A user-friendly decision support tool to assist one-health risk assessors.
Ontology highlight
ABSTRACT:
SUBMITTER: Dewar R
PROVIDER: S-EPMC8141943 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundMicroarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic.ResultsWe have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation.ConclusionSimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from http://www.flychip.org.uk/SimArray/.
| S-EPMC1456992 | biostudies-literature
Project description:Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at http://clusterflow.io.
| S-EPMC5310375 | biostudies-literature
Project description:BackgroundWith the increasing pace of new Genetically Modified Organisms (GMOs) authorized or in pipeline for commercialization worldwide, the task of the laboratories in charge to test the compliance of food, feed or seed samples with their relevant regulations became difficult and costly. Many of them have already adopted the so called "matrix approach" to rationalize the resources and efforts used to increase their efficiency within a limited budget. Most of the time, the "matrix approach" is implemented using limited information and some proprietary (if any) computational tool to efficiently use the available data.ResultsThe developed GMOseek software is designed to support decision making in all the phases of routine GMO laboratory testing, including the interpretation of wet-lab results. The tool makes use of a tabulated matrix of GM events and their genetic elements, of the laboratory analysis history and the available information about the sample at hand. The tool uses an optimization approach to suggest the most suited screening assays for the given sample. The practical GMOseek user interface allows the user to customize the search for a cost-efficient combination of screening assays to be employed on a given sample. It further guides the user to select appropriate analyses to determine the presence of individual GM events in the analyzed sample, and it helps taking a final decision regarding the GMO composition in the sample. GMOseek can also be used to evaluate new, previously unused GMO screening targets and to estimate the profitability of developing new GMO screening methods.ConclusionThe presented freely available software tool offers the GMO testing laboratories the possibility to select combinations of assays (e.g. quantitative real-time PCR tests) needed for their task, by allowing the expert to express his/her preferences in terms of multiplexing and cost. The utility of GMOseek is exemplified by analyzing selected food, feed and seed samples from a national reference laboratory for GMO testing and by comparing its performance to existing tools which use the matrix approach. GMOseek proves superior when tested on real samples in terms of GMO coverage and cost efficiency of its screening strategies, including its capacity of simple interpretation of the testing results.
| S-EPMC4138379 | biostudies-literature
Project description:This study investigated the use of Bayesian Networks (BNs) for left ventricular assist device (LVAD) therapy; a treatment for end-stage heart failure that has been steadily growing in popularity over the past decade. Despite this growth, the number of LVAD implants performed annually remains a small fraction of the estimated population of patients who might benefit from this treatment. We believe that this demonstrates a need for an accurate stratification tool that can help identify LVAD candidates at the most appropriate point in the course of their disease. We derived BNs to predict mortality at five endpoints utilizing the Interagency Registry for Mechanically Assisted Circulatory Support (INTERMACS) database: containing over 12,000 total enrolled patients from 153 hospital sites, collected since 2006 to the present day, and consisting of approximately 230 pre-implant clinical variables. Synthetic minority oversampling technique (SMOTE) was employed to address the uneven proportion of patients with negative outcomes and to improve the performance of the models. The resulting accuracy and area under the ROC curve (%) for predicted mortality were 30 day: 94.9 and 92.5; 90 day: 84.2 and 73.9; 6 month: 78.2 and 70.6; 1 year: 73.1 and 70.6; and 2 years: 71.4 and 70.8. To foster the translation of these models to clinical practice, they have been incorporated into a web-based application, the Cardiac Health Risk Stratification System (CHRiSS). As clinical experience with LVAD therapy continues to grow, and additional data is collected, we aim to continually update these BN models to improve their accuracy and maintain their relevance. Ongoing work also aims to extend the BN models to predict the risk of adverse events post-LVAD implant as additional factors for consideration in decision making.
| S-EPMC4232308 | biostudies-literature
Project description:ObjectiveThe objective of this qualitative study is to gauge physician sentiment about an emergency department (ED) clinical decision support (CDS) system implemented in multiple adult EDs within a university hospital system. This CDS system focuses on predicting patients' likelihood of ED recidivism and/or adverse opioid-related events.MethodsThe study was conducted among adult emergency physicians working in three EDs of a single academic health system in Rhode Island. Qualitative, semistructured interviews were conducted with ED physicians. Interviews assessed physicians' prior experience with predictive analytics, thoughts on the alert's placement, design, and content, the alert's overall impact, and potential areas for improvement. Responses were aggregated and common themes identified.ResultsTwenty-three interviews were conducted (11 preimplementation and 12 postimplementation). Themes were identified regarding each physician familiarity with predictive analytics, alert rollout, alert appearance and content, and on alert sentiments. Most physicians viewed these alerts as a neutral or positive EHR addition, with responses ranging from neutral to positive. The alert placement was noted to be largely intuitive and nonintrusive. The design of the alert was generally viewed positively. The alert's content was believed to be accurate, although the decision to respond to the alert's call-to-action was physician dependent. Those who tended to ignore the alert did so for a few reasons, including already knowing the information the alert contains, the alert offering information that is not relevant to this particular patient, and the alert not containing enough information to be useful.ConclusionUltimately, this alert appears to have a marginally positive effect on ED physician workflow. At its most beneficial, the alert reminded physicians to deeply consider the care provided to high-risk populations and to potentially adjust their care and referrals. At its least beneficial, the alert did not affect physician decision-making but was not intrusive to the point of negatively impacting workflow.
| S-EPMC10482498 | biostudies-literature
Project description:Careful design of experiments using living organisms (e.g. mice) is of critical importance from both an ethical and a scientific standpoint. Randomization should, whenever possible, be an integral part of such experimental design to reduce bias thereby increasing its reliability and reproducibility. To keep the sample size as low as possible, one might take randomization one step further by controlling for baseline variations in the dependent variable(s) and/or certain known covariates. To give an example, in animal experiments aimed to study atherosclerosis development, one would want to control for baseline characteristics such as plasma triglyceride and total cholesterol levels and body weight. This can be done by first defining blocks to create balance among groups in terms of group size and baseline characteristics, followed by random assignment of the blocks to the various control and intervention groups. In the current study we developed a novel, user-friendly tool that allows users to easily randomize animals into blocks and identify random block divisions that are well-balanced based on given baseline characteristics, making randomization time-efficient and easy-to-use. Here, we present the resulting software tool that we have named RandoMice.
| S-EPMC7406044 | biostudies-literature
Project description:BackgroundIndividualized selection of antiretroviral (ARV) therapy is complex, considering drug resistance, comorbidities, drug-drug interactions, and other factors. HIV-ASSIST (www.hivassist.com) is a free, online tool that provides ARV decision support. HIV-ASSIST synthesizes patient and virus-specific attributes to rank ARV combinations based upon a composite objective of achieving viral suppression and maximizing tolerability.ObjectiveTo evaluate concordance of HIV-ASSIST recommendations with ARV selections of experienced HIV clinicians.DesignRetrospective cohort study.PatientsNew and established patients at the Johns Hopkins Bartlett HIV Clinic and San Francisco Veterans Affairs HIV Clinic completing clinic visits were included. Chart reviews were conducted of the most recent clinic visit to generate HIV-ASSIST recommendations, which were compared to prescribed regimens.Main measuresFor each provider-prescribed regimen, we assessed its corresponding HIV-ASSIST "weighted score" (scale of 0 to 10 +, scores of < 2.0 are preferred), rank within HIV-ASSIST's ordered listing of ARV regimens, and concordance with the top five HIV-ASSIST ranked outputs.Key resultsAmong 106 patients (16% female), 23 (22%) were ARV-naïve. HIV-ASSIST outputs for ARV-naïve patients were 100% concordant with prescribed regimens (median rank 1 [IQR 1-3], median weighted score 1.1 [IQR 1-1.2]). For 18 (17%) ARV-experienced patients with ongoing viremia, HIV-ASSIST outputs were 89% concordant with prescribed regimens (median rank 2 [IQR 1-3], median weighted score 1 [IQR 1-1.2]). For 65 (61.3%) patients that were suppressed on a current ARV regimen, HIV-ASSIST recommendations were concordant 88% of the time (median rank 1 [IQR 1-1], median weighted score 1.1 [IQR 1-1.6]). In 18% of cases, HIV-ASSIST weighted score suggested that the prescribed regimen would be considered "less preferred" (score > 2.0) than other available alternatives.ConclusionHIV-ASSIST is an educational decision support tool that provides ARV recommendations concordant with experienced HIV providers from two major academic centers for a diverse set of patient scenarios.
| S-EPMC7210320 | biostudies-literature
Project description:BackgroundPromising health interventions tested in pilot studies will only achieve population-wide impact if they are implemented at scale across communities and health systems. Scaling up effective health interventions is vital as not doing so denies the community the most effective services and programmes. However, there remains a paucity of practical tools to assess the suitability of health interventions for scale-up. The Intervention Scalability Assessment Tool (ISAT) was developed to support policy-makers and practitioners to make systematic assessments of the suitability of health interventions for scale-up.MethodsThe ISAT was developed over three stages; the first stage involved a literature review to identify similar tools and frameworks that could be used to guide scalability assessments, and expert input to develop draft ISAT content. In the second stage, the draft ISAT tool was tested with end users. The third stage involved revising and re-testing the ISAT with end users to further refine the language and structure of the final ISAT.ResultsA variety of information and sources of evidence should be used to complete the ISAT. The ISAT consists of three parts. Part A: 'setting the scene' requires consideration of the context in which the intervention is being considered for scale-up and consists of five domains, as follows: (1) the problem; (2) the intervention; (3) strategic/political context; (4) evidence of effectiveness; and (5) intervention costs and benefits. Part B asks users to assess the potential implementation and scale-up requirements within five domains, namely (1) fidelity and adaptation; (2) reach and acceptability; (3) delivery setting and workforce; (4) implementation infrastructure; and (5) sustainability. Part C generates a graphical representation of the strengths and weaknesses of the readiness of the proposed intervention for scale-up. Users are also prompted for a recommendation as to whether the intervention (1) is recommended for scale-up, (2) is promising but needs further information before scaling up, or (3) does not yet merit scale-up.ConclusionThe ISAT fills an important gap in applied scalability assessment and can become a critical decision support tool for policy-makers and practitioners when selecting health interventions for scale-up. Although the ISAT is designed to be a health policy and practitioner tool, it can also be used by researchers in the design of research to fill important evidence gaps.
| S-EPMC6942323 | biostudies-literature
Project description:Although infection by the pathogenic bacterium Listeria monocytogenes is relatively rare, consequences can be severe, with a high case-fatality rate in vulnerable populations. A quantitative, probabilistic risk assessment tool was developed to compare estimates of the number of invasive listeriosis cases in vulnerable Canadian subpopulations given consumption of contaminated ready-to-eat delicatessen meats and hot dogs, under various user-defined scenarios. The model incorporates variability and uncertainty through Monte Carlo simulation. Processes considered within the model include cross-contamination, growth, risk factor prevalence, subpopulation susceptibilities, and thermal inactivation. Hypothetical contamination events were simulated. Results demonstrated varying risk depending on the consumer risk factors and implicated product (turkey delicatessen meat without growth inhibitors ranked highest for this scenario). The majority (80%) of listeriosis cases were predicted in at-risk subpopulations comprising only 20% of the total Canadian population, with the greatest number of predicted cases in the subpopulation with dialysis and/or liver disease. This tool can be used to simulate conditions and outcomes under different scenarios, such as a contamination event and/or outbreak, to inform public health interventions.
| S-EPMC9150414 | biostudies-literature
Project description:Single-cell and single-molecule measurements indicate the importance of stochastic phenomena in cell biology. Stochasticity creates spontaneous differences in the copy numbers of key macromolecules and the timing of reaction events between genetically-identical cells. Mathematical models are indispensable for the study of phenotypic stochasticity in cellular decision-making and cell survival. There is a demand for versatile, stochastic modeling environments with extensive, preprogrammed statistics functions and plotting capabilities that hide the mathematics from the novice users and offers low-level programming access to the experienced user. Here we present StochPy (Stochastic modeling in Python), which is a flexible software tool for stochastic simulation in cell biology. It provides various stochastic simulation algorithms, SBML support, analyses of the probability distributions of molecule copy numbers and event waiting times, analyses of stochastic time series, and a range of additional statistical functions and plotting facilities for stochastic simulations. We illustrate the functionality of StochPy with stochastic models of gene expression, cell division, and single-molecule enzyme kinetics. StochPy has been successfully tested against the SBML stochastic test suite, passing all tests. StochPy is a comprehensive software package for stochastic simulation of the molecular control networks of living cells. It allows novice and experienced users to study stochastic phenomena in cell biology. The integration with other Python software makes StochPy both a user-friendly and easily extendible simulation tool.
| S-EPMC3832486 | biostudies-literature