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68 results for “SARS CoV-2”
SIRAH-CoV2 initiative: co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ)
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. </p> <p>The files 6WIQ_SIRAHcg_rawdata_0-5us.tar, and 6WIQ_SIRAHcg_rawdata_5-10us.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6WIQ_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6WIQ_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6WIQ_SIRAHcg_10us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd 6WIQ_SIRAHcg_prot.prmtop 6WIQ_SIRAHcg_prot.ncrst 6WIQ_SIRAHcg_10us_prot_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Supplementary Data - MORTALITY RATE DUE TO PULMONERY FIBROSIS ASSOCIATED WITH SARS- COV-2 INFECTION: SCOPE OF BEST FIT REGRESSION
<p>The dataset contains number of infected pateints - Death Frquencies - Mortality rate globally due to pulmonary fibrosis associated with SARS-COV-2 infection with effect from 21st Jan to 28 th April ,2020 . Data analysis report by best fit regression software Curve Expert V.1.4 supported with Spreadsheet ( Excel , Office 2007 ) are included for computation of statistical significance .</p>
Discovery of South African plant-based biomarkers as potential flagships for SARS- CoV-2 receptor
<h1><span>Table S1: </span><span>Distinguished metabolites in the extracts of <em><span>Artemisia annua </span></em><span>and <em>Artemisia afra </em></span>using UPLC-MS/MS set in positive ionization mode.</span></h1> <h1><span>Table S2: Identified and docked compound-based biomarkers from <em><span>Artemisia annua </span></em><span>and <em>Artemisia afra </em></span>(ESI+ scan).</span></h1>
Effects of Mouthrinsing and Gargling to CT Values of SARS CoV-2 DATASET
<p><strong>Background:</strong> Coronavirus disease 2019 can spread rapidly. Surgery in the oral cavity poses a high risk of transmission of severe acute respiratory syndrome coronavirus 2. The American Dental Association and the Centers for Disease Control and Prevention recommend the use of mouthwash containing 1.5% hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) or 0.2% povidone iodine (PI) to reduce the viral load in the upper respiratory tract and decrease the risk of transmission. The aim of the present study was to analyze the effect of mouthrinsing and gargling with mouthwash containing 1% PI, 0.5% PI, 3% H<sub>2</sub>O<sub>2</sub>, or 1.5% H<sub>2</sub>O<sub>2</sub> and water on the cycle threshold (CT) value.</p> <p><strong>Methods:</strong> In total, 69 subjects recruited from Persahabatan General Hospital who met the inclusion criteria were randomly assigned to one of four treatment groups or the control group. The subjects were instructed to gargle with 15 mL of mouthwash for 30 s in the oral cavity followed by 30 s in the back of the throat three times per day for 5 days. CT values were collected on postprocedural days 1, 3, and 5.</p> <p><strong>Results:</strong> The results of the Friedman test significantly differed among the groups. The CT values increased from baseline (day 0) to postprocedural days 1, 3, and 5.</p> <p><strong>Conclusions:</strong> Mouthrinsing and Gargling with mouthwash containing 1% PI, 0.5% PI, 3% H<sub>2</sub>O<sub>2</sub>, or 1.5% H<sub>2</sub>O<sub>2</sub> and water increased the CT value.</p> <p><strong>Background:</strong> Coronavirus disease 2019 can spread rapidly. Surgery in the oral cavity poses a high risk of transmission of severe acute respiratory syndrome coronavirus 2. The American Dental Association and the Centers for Disease Control and Prevention recommend the use of mouthwash containing 1.5% hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) or 0.2% povidone iodine (PI) to reduce the viral load in the upper respiratory tract and decrease the risk of transmission. The aim of the present study was to analyze the effect of mouthrinsing and gargling with mouthwash containing 1% PI, 0.5% PI, 3% H<sub>2</sub>O<sub>2</sub>, or 1.5% H<sub>2</sub>O<sub>2</sub> and water on the cycle threshold (CT) value.</p> <p><strong>Methods:</strong> In total, 69 subjects recruited from Persahabatan General Hospital who met the inclusion criteria were randomly assigned to one of four treatment groups or the control group. The subjects were instructed to gargle with 15 mL of mouthwash for 30 s in the oral cavity followed by 30 s in the back of the throat three times per day for 5 days. CT values were collected on postprocedural days 1, 3, and 5.</p> <p><strong>Results:</strong> The results of the Friedman test significantly differed among the groups. The CT values increased from baseline (day 0) to postprocedural days 1, 3, and 5.</p> <p><strong>Conclusions:</strong> Mouthrinsing and Gargling with mouthwash containing 1% PI, 0.5% PI, 3% H<sub>2</sub>O<sub>2</sub>, or 1.5% H<sub>2</sub>O<sub>2</sub> and water increased the CT value.</p>
Data for Analyses presented in associated publication: Investigating trends in those who experience menstrual bleeding changes after SARS CoV-2 vaccination
<p>This is the data used for analyses presented in our associated publication (details to be provided later). There are three datasets, because we analyzed by specific, biologically relevant subgroups (pre-menopausal people with predictable menstrual cycles, pre-menopausal people who usually do not menstruate, and post-menopausal people). The data provided here has been cleaned and aggregated as described in the associated publication. Specifically,</p> <ul> <li>here we have only included the variables that are included in our analyses</li> <li>we collapsed specific identities (gender, race, ethnicity) into binarized categories (as used in the publication) in order to reduce the likelihood someone could be re-identified from this de-identified data</li> <li>this dataset also does not include unique identifiers for individuals, but instead has row numbers for each dataset (starting at 1 for each data subset). There are no repeated individuals between datasets, as these are mutually exclusive subgroups</li> <li>Additional information regarding the survey and data processes can be found at https://osf.io/6rvxk/?view_only=f91f1247658f49e3bbf59b2f6cfd3898</li> </ul>
SIRAH-CoV2 initiative: Apo ADP ribose phosphatase of NSP3 from SARS CoV-2 (PDB id: 6W02)
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 ADP ribose phosphatase of NSP3 from SARS CoV-2 in its APO form (PDB id: 6W02, Bioassembly 1). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. </p> <p>The file 6W02_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6W02_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W02_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6W02_SIRAHcg_10us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd 6W02_SIRAHcg_prot.prmtop 6W02_SIRAHcg_prot.ncrst 6W02_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Exequiel Barrera (ebarrera@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Dysregulation in mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS- CoV-2 infected cells - Proteomic data obtained with Huh-7 cells
<p>Cultured human Huh-7 cells were infected with SARS-CoV-2 and harvested after 24, 48 and 72 h. The extracted proteins were processed in triplicates preparing for mass spectrometric analysis. Data acquisition was completed, including control samples of non-infected cells, following isobaric tandem mass tag (TMT) chemical labeling and on-line fractionation of the 12 combined biological replicates. The resulted vendor specific raw files (Thermo Scientific) of 12 fractions are provided.</p> <p>The data is further analyzed in order to identify regulated proteins upon SARS-CoV-2 infection to understand the underlying biological processes through pathway analysis. Additional details about the study is going to be completed in the manuscript already submitted for publication.</p>
A Study of SARS CoV-2 Infection and Potential Transmission in Individuals Immunized With Moderna COVID-19 Vaccine
ClinicalTrials.gov study NCT04811664. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Study of Oral Ibrutinib Capsules to Assess Respiratory Failure in Adult Participants With Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and Pulmonary Injury
ClinicalTrials.gov study NCT04375397. IPD Sharing: YES. Countries: 1. Publications: 1.
Live Microbials to Boost Anti-Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Immunity Clinical Trial
ClinicalTrials.gov study NCT04847349. IPD Sharing: YES. Countries: 1. Publications: 1.
COVID-19 Study Assessing the Efficacy and Safety of Anti-Spike SARS CoV-2 Monoclonal Antibodies for Prevention of SARS CoV-2 Infection Asymptomatic in Healthy Adults and Adolescents Who Are Household
ClinicalTrials.gov study NCT04452318. IPD Sharing: YES. Countries: 3. Publications: 8.
F I G U R E 1 in Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS- CoV-2
F I G U R E 1 Structural diagrams of spike glycoproteins of SARS‐CoV, MERS‐CoV, and SARS‐CoV‐2. All spike proteins of coronaviruses contain S1 subunit and S2 subunit, which were divided by the S cleavage sites. FP, fusion peptide; HR, heptad repeat 1 and heptad repeat 2; RBD, receptor‐binding domain, contains core binding motif in the external subdomain; SP, signal peptide
F I G U R E 2 in Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS- CoV-2
F I G U R E 2 Phylogenetic analysis of sequences of coronavirus spike glycoproteins. The sequences of spike glycoproteins of SARS‐CoV‐2, bat SARS‐like CoV, pangolin SARS‐like CoV, and SARS‐CoV were analyzed. The red stars indicate pangolin SARS‐like CoV and bat SARS‐like CoV. Host flags are marked after the clusters. SARS‐CoV‐2, severe respiratory syndrome coronavirus‐2
Transmission Dynamics of COVID-19 Disease among household contacts in Delhi, India (SARS CoV-2 HT Study)
<p>Results from households in the MAMC Delhi FFX Unity study </p>
Vigilancia Intensificada de 100 casos y contactos de Influenza y SARS CoV-2, en Meta, Tolima y Cundinamarca, Colombia, 2020. (Intensified public health surveillance for first 100 cases in Meta, Tolima, and Cundinamarca, Colombia, 2020)
<p>Results from the FFX Unity study in Meta, Tolima, and Cundinamarca, Colombia, 2020.</p>
Dimerization the ACE-2 with Different RBD Mounts: A Dynamic Simulation Perspective on SARS-Cov-2 Infecting Details
<p>The system construction and dynamic simulation data of paper "Dimerization the ACE-2 with Different RBD Mounts: A Dynamic Simulation Perspective on SARS-Cov-2 Infecting Details"(manuscript, ci-2023-00041c) are prepared.</p>
LAMMPS trajectories for "The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA"
<p><strong>LAMMPS trajectory data for:</strong><br> <strong>The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA</strong><br> Jasmine Cubuk<sup>1,2</sup>, Jhullian J. Alston<sup>1,2</sup>, J. Jeremías Incicco<sup>1,2</sup>, Alex S. Holehouse<sup>1,2</sup>, Kathleen B Hall<sup>1</sup>, Melissa D. Stuchell-Brereton<sup>1,2</sup>, Andrea Soranno<sup>1,2,*</sup></p> <p><sup>1</sup>Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110, Saint Louis, MO, USA</p> <p><sup>2</sup>Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA</p> <p><strong>Corresponding author: </strong>Andrea Soranno (soranno@wustl.edu)<br> <strong>Questions about simulations: </strong>Alex Holehouse (alex.holehouse@wustl.edu)</p> <p><strong>Preprint link: </strong><a href="https://doi.org/10.1101/2023.02.10.527914">https://doi.org/10.1101/2023.02.10.527914</a></p> <p><strong>GitHub link to simulation info:</strong> <a href="https://github.com/holehouse-lab/supportingdata/tree/master/2023/cubuk_2023">https://github.com/holehouse-lab/supportingdata/tree/master/2023/cubuk_2023</a></p> <p><strong>Funding: </strong>This research was supported by the NIH National Institute on Allergic and Infectious Diseases with R01AI163142 (to A.S., A.S.H.) and by the NIH National Cancer Institute F99CA264413 (to J.J.A.).</p> <p> </p>
Study of a Severe Acute Respiratory Syndrome CoV-2 (SARS-CoV-2) Virus-like Particle (VLP) Vaccine in Healthy Adults
ClinicalTrials.gov study NCT04818281. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study of a Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Virus-like Particle (VLP) Vaccine
ClinicalTrials.gov study NCT04962893. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Risk of Infection of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), COVID-19, in a Massive Musical Show With Transmission Prevention Measures
ClinicalTrials.gov study NCT04668625. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.