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2,489 results for “SARS-CoV-2”
Training data for 'Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads' tutorial (Galaxy Training Material)
<p>The data here is a copy of the corresponding SRR records in the NCBI SRA. The duplication serves a dual purpose:</p> <ol> <li>as a backup should there be problems connecting to NCBI servers, e.g., during Galaxy user trainings.</li> <li>to illustrate how to obtain raw sequencing data from alternative sources, and to organize the data into the same collection structure in a Galaxy history that is generated by specialized Galaxy SRA download tools.</li> </ol>
The airborne lifetime of small speech droplets and their potential importance to SARS-CoV-2 transmission
<p> Movies that show the experimental setup and the full 85-minute observation of speech droplet nuclei.</p> <p> </p> <p>The full movie recording of highly sensitive laser light scattering observations that indicate loud-speaking generates, in addition to hundreds of regular droplets, also many thousands of micro-droplets per second. This movie clip shows the decay of airborne particles.</p> <p> </p> <p>Note: some parts of the audio of the clips were muted for privacy.</p>
Haruspex Analysis for SARS-CoV-2 rna_polymerase-nsp7-nsp8 pdb entry 7bv1 emdb 30209
<p>Haruspex (version 1.0 190116) analysis for SARS-CoV-2 rna_polymerase-nsp7-nsp8 , pdb entry 7bv1 , emdb 30209. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421</p>
Haruspex Analysis for SARS-CoV-2 surface_glycoprotein pdb entry 6m17 emdb 30039
<p>Haruspex (version 1.0 190116) analysis for SARS-CoV-2 surface_glycoprotein , pdb entry 6m17 , emdb 30039. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421</p>
Haruspex Analysis for SARS-CoV-2 surface_glycoprotein pdb entry 6vsj emdb 21377
<p>Haruspex (version 1.0 190116) analysis for SARS-CoV-2 surface_glycoprotein , pdb entry 6vsj , emdb 21377. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421</p>
Haruspex Analysis for SARS-CoV-2 surface_glycoprotein pdb entry 6vsb emdb 21375
<p>Haruspex (version 1.0 190116) analysis for SARS-CoV-2 surface_glycoprotein , pdb entry 6vsb , emdb 21375. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421</p>
Haruspex Analysis for SARS-CoV-2 rna_polymerase-nsp7-nsp8 pdb entry 6m71 emdb 30127
<p>Haruspex (version 1.0 190116) analysis for SARS-CoV-2 rna_polymerase-nsp7-nsp8 , pdb entry 6m71 , emdb 30127. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421</p>
Investigating evolution at the catalytic site of the main SARS-CoV-2 protease using over 15,000 genomes
<p>We investigated evolution and genomic variation of SARS-CoV-2 within the current pandemic at the catalytic site of the main SARS-CoV-2 protease (see https://zenodo.org/record/3834875#.Xs1IHsZ7nyk and <a href="https://openlabnotebooks.org/mapping-the-genetic-variations-of-sars-cov-2-onto-its-proteins-crystal-structures-post-1/">https://openlabnotebooks.org/mapping-the-genetic-variations-of-sars-cov-2-onto-its-proteins-crystal-structures-post-1/ </a>).<br> We used more than 15,000 genomic sequences from GISAID (<a href="https://www.epicov.org/">https://www.epicov.org/</a>) available on the 17th of May 2020.<br> We use a new approach based on phylogenetic inference of homoplasy, clustering of mutations, and ambiguous consensus sequence characters, to identify sites that are likely affected by sequencing artefacts.<br> We find that these sites are mostly conserved, and the amino acid variants observed are only M49I, P52S, N142S, and P168S, all of which appear only at extremely low frequencies (maximum of two samples each).</p>
Datasets for GTN tutorial on SARS-CoV-2 variant analysis
<p>A reference genome in FASTA format is provided for SARS-CoV-2, "Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome", having the accession ID of NC_045512.2.</p> <p>This file was obtained from NCBI within this Galaxy history: https://usegalaxy.org/u/dan/h/nc0455122-from-ncbi</p>
QM/MM MD simulations of the ES complexes of SARS-CoV-2 main protease and oligopeptide substrates
<p>qmdcd.7z : QM/MM MD trajectories for all considered systems in dcd format for QM parts without link atoms (QMpart_nolink.pdb)</p> <p>frames.7z : QM parts of the MD frames selected for the electron density analysis.</p> <p> </p> <p> </p>
ekoraytascilar/naturecommunicationscovid: Data and analysis code to accompany "Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion"
<p>This release contains raw datasets and analysis code for the research paper titled "Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion"</p>
SARS-CoV-2 detection dogs - a pilot study
<p>The outstanding olfactory acuity of canines led us to consider whether dogs are able to reliably detect the odour of respiratory diseases associated with a SARS-CoV-2 infection in saliva or tracheobronchial secretion of hospitalized COVID-19 patients. Furthermore, we examined if SARS-CoV-2 detection dogs could provide an appropriate screening method for the human virus.The aim of this data publication is to provide the data acquired in the controlled, randomized and double-blinded pilot study `Scent dog identification of SARS-CoV-2 infection’ (submitted to BMC Infectious Diseases).</p>
On the evolutionary epidemiology of SARS-CoV-2
<p><span><span><span><span><span><span><span><span><span><span><span>There is no doubt that the novel coronavirus SARS-CoV-2 that causes COVID-19 is mutating and thus has the potential to adapt during the current pandemic. Whether this evolution will lead to changes in the transmission, the duration, or the severity of the disease is not clear. This has led to considerable scientific and media debate, from raising alarms about evolutionary change to dismissing it. Here we review what little is currently known about the evolution of SARS-CoV-2 and extend existing evolutionary theory to consider how this disease might evolve during the COVID-19 pandemic. While there is currently no definitive evidence that SARS-CoV-2 is undergoing further adaptation, continued, evidence-based, analysis of evolutionary change is important so that public health measures can be adjusted in response to substantive changes in the infectivity or severity of COVID-19.</span></span></span></span></span></span></span></span></span></span></span></p>
Electron microscopy of SARS-CoV-2 particles - Dataset 03
<p>The dataset contains 122 transmission electron microscopy images of ultrathin (60-70 nm) plastic sections through extracellular SARS-CoV-2 particles in Vero cell cultures. Images were recorded with 1376 x 1032 pixel dimensions at 0.64 nm pixel size (12 bit) and stored in 16 bit TIF format. For visualization of the images, use an image viewer capable of reading 16 bit images (e.g. IrfanView). Image files are size calibrated and can be opened with the correct size calibration using ImageJ or Fiji using the Bioformats importer. The image files are accompanied by a PDF document which describes the methods which were used for generation of the images. The dataset was produced as dataset 03 for a comparative morphometric analysis of SARS-CoV and SARS-CoV-2. Further datasets which were used for the analysis are available in this repository (see dataset description document).</p> <p>Related publication: Laue M, Kauter A, Hoffmann T, Möller L, Michel J, Nitsche A. Morphometry of SARS-CoV and SARS-CoV-2 particles in ultrathin plastic sections of infected Vero cell cultures. Sci Rep. 2021 Feb 10;11(1):3515. doi: 10.1038/s41598-021-82852-7. PMID: 33568700; PMCID: PMC7876034.</p>
Electron microscopy of SARS-CoV-2 particles - Dataset 07
<p>The dataset contains 134 transmission electron microscopy images of ultrathin (45 nm) plastic sections through extracellular SARS-CoV-2 particles in Vero cell cultures. Images were recorded with 1376 x 1032 pixel dimensions at 0.54 nm pixel size (12 bit) and stored in 16 bit TIF format. For visualization of the images, use an image viewer capable of reading 16 bit images (e.g. IrfanView). Image files are size calibrated and can be opened with the correct size calibration using ImageJ or Fiji using the Bioformats importer. The image files are accompanied by a PDF document which describes the methods which were used for generation of the images. The dataset was produced as dataset 07 for a comparative morphometric analysis of SARS-CoV and SARS-CoV-2. Further datasets which were used for the analysis are available in this repository (see dataset description document).</p> <p>Related publication: Laue M, Kauter A, Hoffmann T, Möller L, Michel J, Nitsche A. Morphometry of SARS-CoV and SARS-CoV-2 particles in ultrathin plastic sections of infected Vero cell cultures. Sci Rep. 2021 Feb 10;11(1):3515. doi: 10.1038/s41598-021-82852-7. PMID: 33568700; PMCID: PMC7876034.</p>
A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs.
<p>The spectra were provided as unprocessed raw data in the manufacturers data format (Bruker), as labelled two zip archives with SARS CoV 2 positives and negative, according to the reviewer's recommendation.</p> <p>This information belongs to the publication (in review in <em>Journal of Virological Methods</em>)<br> "A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs"<br> All the information belongs to the National Reference Institute, INEI-ANLIS DR CARLOS G MALBRAN, BUENOS AIRES, ARGENTINA.</p>
SARS-CoV-2 transmission via speech-generated respiratory droplets
<p>The physics of generating acoustic waves involves the high-speed passage of air pressurized by the lungs through narrow passages, past the mucosal epithelial layers of the vibrating vocal folds. Sounds are further modulated by the passage of this air through narrow passages between the tongue, lips, and teeth, dislodging oral fluid at all of these locations. Generation of droplets is inevitably linked to the physics of speech generation, and not limited to one person as is highlighted in a short video recording</p>
Supplementary material from "Possible fates of the dispersion of SARS-COV-2 in the Mexican context"
<p>The determination of the adequate time for house confinement and when social distancing restrictions should end are now two of the main challenges that any country has to face in an effective battle against. The possibility of a new outbreak of the pandemic and how to avoid it is, nowadays, one of the primary objectives of epidemiological research. In this work, we go deep in this subject by presenting an innovative compartmental model, that explicitly introduces the number of active cases, and employing it as a conceptual tool to explore the possible fates of the dispersion of SARS-COV-2 in the Mexican context. We incorporated the impact of starting, inattention, and end of restrictive social policies on the time evolution of the pandemics via time-in-run corrections to the infection rates. The magnitude and impact on the epidemic due to post-social restrictive policies are also studied. The scenarios generated by the model can help authorities to determine an adequate time and population load that may be allowed to reassume normal activities.</p>
VTR case studies datasets: myoglobin against hemoglobin, RBDs of SARS-CoV-1 vs. SARS-CoV-2, and glucose-tolerant vs. non-tolerant β-glucosidases
<p>Description of the four files:</p> <ol> <li><strong>contacts.xlsx</strong> <ul> <li>List of detected contacts for the three case studies</li> </ul> </li> <li><strong>pymol_files_case_study_1.zip</strong> <ul> <li>Contains files in PDB format of the analyzed structures, and files in PML format used to display visualizations in the PyMOL tool for the case study 1: comparison between contacts of myoglobin against hemoglobin</li> </ul> </li> <li><strong>pymol_files_case_study_2.zip</strong> <ul> <li>Contains files in PDB format of the analyzed structures, and files in PML format used to display visualizations in the PyMOL tool for the case study 2: comparison between contacts of RBDs of SARS-CoV-1 vs. SARS-CoV-2 both complexed with the cell receptor ACE2</li> </ul> </li> <li><strong>pymol_files_case_study_3.zip</strong> <ul> <li>Contains files in PDB format of the analyzed structures, and files in PML format used to display visualizations in the PyMOL tool for the case study 3: comparison between contacts of glucose-tolerant vs. non-tolerant β-glucosidases </li> </ul> </li> </ol>
Pandemic-related Attitudes, Stressors and Work Outcomes among Medical Assistants during the SARS-CoV-2 ("Coronavirus") Pandemic in Germany: a cross-sectional Study
<p>File type: SPSS file (.sav)</p> <p>Study type: Cross-sectional study</p> <p>Population: Medical assistants in Germany</p> <p>Study period: April 7th-April 14th, 2020</p> <p>Number of participants: 2150</p> <p>Research question: Investigation of pandemic-related attitudes, stressors and work outcomes among medical assistants during the SARS-CoV-2 (“Coronavirus”) pandemic</p> <p>Missing values: None (due to online survey) </p> <p>Original variables: v_982, v_1, v_2, v_3, v_5, v_6, v_7, v_13, v_14, v_21, v_22, v_23, v_24, v_26, v_27, v_28, v_29, v_31, v_32, v_33, v_40, v_41, v_42, v_43, v_46, v_47, v_48 v_49, v_52, v_57, Beruf_MFA</p> <p>All other variables were calculated from the original variables either by rescaling or dichotomization. </p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.