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2,489 results for “Sars-CoV-2”
Figure 2 from: Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY (2021) Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia 68(3): 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Figure 2 The structure of the PLpro SARS-CoV-2 receptor (PDB ID: 5TL6) along with the distribution of residues on the Ramachandran plot. The PLpro receptor structure is composed of 10 α-helix structures and 19 β-sheet structures. The PLpro receptor structure is ready to use in molecular docking simulations with 96.55% of the residue in the protein-forming region.
Figure 1 from: Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY (2021) Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia 68(3): 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Figure 1 The structure of the Mpro SARS-CoV-2 receptor (PDB ID: 6LU7) along with the distribution of residues on the Ramachandran plot. The Mpro receptor structure is composed of 10 α-helix structures and 13 β-sheet structures. The Mpro receptor structure is ready to use in molecular docking simulations with 92.15% of the residue in the protein-forming region.
Figure 3 from: Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY (2021) Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia 68(3): 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Figure 3 Structure of the ACE 2 receptor h receptor (PDB ID: 1R42) along with the distribution of residues on the Ramachandran plot. The ACE-2 receptor structure is composed of 31 α-helix structures and six β-sheet structures. The structure of the hACE-2 receptor is ready to be used in molecular docking simulations with 98.37% of the residue in the protein-forming region.
Preterm birth is not associated with asymptomatic/mild SARS-CoV-2 infection per se: pre-pregnancy state is what matters
<p><span><span><span><span><span><span><span><span><span><span><span>Evidence for the real impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on preterm birth is unclear, as available series report composite pregnancy outcomes and/or do not stratify patients according to disease severity.The purpose of the research was to determine the real impact of asymptomatic/mild SARS-CoV-2 infection on preterm birth not due to maternal respiratory failure. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>This case-control study involved women admitted to a hospital for delivery between 20 September 2020 and 9 January 2021 in northern Italy. The cumulative incidence of Coronavirus disease-19 was compared between preterm birth (case group, n = 102) and full-term delivery (control group, n = 127). Only women with spontaneous or medically-indicated preterm birth because of placental vascular malperfusion (pregnancy-related hypertension and its complications) were included. Current or past SARS-CoV-2 infection was determined by nasopharyngeal swab testing and detection of IgM/IgG antibodies in blood samples. </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>A significant difference in the cumulative incidence of Coronavirus disease-19 between the case (21/102, 20.5%) and the control group (32/127, 25.1%) (<i>P</i>= 0.50) was not observed, although the case group was burdened by a higher prevalence of three known risk factors (body mass index > 24.9, asthma, chronic hypertension) for severe Coronavirus disease-19. Logistic regression analysis showed that asymptomatic/mild SARS-CoV-2 infection was not an independent predictor of spontaneous and medically-indicated preterm birth due to pregnancy-related hypertension and its complications (0.77; 95% confidence interval, 0.41-1.43). </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Pregnant patients without comorbidities need to be reassured that asymptomatic/mild SARS-CoV-2 infection does not increase the risk of preterm delivery. Preterm birth and severeCoronavirus disease-19 share common risk factors (i.e., body mass index > 24.9, asthma, chronic hypertension), which may explain the high rate of indicated preterm birth due to maternal conditions reported in the literature. </span></span></span></span></span></span></span></span></span></span></span></p>
Nafamostat-interferon-alpha combination suppresses SARS-CoV-2 infection by targeting cooperatively host TMPRSS2 in vitro and in vivo
<p>raw data</p>
SARS-CoV-2 TREE DATA
<p>Demo</p>
Supplementary data --The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner
<p>Supplementary data for the Cell Systems manuscript 'The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner', by Hamelin <em>et al.</em></p> <p><strong>GISAID_Authors_Recognition_2021-01-19. </strong>Metadata concerning the SARS-CoV-2 viral sequences analysed, and generously provided by GISAID. </p> <p><strong>Table S1. </strong>SARS-CoV-2 mutations identified from 330,246 GISAID entries (December 31<sup>st</sup> 2020), Related to Figure 1 and Figure 2. SARS-CoV-2 mutations at the nucleic and amino acid level are indicated. Number of genomes carrying mutation show the frequency of individual mutations among all SARS-CoV-2 variants. </p> <p><strong>Table S2. </strong>SARS-CoV-2 prevalent mutations identified from 330,246 GISAID entries (December 31<sup>st</sup> 2020) and detected in at least 100 individuals, Related to Figure 2.</p> <p><strong>Table S3.</strong> Previously validated SARS-CoV-2 CD8+ T cell epitopes and their matching mutated forms identified in this study, Related to Figure 1 and Figure 2.</p> <p><strong>Table S4.</strong> List of previously validated SARS-CoV-2 CD8+ T cell epitopes. Epitopes were downloaded from https://www.mckayspcb.com/SARS2TcellEpitopes/ (as of January 2021). This database has effectively catalogued all SARS-CoV-2 CD8+ epitopes validated by 18 separate studies. See Quadeer et al. 2021 for details, Related to Figure 1 and Figure 2. </p>
Emerging variants of SARS-CoV-2 NSP10 highlight strong and functional conservation of its binding to two non-structural protein, NSP14 and NSP16
<p>The data set contains: (1) topology (prmtop), (2) coordinate files to the run the simulation (3) A plumed.dat file (4) COLVAR and (5) HILLS files; (6) Trajectory (xtc) file and (7) corresponding pdb file. </p> <p>The simulations were run as replicates.</p>
Supporting data for Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater
<p>This dataset contains the FASTQ files used in the paper <em>Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater</em>. </p> <p>The FASTQ files are classified in 2 different folders: MinION and MiSeq. Inside the MinION folder, there are two more folders, one for the R9.4.1 flow cell data and the other for the R10.4.1 flow cell data. </p> <p>Twist synthetic RNA mixtures are named as mix1, mix2, etc. </p> <p>Twist synthetic RNA corresponding to the Wuhan sequence is named as mix11_WH</p> <p>Wastewater samples are named as WWTP_1, WWTP_2, etc. </p>
Differences in SARS-CoV-2 specific humoral and cellular immune responses after contralateral and ipsilateral COVID-19 vaccination
<p>In an observational study, 303 previously naive individuals were recruited, who received the second dose of the COVID-19 vaccine BNT162b2 on either the ipsilateral (n=147) or the contralateral side (n=156). Spike-specific IgG, IgG-avidity, and neutralizing antibodies were quantified using ELISA and a surrogate assay 2 weeks after dose 2. A subgroup of 143 individuals (64 ipsilateral, 79 contralateral) was analysed for spike-specific CD4 and CD8 T-cells using flow-cytometry.</p>
A large-scale serological survey in pets from October 2020 through June 2021 in France shows significantly higher exposure to SARS-CoV-2 in cats
<p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect many animals, including pets such as dogs and cats. Many studies have documented infection in companion animals by bio-molecular and serological methods. However, only a few have compared seroprevalence in cats and dogs from the general population, and these studies were limited by small sample sizes and collections over short periods. Our goal was to obtain a more accurate evaluation of seroprevalence in companion animals in France and to determine whether cats and dogs differ in their exposure to SARS-CoV-2. For this purpose, we conducted an extensive SARS-CoV-2 serological survey of 2036 cats and 3577 dogs sampled by veterinarians during medical examinations in clinics throughout France. Sampling was carried out from October 2020 through June 2021, a period encompassing the second and third waves of SARS-CoV-2 infections in humans in the country. Using a microsphere immunoassay targeting receptor binding domain and trimeric spike protein, we found 7.1% seroprevalence in pets, in a subset of 308 seropositive samples, 26.3% had neutralizing antibodies. We found that cats were significantly more likely to test positive than dogs, with seropositivity rates of 9.3% and 5.9% in cats and dogs, respectively. Finally, data for both species showed that seroprevalence was lower in older animals and was not associated with the date of sampling or the sex of the animal. Our results show that cats are significantly more sensitive to SARS-CoV-2 than dogs, in line with experimental studies showing that cats are more susceptible than dogs. This study reinforces that pets are commonly infected or exposed to SARS-CoV-2, emphasizing the importance of a One-Health approach to the SARS-CoV-2 pandemic and raising the question of vaccination of companion animals in close contact with humans.</p>
Metabolic dysregulation in term infants from SARS-CoV-2 infected mothers
<p><strong>Background </strong></p> <p>Pregnant women are one of the most vulnerable groups that require additional precautions against SARS-CoV-2 infection. We hypothesized that SARS-CoV-2 virus infection has an impact on newborns from mothers infected in late stages of pregnancy and that this will be reflected in the urinary metabolomic fingerprint of newborns.</p> <p><strong>Methods</strong></p> <p>Term infants born to mothers with SARS-CoV2 at delivery and control term infants born to negative pregnant women during the same period in the same period were recruited and urine samples were collected in the first 48 - 72 hours after delivery. Untargeted metabolomic fingerprinting of urine samples was performed employing liquid chromatography-time-of-flight mass spectrometry</p> <p><strong>Results</strong></p> <p>A total of 49 term newborns were included in this study, 26 from mothers with acquired SARS-CoV-2 infection (GA= 40 weeks, IQR (38-40)) and 23 newborns from mothers without SARS-CoV-2 infection (GA= 40 weeks, IQR (39-40)).</p> <p>Sample analysis using two complementary methods allowed the annotation of 980 features. Differences in the urinary metabolomes between cases and controls were observed. Functional analysis indicated that metabolic pathways were altered, including pyrimidine metabolism, drug metabolism by cytochrome P450, a total of eight pathways related to amino acids metabolism and translation, and four pathways related to the metabolism of cofactors and vitamins. Also, Chemical Similarity Enrichment Analysis (ChemRICH) complemented the pathway enrichment analysis, indicating that several clusters of metabolites, such as dipeptides, fatty acids and chromans, are downregulated in urines samples from newborns with mothers affected by SARS-CoV-2.</p> <p><strong>Conclusions</strong></p> <p>This is the first study of the urinary metabolome of newborns from mothers with and without SARS-CoV-2 infection. Alterations on metabolic pathways and metabolite clusters confirm that neonates exhibited metabolic dysregulations when their mothers were infected late in pregnancy, although no intrauterine or transplacental transmission or clinical evidence was observed.</p>
Fig. 3. Dixon plots for biflavone 1–9 in Natural biflavones are potent inhibitors against SARS-CoV-2 papain-like protease
Fig. 3. Dixon plots for biflavone 1–9.
Fig. 2 in Natural biflavones are potent inhibitors against SARS-CoV-2 papain-like protease
Fig. 2. Structures of the biflavones (1–9) from NCLTCMs and the flavone monomers.
SARS-CoV-2 replicates in the placenta after maternal infection during pregnancy
<p>Study datasheet</p>
European Pregnancy and Paediatric Infections Cohort Collaboration (EPPICC) SARS-CoV-2 Antibody Study Protocol. Covid-19
ClinicalTrials.gov study NCT04726137. IPD Sharing: NO. Countries: 6. Publications: 0.
Safety and Efficacy of Trans Sodium Crocetinate (TSC) in SARS-CoV-2 (COVID-19) Infected Subjects
ClinicalTrials.gov study NCT04573322. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Adipose Mesenchymal Cells for Abatement of SARS-CoV-2 Respiratory Compromise in COVID-19 Disease
ClinicalTrials.gov study NCT04352803. IPD Sharing: UNDECIDED. Countries: 0. Publications: 9.
Study of the Efficacy and Safety of a Single Administration of Olokizumab and RPH-104 With Standard Therapy in Patients With Severe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infecti
ClinicalTrials.gov study NCT04380519. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Povidone Iodine Nasal Application to Prevent Intraoperative Spread of SARS-CoV-2
ClinicalTrials.gov study NCT05745467. IPD Sharing: YES. Countries: 0. Publications: 14.
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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.