an analysis of the noncovalent homopentameric complex of CTx B chain (CTx B5) using electrospray ionization triple quadrupole mass spectrometry and tandem mass spectrometry and the analysis of the noncovalent hexameric holotoxin usingelectrospray ionization time-of-flight mass spectrometry over a range of pH values that correlate with those encountered by this toxin after cellular uptake. We show that noncovalent interactions within the toxin assemblies were maintained under both acidic and neutral conditions in the gas phase. However, unlike the related Escherichia coli Shiga-like toxin B5 pentamer (SLTx B), the CTx B5 pentamer was stable at low pH, indicating that additional interactions must be present within the latter. Structural comparison of the CTx B monomer interface reveals an additional α-helix that is absent in the SLTx B monomer. In silico energy calculations support interactions between this helix and the adjacent monomer. These data provide insight into the apparent stabilization of CTx B relative to SLTx B

DIYA: a bacterial annotation pipeline for any genomics lab

Summary:DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. The software is currently used to take DNA contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in Genbank file format as output

Treatments used for obsessive-compulsive disorder-An international perspective

© 2019 John Wiley & Sons, Ltd.OBJECTIVE: The objective of this study was to characterise international trends in the use of psychotropic medication, psychological therapies, and novel therapies used to treat obsessive-compulsive disorder (OCD). METHODS: Researchers in the field of OCD were invited to contribute summary statistics on the characteristics of their samples. Consistency of summary statistics across countries was evaluated. RESULTS: The study surveyed 19 expert centres from 15 countries (Argentina, Australia, Brazil, China, Germany, Greece, India, Italy, Japan, Mexico, Portugal, South Africa, Spain, the United Kingdom, and the United States) providing a total sample of 7,340 participants. Fluoxetine (n = 972; 13.2%) and fluvoxamine (n = 913; 12.4%) were the most commonly used selective serotonin reuptake inhibitor medications. Risperidone (n = 428; 7.3%) and aripiprazole (n = 415; 7.1%) were the most commonly used antipsychotic agents. Neurostimulation techniques such as transcranial magnetic stimulation, deep brain stimulation, gamma knife surgery, and psychosurgery were used in less than 1% of the sample. There was significant variation in the use and accessibility of exposure and response prevention for OCD. CONCLUSIONS: The variation between countries in treatments used for OCD needs further evaluation. Exposure and response prevention is not used as frequently as guidelines suggest and appears difficult to access in most countries. Updated treatment guidelines are recommended.Peer reviewe

Use of ZDR columns for early detection of severe convection within the operational radar network of the United Kingdom

Differential reflectivity () columns were observed using a Met Office three‐dimensional radar composite. An algorithm for automatic detection of columns was developed, based on dB and dBZ. Across three case days, detected columns were found to precede severe convection in tracked convective cells with a range of lead times from 0 to 20 min depending on the case day. Requiring maxima above 1.4 dB and 30 dBZ of and respectively was an appropriate second condition for all three cases although the skill in the early detection of severe convection varied across case days. Despite the high probability of detections, the high false alarm rate accompanied by low critical success index and data latency limit performance based on the three cases considered in this study. Nevertheless, the ability to detect columns in operational radar data with a useful lead time prior to severe convection in certain conditions is a promising development towards advancing nowcasting of severe convection in the United Kingdom

Investigation of transverse collective flow of intermediate mass fragments

The transverse flow of intermediate mass fragments (IMFs) has been investigated for the 35 MeV/u ${}^{70}\mathrm{Zn}+{}^{70}\mathrm{Zn}$, ${}^{64}\mathrm{Zn}+{}^{64}\mathrm{Zn}$, and ${}^{64}\mathrm{Ni}+{}^{64}\mathrm{Ni}$ systems. A transition from the IMF transverse flow strongly depending on the mass of the system, in the most violent collisions, to a dependence on the charge of the system, for the peripheral reactions, is shown. This transition was shown to be sensitive to the density dependence of the symmetry energy using the antisymmetrized molecular-dynamics model. The results present an observable, the IMF transverse flow, that can be used to probe the nuclear equation of state. Comparison with the simulation demonstrated a preference for a stiff density dependence of the symmetry energy