2671 research outputs found
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Data for "Checklist and guidance on creating codelists for electronic health records research"
No full textData, collection tools, and processing scripts associated with the manuscript, "Checklist and guidance on creating codelists for electronic health records research"
Kinetic properties of the recombinantly expressed PfPKGWT, PfPKGY214, PfPKGSTmut, PfPKGT695A, PfPKGT695E and CD analysis of PfPKGWT and PfPKGSTmut
No full textDataset showing the kinetic properties of the recombinantly expressed PfPKGWT, PfPKGY214, PfPKGSTmut, PfPKGT695A, PfPKGT695E and CD analysis of PfPKGWT and PfPKGSTmut for: "Activation loop phosphorylation and cGMP saturation of PKG regulate egress of malaria parasites"
Phosphoproteome analyses of PKG_GFP, PKG_T695A and PKG_T695E in P. falciparum schizonts
No full textDataset showing phosphoproteome analyses of PKG_GFP, PKG_T695A and PKG_T695E in P. falciparum schizonts for: "Activation loop phosphorylation and cGMP saturation of PKG regulate egress of malaria parasites"
Dynamics of SARS-CoV-2 infection over two epidemic waves in Manaus, Brazil: a serological study of seven thousand blood donors
No full textMost longitudinal studies of COVID-19 incidence have used unlinked samples. The city of Manaus, Brazil, has a blood donation program which allows sample linkage, and was struck by two large COVID-19 epidemic waves between mid-2020 and early 2021. We estimated the changing force of infection, i.e. incidence in susceptible individuals. Seroconversion was inferred by a mixture model for serial values from the Abbott Architect SARS-CoV-2 nucleocapsid (N) IgG assay. We estimated the number of suspected COVID-19 hospitalizations arising from each infection over calendar time. Whole blood donations between April 2020 and March 2021 were included from 6734 people, 2747 with two or more donations. The inferred criterion for seroconversion, and thus an incident infection, was a 6.07 fold increase in N IgG reactivity. The overall force of infection was 1.19 per person year (95% confidence interval 1.14-1.24) during the two main waves. The estimated number of suspected hospitalizations per infection, was approximately 4.1 times higher in the second wave than in the first. Serial values from this assay can be used to infer seroconversion over time, and in Manaus show a higher number of suspected COVID-19 hospitalizations per infection in the second wave relative to the first
Data file for Are migrant workers at greater risk of workplace deaths? A systematic review and meta-analysis of mortality risks and social determinants among migrant workers
No full textThis is the data file for the manuscript titled "Are migrant workers at greater risk of workplace deaths? A systematic review and meta-analysis of mortality risks and social determinants among migrant workers". The study is a systematic review and meta-analysis of peer-reviewed literature to examine mortality outcomes among migrant workers and associated risk factors. Studies published between 1 January 2000 to 17 January 2023 in English language were searched in MEDLINE, Embase, PsycINFO, and Ovid Global Health. The registered protocol is available at PROSPERO: https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=372893
Impact of commercial gut health interventions on caecal metagenome and broiler performance
No full textMaintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores as control against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use. Using a binning strategy, 84 (≥75% completeness, ≤ 5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n = 52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European Poultry Efficiency Factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of Probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected abundance of microbial enzymes relating to carbohydrate and protein digestion, and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria including Rikenella microfusus and UBA7160 species. All GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health
BonoboFlow: Streamlined Viral Genome Assembly and Haplotype Reconstruction from Nanopore Reads
No full textViral genome analysis is crucial for understanding global virus diversity. Traditional methods are labor-intensive and unsuitable for large-scale studies, while next-generation sequencing faces challenges with genome fragmentation. Third-generation sequencing, like Oxford Nanopore (ONT), offers long reads but has high error rates. Our Nextflow pipeline, BonoboFlow, addresses these issues by standardizing error correction, genome assembly, and haplotype reconstruction, improving the accuracy and efficiency of viral genome analysis
Multimodal mucosal and systemic immune characterization of a non-human primate trachoma model highlights the critical role of local immunity during acute phase disease
No full textThis dataset contains results characterizing our model of trachoma (non-human primate). Those results comprise clinical scoring to assess the clinical signs, bacterial quantification to assess the conjunctival infection by Chlamydia trachomatis, as well as local and systemic immune assessment (conjunctival immune population with flow cytometry, immunoglobulin, and cytokines quantifications). Results are organized by type of data, each data type in a different folder. Clinical scoring is compiled in a single Excel file of clinical scoring results (on a scale of 0 to 8 for total scoring, 0 to 3 for inflammation score, and 0 to 5 for follicles score). Bacterial loads of conjunctival Chlamydia trachomatis are compiled in a single Excel file with qPCR results expressed in equivalent copies of IFU (inclusion forming unit) per µL. Flow cytometry results are put as FCS files raw from any analysis with a separate folder for each timepoint and a different folder for compensation files. Each animal is a different FCS file. Cytokine quantifications are compiled in a single Excel file. Each cytokine is expressed in pg per µL. Immunoglobulin quantifications are compiled in a single Excel file and expressed in titers. For every Excel file, cells were left blank when the data wasn't available
cleanepi: Clean and Standardize Epidemiological Data
No full textCleaning and standardizing tabular data package, tailored specifically for curating epidemiological data. It streamlines various data cleaning tasks that are typically expected when working with datasets in epidemiology. It returns the processed data in the same format, ensuring seamless integration into existing workflows. Additionally, it generates a comprehensive report detailing the outcomes of each cleaning task
Women’s subsistence strategies predict fertility across cultures, but context matters
No full textAnonymized dataset for: "Women’s subsistence strategies predict fertility across cultures, but context matters.