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5,809 results for “Viruses”
Supplementary dataset to publication: "Neuroglia Infection by Rabies Virus after Anterograde Virus Spread in Peripheral Neurons"
<p>Supplementary data to the publication: Potratz M., Zaeck L.M., Weigel C., Klein A., Freuling C.M., Müller T., <strong>Finke S.</strong> <strong>2020. </strong>Neuroglia Infection by Rabies Virus after Anterograde Virus Spread in Peripheral Neurons. <strong>Acta Neuropathologica Communications. </strong>8:199. doi.org/10.1186/s40478-020-01074-6.</p>
Microbiological data from studies to optimise depuration of viruses from Pacific oysters (Crassotrea gigas)
<p>Viral contamination of bivalve molluscan shellfish is a recognised cause of foodborne gastroenteritis. Unlike bacterial contaminants, viruses such as norovirus are not easily removed once shellfish become contaminated. Therefore the normal practice of depurating following harvest may not effectively reduce the risk of become ill following consumption of shellfish.</p> <p>As part of the SeafoodTomorrow consortium project (Horizon 2020), studies were undertaken to determine the optimal conditions under which Pacific oysters (Crassostrea gigas) are depurated (purified) following harvest.</p> <p>This dataset includes levels of norovirus, F specific coliphage genogroup II and E. coli found in oysters following several experiments in which depuration conditions were varied.</p>
Diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice
<p>Data and analysis files for diallel analysis of weight loss in 8-12 week old male and female mice (n=1,043), mock treated or infected with influenza A virus (H1N1, PR8) across 4 days post-infection, as well as founder haplotype effect analysis at Mx1 for pre-CC and CC-RIX.</p>
West Nile Virus Predictions output data
<p><span>The testSubmission.csv was meant for validating the results in the Kaggle competition. It is a csv with 2 columns, one being a probability value from 0 to 1 and the second being an id to which that probability refers to. Those probabilities are the result of the classifications of a trained XGBoost classifier. </span></p>
Supplementary dataset to publication: Approaching the complexity of Crimean-Congo hemorrhagic fever virus serology: a study in swine
<p>For the detection of anti-CCHFV antibodies in swine, we established a swine-specific in-house ELISA, indirect immunofluorescence assay and a virus neutralization test. Uploaded data contains sample performance in each test. Samples used in this study include swine serum samples from Germany and Spain.</p>
Continuous phylogeography analysis of Rift Valley fever virus (RVFV) in Africa and the Arabian Peninsula
<p>Spatiotemporal-explicit Bayesian phylogenetic trees and MCMC log files for Rift Valley fever virus large, medium and non-structural genetic sequences generated by BEAST v1.10</p> <ol> <li>Log files (logs.zip)</li> <li>Tree files (trees.zip)</li> </ol>
Alignments and ML trees of cassava brown streak virus and Ugandana cassava brown streak virus polyprotein nucleotide sequences
<p>Alignments of full and nearly full polyprotein-length nucleotide sequences from GenBank for the two ipomoviruses that cause cassava brown streak disease, in fasta format. Separate alignments for 67 cassava brown streak virus sequences and 81 Ugandan cassava brown streak virus sequences are provided, as well as a combined alignment of 148 sequences. Alignments were created with MUSCLE and then modified by eye in AliView.</p> <p>Also, two tree files (in nexus) format are supplied, resulting from a maximum likelihood analysis with IQTree on each of the two single-species datasets. Support for nodes with aLRT and 100 actual bootstrap replicates are provided (aLRT/bootstrap).</p>
Recombinant Hepatitis E Viruses Harboring Tags in the ORF1 Protein
<p>Hepatitis E virus (HEV) is one of the most common causes of acute hepatitis and jaundice in the world. Current understanding of the molecular virology and pathogenesis of hepatitis E is incomplete, especially due to the limited availability of functional tools. Here, we report the development of tagged HEV genomes as a novel tool to investigate the viral life cycle. A selectable subgenomic HEV replicon was subjected to random 15-nucleotide sequence insertion using transposon-based technology. Viable insertions in the open reading frame 1 (ORF1) protein were selected in a hepatoblastoma cell line. Functional insertion sites were identified downstream of the methyltransferase domain, in the hypervariable region (HVR) and between the helicase and RNA-dependent RNA polymerase domains. HEV genomes harboring a hemagglutinin (HA) epitope tag or a small luciferase (NanoLuc) in the HVR were found to be fully functional and to allow for the production of infectious virus. NanoLuc allowed to quantitatively monitor HEV infection and replication by luciferase assay. HA-tagged replicons and full-length genomes allowed to localize putative sites of HEV RNA replication by the simultaneous detection of viral RNA by fluorescence in situ hybridization and of ORF1 protein by immunofluorescence. Candidate HEV replication complexes were found in cytoplasmic dot-like structures which partially overlap with ORF2 and ORF3 proteins as well as exosomal markers. Hence, tagged HEV genomes yield new insights into the viral life cycle and should allow to further investigate the structure and composition of the viral replication complex.</p>
Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of (RNA) viruses
<p>Fasta file (blackfly_viral_genomes.fasta) with identified virus sequences in Cameroonian blackflies and a corresponding table with their taxonomy when possible (taxonomy_data.tsv). Viruses were identified with geNomad v1.7.0 and Diamond blastx v2.0.11 with the NCBI nr database (accessed 23-03-2023).</p> <p>We also included a fata file with all assembled sequences across all blackfly samples (blackfly.all.fasta)</p>
vPro-MS peptide spectral library for the identification of human-pathogenic viruses by untargeted proteomics
<p>The viral proteomics workflow (vPro-MS) enables identification of human-pathogenic viruses from patient samples by untargeted proteomics. vPro-MS is based on an in-silico derived peptide library covering the human virome in <a href="https://www.uniprot.org/" rel="nofollow">UniProtKB</a> (331 viruses, 20,386 genomes, 121,977 peptides). vPro-MS is intended to identify human-pathogenic viruses from DiaNN (<a href="https://github.com/vdemichev/DiaNN">https://github.com/vdemichev/DiaNN</a>) outputs of either DIA or diaPASEF data. A scoring algorithm (vProID) assesses the confidence of virus identification and the results are finally summarized in a report table. </p> <p>The vPro Peptide Library folder contains 3 peptide FASTA files (Contaminants.fasta, Human.fasta, vPro.Virus.fasta), which were used to predict the spectral library (vPro-lib.predicted.speclib). Please note, that the additional commands “--cut” and “--duplicate-proteins” are needed to reprocess the prediction in DiaNN. This spectral library should be used to identify peptide sequences from samples of human origin using DiaNN. Furthermore, the folder contains the metadata file of the viral peptide sequences (vPro.Peptide.Library.txt) and a summary file of the virus taxonomy covered by the library (Taxonomy.Summary.txt). The metadata file is used by the vPro script to identify viruses from the DiaNN main report.</p>
PhasAGE Training School 1 - Phase separation in virus-host interactions- LECTURE
<p>The Training School 1 <strong>“Computational Methods to Study Protein Phase Separation”</strong> is the first edition of a series of PhasAGE training activities.</p> <p>The goal of this course is to provide participants with the basic knowledge to understand the phenomenon of <strong>Phase Separation</strong>, its role in biological processes and diseases. In addition, the course will provide <strong>an overview of the available computational resources</strong> to navigate this knowledge. Participants will have <strong>hands-on training</strong> in tools and resources available for life sciences, to collect information from the literature on biomolecular phase transitions, identify features triggering phase transitions, mutations associated with diseases, known or predicted PTMs and molecular interaction sites.</p>
Experience of COVID-19 disease and fear of the SARS-CoV-2 virus among Polish students
<p>The deposited files contain a database related to the study of the fear of COVID-19 among Polish students and a code book. It is connected with the article titled <em>Experience of COVID-19 disease and fear of the SARS-CoV-2 virus among Polish students</em></p>
Data for Li et al., Waterborne virus transport and the associated risks in a large lake, Water Research; DOI: 10.1016/j.watres.2022.119437
<p>Experimental data (virus concentrations measured in sewage, in units of genome copies per mL sewage) </p> <p>Code (written in R) used to model virus concentration distributions</p> <p>Code (Delft3D and Matlab) used for hydrodynamic, water quality and QMRA simulations. Input files are for the "winter scenario" shown in the publication.</p>
Data for: Luo et al., Expiratory aerosol pH: the overlooked driver of airborne virus inactivation, Environmental Science and Technology, 10.1021/acs.est.2c05777
<p><strong>Experimental data </strong></p> <p>This folder contains the experimental data to the figures shown in the main manuscript and Supporting Information.</p> <p>Figures 1 and S3 (inactivation curves for IAV, SARS-CoV-2 and HCoV-229E)</p> <p>Figure 1 (rate constants)</p> <p>Figure 2 (EDB analysis of SLF)</p> <p>Figure S1A (zetasizer analysis to measure virus aggregation)</p> <p>Figure S1B (renilla and plaque assay data for viruses exposed to pH 5, 6 and 7)</p> <p>Figure S4A (EDB analysis of different SLF samples; raw data)</p> <p>Figure S4Amean (EDB analysis of different SLF samples; mean values)</p> <p>Figure S5 (EDB analysis of nasal mucus)</p> <p>Figure S8 (EDB analysis of slow crystal growth stage of SLF and nasal mucus)</p> <p>Figure S13 and S14 (literature data on inactivation of IAV and SARS-CoV-2 in aerosol particles)</p> <p> </p> <p> </p>
CRISPR-based engineering of RNA viruses
<p>CRISPR RNA-guided endonucleases have enabled precise editing of DNA. However, options for editing RNA remain limited. Here, we combine sequence-specific RNA cleavage by CRISPR ribonucleases with programmable RNA repair to make precise deletions and insertions in RNA. This work establishes a new recombinant RNA technology with immediate applications for the facile engineering of RNA viruses.</p> <p> </p> <p>This dataset contains code for analyzing sequencing data and generating figures in the manuscript.</p>
Virus operational taxonomic units (vOTUs) from Stordalen Mire, Sweden
<p>This file is a collection of 5,051 virus operational taxonomy units (vOTUs) that were identified from samples collected from Stordalen Mire, a long-term ecological research site in Abisko, Sweden. Peat soil was sampled from the active layer across 3 different thaw stages (palsa, bog, and fen) between 2010-2017. From 379 bulk metagenomes, virus sequences were identified <em>in silico</em> using VirSorter1 (with additional stringent filtering criteria). Virus sequences above 5kb in length were then clustered into vOTUs (using a threshold of 95% identity and 80% coverage). This vOTU dataset is the basis of a research paper, entitled 'Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient,' (Sun and Pratama, <em>et al.</em>, <em>in prep.</em>), which provides insights into permafrost viruses and their role in terrestrial carbon cycling.</p> <p> </p> <p>FUNDING:</p> <p>This research is a contribution of the EMERGE Biology Integration Institute (<a href="https://emerge-bii.github.io">https://emerge-bii.github.io/</a>), funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070.<br> We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164.<br> This study was also funded by the Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research, grant #s DE-SC0004632. DE-SC0010580. and DE-SC0016440.<br> A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal: 10.46936/10.25585/60001148) and used resources at the DOE Joint Genome Institute (<a href="https://www.google.com/url?q=https://ror.org/04xm1d337&sa=D&source=docs&ust=1674859614742521&usg=AOvVaw2XgXYw9eI4JIXRMKn3S9Se">https://ror.org/04xm1d337</a>) and the Environmental Molecular Sciences Laboratory (<a href="https://www.google.com/url?q=https://ror.org/04rc0xn13&sa=D&source=docs&ust=1674859614742655&usg=AOvVaw3UXdoHIFmVjc-mXUhDXYQt">https://ror.org/04rc0xn13</a>), which are DOE Office of Science User Facilities operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).</p>
Soil nitrogen and phosphorus effects on plant virus density, transmission, and species interactions
This data package includes data and code from an experiment testing the effects of nitrogen and phosphorus addition on interactions between two grass viruses (BYDV-PAV and CYDV-RPV). Data include virus density within oats (Avena sativa) and transmission of viruses to a second set of oats. Data were collected by Amy E. Kendig and collaborators between February 2014 and August 2014 at the University of Minnesota in St. Paul Minnesota, USA. Experiments were performed in growth chambers, virus density data were obtained using one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and transmission data were obtained using RT-PCR. The code includes statistical analyses and figures. Model objects created through statistical analyses are also included. The code was run using R (version 3.5.2).
Virus alignments found in human cancer - aidinfo table
<p>The file contains one row for every analysis_id (column name 'aid') analyzed for the paper. An analysis_id is a unique TCGA BAM file.</p>
Diagnostic electron microscopy of viruses with low-voltage electron microscopes. Raw image files with brief description.
<p>The zipped data container contains the raw (unprocessed) images that we have used for the preparation of our manuscript entiteled:</p> <p>"Diagnostic electron microscopy of viruses with low-voltage electron microscopes" <a href="https://doi.org/10.1369%2F0022155420929438">https://doi.org/10.1369/0022155420929438</a></p> <p>Lars Möller, Gudrun Holland, Michael Laue</p> <p>Advanced Light and Electron Microscopy (ZBS 4), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, D-13353 Berlin, Germany</p> <p>The brief description of the data set comprises the abstract of the manuscript, the figures (including captions) and a description of the materials and methods used for their generation.</p>
The virus and socioeconomic inequality: An agent-based model to simulate and assess the impact of interventions to reduce the spread of COVID-19 in Rio de Janeiro, Brazil
<p>This video shows de simulation of scenarios presented in the article "The virus and socioeconomic inequality: An agent-based model to simulate and assess the impact of interventions to reduce the spread of COVID-19 in Rio de Janeiro, Brazil"</p>
ScienceDex guides
Understand access before you commit
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.