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2,489 results for “Sars-CoV-2”
Inhibition Mechanism of SARS-CoV-2 Main Protease: A Molecular Modeling Approach
<p>Structural basis for the inhibition of SARS-CoV-2 main protease; Molecular Docking; Classical MD Simulations</p>
Lung Ultrasound in Patients With SARS-COV-2 Pneumonia Correlations With Chest Computed Tomography, Respiratory Impairment, and Inflammatory Cascade
<p>Objectives—Lung ultrasound (LUS) might be comparable to chest computed tomography (CT) in detecting parenchymal and pleural pathology, and in monitoring interstitial lung disease. We aimed to describe LUS characteristics of patients during the hospitalization for COVID-19 pneumonia, and to compare the extent of lung involvement at LUS and chest-CT with inflammatory response and the severity of respiration impairment.<br> Methods—During a 2-week period, we performed LUS and chest CT in hospitalized patients affected by COVID-19 pneumonia. Dosages of high sensitivity C-reactive protein (HS-CRP), D-dimer, and interleukin-6 (IL-6) were also obtained. The index of lung function (P/F ratio) was calculated from the blood gas test. LUS and CT scoring were assessed using previously validated scores. <br> Results—Twenty-six consecutive patients (3 women) underwent LUS 34 - 14 days from the early symptoms. Among them, 21 underwent CT on the same day of LUS. A fair association was found between LUS and CT scores (R = 0.45, P = .049), which became stronger if the B-lines score on LUS was not considered (R = 0.57, P = .024). LUS B-lines score correlated with IL-6 levels (R = 0.75, P = 0.011), and the number of involved lung segments detected by LUS correlated with the P/F ratio (R = 0.60, P = .019) but not with HS-CRP and D-Dimer levels. No correlations were found between CT scores and inflammations markers or P/F.<br> Conclusion—In patients with COVID-19 pneumonia, LUS was correlated with both the extent of the inflammatory response and the P/F ratio. </p>
Data and code archive for project "Tracing caffeine and its metabolite in wastewater to understand the spread of SARS-CoV-2"
<p>This dataset/code archive included all the data and R codes that were used to explore the universal and robust wastewater biomarkers for population normalization in the SARS-CoV-2 wastewater-based epidemiology. There are nine R code files to produce figures and tables. The data included:</p> <ol> <li>Raw data of weekly biomarkers (caffeine, paraxanthine, and PMMoV) wastewater concentrations, weekly new COVID-19 case numbers, SARS-CoV-2 N1/N2 copies in wastewater, wastewater flow rate <ul> <li>A total of 2,624 wastewater samples (41 weeks) were collected weekly from May 2021- April 2022 from 64 wastewater treatment plants across Missouri, US;</li> <li>pMMoV data was only available from Sep 13 2021-April 2022 for Missouri data;</li> <li>Validation dataset from 10 wastewater treatment plants across Wisconsin, US, to test the relationship between wastewater biomarkers and population. </li> </ul> </li> <li>Downloaded Apple mobility data during the pandemic </li> <li>Validation dataset for wastewater flowrate estimation using paraxanthine concentrations.</li> </ol>
Genomic surveillance of SARS-CoV-2 in healthcare workers: a critical sentinel group for monitoring the SARS-CoV-2 variant shift
<p>Figure S1. Phylogenetic reconstruction of SARS-CoV-2 sequences distinguished between general population and healthcare workers. Samples correspond to the period of November 17th, 2021 and February 21st, 2022. The phylogenetic tree was reconstructed with 1,000 iterations for Ultra-Fast Bootstrap and SH-like approximate likelihood ratio test (SH-aLRT). Reference (SARS-CoV-2 reference genome - NC_045512).</p>
Data for the manuscript "Identification and structural studies of the crucial RNAi target of SARS-CoV-2 through molecular dynamics simulations"
<p>Simulation datasets for manuscript titled "<strong>Identification and structural studies of the crucial RNAi target of SARS-CoV-2 through molecular dynamics simulations"</strong></p>
Data set related to the article: "SARS-CoV-2 Lysate Stimulation Impairs the Release of Platelet-like Particles and Megakaryopoiesis in the MEG-01 Cell Line."
<p>Abstract:</p> <p>SARS-CoV-2 infection causes a considerable inflammatory response coupled with impaired platelet reactivity, which can lead to platelet disorders recognized as negative prognostic factors in COVID-19 patients. The virus may cause thrombocytopenia or thrombocytosis during the different disease stages by destroying or activating platelets and influencing platelet production. While it is known that several viruses can impair megakaryopoiesis by generating an improper production and activation of platelets, the potential involvement of SARS-CoV-2 in affecting megakaryopoiesis is poorly understood. To this purpose, we explored, in vitro, the impact of SARS-CoV-2 stimulation in the MEG-01 cell line, a human megakaryoblastic leukemia cell line, considering its spontaneous capacity of releasing platelet-like particles (PLPs). We interrogated the effect of heat-inactivated SARS- CoV-2 lysate in the release of PLPs and activation from MEG-01, the signaling pathway influenced by SARS-CoV-2, and the functional effect on macrophagic skewing. The results highlight the potential influence of SARS-CoV-2 in the early stages of megakaryopoiesis by enhancing the production and activation of platelets, very likely due to the impairment of STATs signaling and AMPK activity. Overall, these findings provide new insight into the role of SARS-CoV-2 in affecting megakaryocyte– platelet compartment, possibly unlocking another avenue by which SARS-CoV-2 moves.</p>
Dataset related to article "Transcriptomic profile of TNFhigh MAIT cells is linked to B cell response following SARS-CoV-2 vaccination"
<p>This record contains raw data related to article “<em>Transcriptomic profile of TNF<sup>high</sup> MAIT cells is linked to B cell response following SARS-CoV-2 vaccination"</em></p> <p><strong>ABSTRACT</strong></p> <p><strong>Introduction:</strong> Higher frequencies of Mucosal-associated invariant T (MAIT) cells were associated with an increased adaptive response to mRNA <em>BNT162b2</em> SARS-CoV-2 vaccine, however, the mechanistic insights into this relationship are unknown. Here, we hypothesized that the TNF response of MAIT cells supports B cell activation following SARS-CoV-2 immunization.</p> <p><strong>Methods:</strong> To investigate the effects of repeated SARS-CoV-2 vaccinations on the peripheral blood mononuclear cells (PBMCs), we performed a longitudinal single cell (sc)RNA-seq and scTCR-seq analysis of SARS-CoV-2 vaccinated healthy adults with two doses of the Pfizer-BioNTech <em>BNT162b2 </em>mRNA vaccine. Collection of PBMCs was performed 1 day before, 3- and 17-days after prime vaccination, and 3-days and 3-months following vaccine-boost. Based on scRNA/TCR-seq data related to regulatory signals induced by the vaccine, we used computational approaches for the functional pathway enrichment analysis (Reactome), dynamics of the effector cell-polarization (RNA Velocity and CellRank) and cell-cell communication (NicheNet).</p> <p><strong>Results:</strong> We identified MAIT cells as an important source of TNF across circulating lymphocytes in response to repeated SARS-CoV-2 <em>BNT162b2</em> vaccination. The <em>TNF<sup>high</sup></em> signature of MAIT cells was induced by the second administration of the vaccine. Notably, the increased <em>TNF</em> expression was associated with MAIT cell proliferation and efficient anti-SARS-CoV-2 antibody production. Finally, by decoding the ligand-receptor interactions and incorporating intracellular signaling, we predicted <em>TNF<sup>high</sup></em> MAIT cell interplay with different B cell subsets. In specific, predicted <em>TNF</em>-mediated activation was selectively directed to conventional switched memory B cells, which are deputed to high-affinity long-term memory.</p> <p><strong>Discussion:</strong> Overall, our results indicate that SARS-CoV-2 <em>BNT162b2</em> vaccination influences MAIT cell frequencies and their transcriptional effector profile with the potential to promote B cell activation. This work also provides a blueprint for the promising use of MAIT cells as cellular adjuvants in mRNA-based vaccines.</p>
SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs
GEO Series GSE159191. Homo sapiens; Severe acute respiratory syndrome coronavirus 2. 16 samples. Type: Expression profiling by high throughput sequencing.
Mild SARS-CoV-2 maternal infection in mice induces transient offspring neurodevelopmental aberrance
GEO Series GSE317803. Mus musculus. 140 samples. Type: Expression profiling by high throughput sequencing.
SARS-CoV-2 infection
GEO Series GSE234487. Homo sapiens. 50 samples. Type: Expression profiling by high throughput sequencing.
Host transcriptome in human lung A549 cells infected with SARS-CoV-2 expressing wild-type and mutant (H234A and N277A) Nsp15
GEO Series GSE274310. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
SARS-CoV-2 nsp13 restricts episomal DNA transcription without affecting chromosomal DNA
GEO Series GSE211851. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Role of Top1 and Genome structure in SARS-CoV-2 infection
GEO Series GSE162619. Mesocricetus auratus; Homo sapiens. 39 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Probiotic consortia improve anti-viral immunity to SARS-CoV-2 in Ferrets [RT-PCR]
GEO Series GSE180390. Mustela putorius furo. 143 samples. Type: Expression profiling by RT-PCR.
Plasma Levels of Glycohydrolase Activities in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Patients
<p>Dataset from Massaccesi L, Vianello E, Ranucci M, Galliera E, Sitzia C, Romanelli MMC. Plasma Levels of Glycohydrolase Activities in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Patients. Arch Pathol Lab Med. 2021 Aug 1;145(8):922-923. doi: 10.5858/arpa.2021-0037-LE. PMID: 34313714.</p> <p> </p>
Cardiovascular tissue banking activity during SARS-CoV-2 pandemic: evolution of national protocols and Lombardy experience
<p>Cardiovascular tissue banking activity during SARS-CoV-2 pandemic: evolution of national protocols and Lombardy experience</p> <p>The worldwide pandemic outbreak due to severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has created unprecedented challenges for public health services. Lombardy, region of the Northern Italy, has been the first area in the Western world whose organs and tissues procurement programs have had to face the virus pandemic emergency. We retrospectively collected and analyzed data about cardiovascular tissues (CT) in 2019 and in 2020. We aimed to describe the rapid evolution of SARS-CoV-2 regulation laws for tissue donor’s selection and harvesting from February 2020 until January 2021. As expected the number of CT donors in 2020 was significantly lower than those of 2019 (66 vs. 99, p value 0.02). The total number of CT collected from donors have been 254 in 2019 and 206 in 2020 (p 0.28). Femoral arteries were the most required vascular tissues (55.5% in 2019 and 40% in 2020). Fifty-five and forty-eight pulmonary valves were implanted in 2019 and 2020, respectively. No differences were found for the types of CT requests between the 2 years. The median age of receivers of vascular tissues was 69.6 ± 14.6 years in the 2019 and 63.3 ± 14.9 years in 2020 (p \0.01). The median age of receivers of pulmonary and aortic valves did not differ between the 2 years (9.32 ± 11.49 vs. 8.36 ± 10.66 and 48.67 ± 27.19 vs. 37.14 ± 31.97 respectively). Despite the dramatically reduction of donors, the number of CT collected has not decreased significantly and so far the CT distribution rate is comparable to those of 2019</p>
Geneticin shows selective antiviral activity against SARS-CoV-2 by targeting programmed -1 ribosomal frameshifting
<p>Raw data of the experiments presented in "Geneticin shows selective antiviral activity against SARS-CoV-2 by targeting programmed -1 ribosomal frameshifting"</p>
Ligation-based Assay for Variant-Typing without Sequencing: Application to SARS-CoV-2 Variants of Concern [Data Deposit]
<p>Data analyzed for the results of the original research article "<strong>Ligation-based Assay for Variant-Typing without Sequencing: Application to SARS-CoV-2 Variants of Concern</strong>".</p>
Molecular dynamics trajectories for "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessiblity"
<p>Dataset of molecular dynamics trajectories obtained for "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessiblity"</p> <p>Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is causing a devastating social and economic impact all over the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, and increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes, via its receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2). In an attempt to understand the effect of RBD mutations in the VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some VOCs mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (alpha, beta, delta, and omicron). Our results show that, in solution, wt RBD presents two distinct conformations: an “open” conformation where it is free to bind ACE2; and a “closed” conformation, where the RBM ridge blocks the binding surface. The alpha and beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the delta and omicron variants showed extreme results, with the closed conformation either barely observed or not observed at all. The delta variant also differed from the other variants substantially, alternating between the open conformation and an alternative “reversed” one, with a significantly changed orientation of the RBM ridge. This alternate conformation could potentially provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the omicron and delta variant, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of delta, antibody escape.</p>
Dataset related to article "The antibody response to SARS-CoV-2 infection persists over at least 8 months in symptomatic patients"
<p>This set of data is related to article "The antibody response to SARS-CoV-2 infection persists over at least 8 months in symptomatic patients"</p> <p>Abstract</p> <p>The factors involved in the persistence of antibodies to SARS-CoV-2 are unknown. We evaluated the antibody response to SARS-CoV-2 in personnel from 10 healthcare facilities and its association with individuals’ characteristics and COVID-19 symptoms in an observational study. We enrolled 4735 subjects (corresponding to 80% of all personnel) over a period of 5 months when the spreading of the virus was drastically reduced. For each participant, we determined the rate of antibody increase or decrease over time in relation to 93 features analyzed in univariate and multivariate analyses through a machine learning approach. In individuals positive for IgG ( ≥ 12 AU/mL) at the beginning of th study, we found an increase [p= 0.0002] in antibody response in symptomatic subjects, particularly with anosmia/dysgeusia (OR 2.75, 95% CI 1.753 – 4.301), in a multivariate logistic regression analysis. This may be linked to the persistence of SARS-CoV-2 in the olfactory bulb.</p>
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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.