COSMOS: Python library for massively parallel workflows

Summary: Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Availability and implementation: Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. Contact: [email protected] or [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online

Measuring patient-perceived quality of care in US hospitals using Twitter

ABSTRACT Background Patients routinely use Twitter to share feedback about their experience receiving healthcare. Identifying and analysing the content of posts sent to hospitals may provide a novel real-time measure of quality, supplementing traditional, survey-based approaches. Objective To assess the use of Twitter as a supplemental data stream for measuring patientperceived quality of care in US hospitals and compare patient sentiments about hospitals with established quality measures. Design 404 065 tweets directed to 2349 US hospitals over a 1-year period were classified as having to do with patient experience using a machine learning approach. Sentiment was calculated for these tweets using natural language processing. 11 602 tweets were manually categorised into patient experience topics. Finally, hospitals with ≥50 patient experience tweets were surveyed to understand how they use Twitter to interact with patients. Key results Roughly half of the hospitals in the US have a presence on Twitter. Of the tweets directed toward these hospitals, 34 725 (9.4%) were related to patient experience and covered diverse topics. Analyses limited to hospitals with ≥50 patient experience tweets revealed that they were more active on Twitter, more likely to be below the national median of Medicare patients ( p<0.001) and above the national median for nurse/patient ratio ( p=0.006), and to be a nonprofit hospital ( p<0.001). After adjusting for hospital characteristics, we found that Twitter sentiment was not associated with Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) ratings (but having a Twitter account was), although there was a weak association with 30-day hospital readmission rates ( p=0.003). Conclusions Tweets describing patient experiences in hospitals cover a wide range of patient care aspects and can be identified using automated approaches. These tweets represen

Evaluating the Implementation of a Twitter-Based Foodborne Illness Reporting Tool in the City of St. Louis Department of Health

Foodborne illness is a serious and preventable public health problem affecting 1 in 6 Americans with cost estimates over $50 billion annually. Local health departments license and inspect restaurants to ensure food safety and respond to reports of suspected foodborne illness. The City of St. Louis Department of Health adopted the HealthMap Foodborne Dashboard (Dashboard), a tool that monitors Twitter for tweets about food poisoning in a geographic area and allows the health department to respond. We evaluated the implementation by interviewing employees of the City of St. Louis Department of Health involved in food safety. We interviewed epidemiologists, environmental health specialists, health services specialists, food inspectors, and public information officers. Participants viewed engaging innovation participants and executing the innovation as challenges while they felt the Dashboard had relative advantage over existing reporting methods and was not complex once in place. This study is the first to examine practitioner perceptions of the implementation of a new technology in a local health department. Similar implementation projects should focus more on process by developing clear and comprehensive plans to educate and involve stakeholders prior to implementation

Analysis of changing statistical significance from .05 to .005 in foot and ankle randomized controlled trials

Background: Misinterpretation of p-values in RCTs is extremely problematic since they are the core basis for high levels of recommendation in clinical practice guidelines, especially Orthopaedics. Benjamin et al. proposed a universal protocol change, moving statistical significance from a p-value of .05 to .005 to combat the misinterpretation that is happening in medical literature. In this study, we are looking to evaluate the effect of the protocol suggested by Benjamin et al. on foot and ankle-related RCTs in the top 3 Foot and Ankle-related journals.Methods: We conducted a Pubmed search looking at studies published from January 1st, 2016 to November 10, 2021, in the following three journals; Foot and Ankle International, Journal of Foot and Ankle Surgery, and Foot & Ankle International. The inclusion criteria for the study were RCTs published in the above journals with specifically stated primary endpoints. If a study has multiple primary endpoints, all were included. Exclusion criteria were any study that was not prospective and randomized by design, also any study that did not state primary endpoints was excluded. Two authors extracted the data using a pilot-tested Google form, any disagreements or questions were resolved by published methodologic orthopaedic authors.Results: Of the 222 endpoints, 101 endpoints (45.5%; 101/222) were at or below the .05 threshold while 121 endpoints (54.5%; 121/222) were above the .05 threshold. We also found that 59 endpoints (26.6%; 59/222) were below .005.Conclusion: Our results suggest that changing the threshold for statistical significance from .05 to .005 in foot and ankle RCTs would heavily alter literature published in the field. By implementing this methodology, it is a promising measure to be able to increase RCT quality until a more substantial solution can be found. With that being said, caution must be taken when interpreting our results, also requiring further evaluation

Data curation during a pandemic and lessons learned from COVID-19

Detailed, accurate data related to a disease outbreak enable informed public health decision making. Given the variety of data types available across different regions, global data curation and standardization efforts are essential to guarantee rapid data integration and dissemination in times of a pandemic.Data availability The underlying dataset for Fig. 1a is available open access from the supplemental material in ref. 5, and datasets for Fig. 1b,c from the UNESCO World Heritage List 2021 in ref. 32.https://www.nature.com/natcomputscihj2023Computer Scienc

A Simple, Inexpensive Device for Nucleic Acid Amplification without Electricity—Toward Instrument-Free Molecular Diagnostics in Low-Resource Settings

Molecular assays targeted to nucleic acid (NA) markers are becoming increasingly important to medical diagnostics. However, these are typically confined to wealthy, developed countries; or, to the national reference laboratories of developing-world countries. There are many infectious diseases that are endemic in low-resource settings (LRS) where the lack of simple, instrument-free, NA diagnostic tests is a critical barrier to timely treatment. One of the primary barriers to the practicality and availability of NA assays in LRS has been the complexity and power requirements of polymerase chain reaction (PCR) instrumentation (another is sample preparation).In this article, we investigate the hypothesis that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays. We assess the heater's equivalence to commercially available PCR instruments through the characterization of the temperature profiles produced, and a minimal method comparison. Versions of the prototype for several different isothermal techniques are presented.We demonstrate that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays, and that the results of those assays are not significantly different from ones incubated in parallel in commercially available PCR instruments. These results clearly suggest the potential of the non-instrumented nucleic acid amplification (NINA) heater for molecular diagnostics in LRS. When combined with other innovations in development that eliminate power requirements for sample preparation, cold reagent storage, and readout, the NINA heater will comprise part of a kit that should enable electricity-free NA testing for many important analytes

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC

Measurements are presented of production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs, H →γ γ, H → Z Z∗ →4l and H →W W∗ →lνlν. The results are based on the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV, corresponding to an integrated luminosity of about 25 fb−1. Evidence for Higgs boson production through vector-boson fusion is reported. Results of combined fits probing Higgs boson couplings to fermions and bosons, as well as anomalous contributions to loop-induced production and decay modes, are presented. All measurements are consistent with expectations for the Standard Model Higgs boson