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944 results for “antiviral”
Diffraction images used to solve the structures published in the article "Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host-glycosylation target"
<p>Raw diffraction images used for generating the structures published in the article "Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host-glycosylation target" (available <a href="https://doi.org/10.1073/pnas.2013620117">here</a>). Full single-crystal datasets, including images that were not used in the final analyses, are published. The software used for the processing of each dataset is listed in their respective PDB entries. Datasets 6ZJ1 and 6ZJ5 were cut anisotropically using STARANISO, other datasets were processed isotropically.</p> <p> </p> <p>If you find this useful, please contact me at <a href="mailto:lukasz.sobala@hirszfeld.pl">lukasz.sobala@hirszfeld.pl</a>, I am just interested in how these data are used!</p>
Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity
<p>The data present in this repository reflect intermediate and processed data presented in the manuscript, <em>Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity. </em>This manuscript is still under review; as such, this page will be updated upon publication.</p> <p> </p> <p><strong>Manuscript Abstract:</strong></p> <p>Evolutionary perspectives on the deployment of immune factors following infection have been shaped by studies on a limited number of biomedical model systems with a heavy emphasis on vertebrate species. Though their contributions to contemporary immunology cannot be understated, a broader phylogenetic perspective is needed to understand the evolution of immune systems across Metazoa. In our study, we leverage differential gene expression analyses to identify genes implicated in the antiviral immune response of the acorn worm hemichordate, <em>Saccoglossus kowalevskii</em>, and place them in the context of immunity evolution within deuterostomes – the animal clade composed of chordates, hemichordates, and echinoderms. Following acute exposure to the synthetic viral dsRNA analog, poly(I:C), we show that <em>S. kowalevskii </em>responds by regulating the transcription of genes associated with canonical innate immunity signaling pathways (e.g., NF-κB and IRF signaling) and metabolic processes (e.g., lipid metabolism), as well as many genes without clear evidence of orthology with those of model species. Aggregated across all experimental time point contrasts, we identify 423 genes that are differentially expressed in response to poly(I:C). We also identify 147 genes with altered temporal patterns of expression in response to immune challenge. By characterizing the molecular toolkit involved in hemichordate antiviral immunity, our findings provide vital evolutionary context for understanding the origins of immune systems within Deuterostomia.</p> <p> </p> <p><strong>Repository contents:</strong></p> <p>### Processed Data ###</p> <ul> <li><em>Full_DESeq2_matrix.csv </em>--> DESeq2 results for each contrast (e.g., 2hpi treatment vs. control)</li> <li><em>MaSigPro.Clusters.csv</em> --> Mean expression for each gene placed within a pDEG cluster</li> <li><em>MaSigPro.SigGenes.TreatmentvsControl.Robj</em> --> T.fit() R-object output from MaSigPro pipeline. This can be opened in R using the load() function.</li> </ul> <p>### Homology Assessment ###</p> <ul> <li><em>Orthofinder.tar.gz</em> --> OrthoFinder results</li> <li><em>Skowalevskii_Genome_Annotation.SPHuman_and_HOG.csv</em> --> Assignment of IDs to Skow1.1 genes conforming to "PANTHER-Human" and "HOG" output described in the main text of the paper</li> <li><em>Skowalevskii_Genome_Annotation.SPPANTHER.csv </em>--> Assignment of IDs to Skow1.1 genes conforming to "PANTHER-SwissProt" output described in the main text of the paper</li> </ul> <p>### Functional Annotation ###</p> <ul> <li><em>Skow.HMMER_Pfam.domtblout.tsv</em> --> Pfam annotation of the Skow1.1 genome assembly in HMMER's domblout format</li> <li><em>Skow.KofamKOALA.detail.tsv</em> --> KO annotation of the Skow1.1 genome assembly using KofamKOALA (detailed output)</li> <li><em>Skow.KofamKOALA.detail.tsv </em>--> KO annotation of the Skow1.1 genome assembly using KofamKOALA (mapper output)</li> <li><em>SkowAnnotations.GO.tsv</em> --> GO annotation of the Skow1.1 genome assembly</li> <li><em>SkowAnnotations.PF.tsv</em> --> PF annotation of the Skow1.1 genome assembly</li> <li><em>SkowAnnotations.PP.tsv</em> --> PP annotation of the Skow1.1 genome assembly</li> </ul> <p>### Enrichment Data ###</p> <ul> <li><em>DESeqEnrichments.tsv</em> --> Pearson's chi-squared enrichment calculations for every annotation present in the Skow1.1 genome assembly for genes resolved as significantly differentially expressed by DESeq2.</li> <li><em>MaSigProEnrichments.tsv</em> --> Pearson's chi-squared enrichment calculations for every annotation present in the Skow1.1 genome assembly for genes resolved as significantly differentially expressed by MaSigPro.</li> </ul>
Polyphenols' Inflammation-mediated Deglucuronidation and Promiscuous-binding Behavior for Antiviral Assaying and Trialing
<p>Dataset based on EMSKE Phytochem's pre-existing library of more than 250 Pubchem compounds that supports the research work Polyphenols’ Inflammation-mediated Deglucuronidation and Promiscuous-binding Behavior for Antiviral Assaying and Trialing. It refers to Jasial et al. 2016's dataset uploaded to Zenodo, <br> <br> Jasial, S.; Hu, Y.; Bajorath, J. PubChem Compounds Tested in Primary and Confirmatory Assays, 2016<br> <br> located at https://doi.org/10.5281/zenodo.44593 , which itself supports their work Jasial et al 2017: <br> <br> Jasial, S.; Hu, Y.; Bajorath, J. Determining the Degree of Promiscuity of Extensively Assayed Compounds. PLOS ONE 2016, 11 (4), e0153873. https://doi.org/10.1371/journal.pone.0153873.</p>
Antiviral activity of HIV-1 integrase strand-transfer inhibitors against mutants with integrase resistance-associated mutations and their frequency in treatment-naïve individuals
<p>The development of resistance to human immunodeficiency virus 1 (HIV-1) integrase strand-transfer inhibitors (INSTI) has been documented; however, knowledge of the impact of pre-existing integrase (IN) mutations on INSTI resistance (INSTI-R) is still evolving. The frequency of HIV-1 IN mutations in 2177 treatment-naïve subjects was investigated, along with the INSTI susceptibility of site-directed mutant viruses containing major and minor INSTI-R mutations. Total 6 of 39 minor INSTI-R mutations (M50I, S119P/G/T/R, and E157Q) were found in >1% of IN-treatment-naïve subjects with no impact on INSTI susceptibility. When each combined with major INSTI-R mutation, M50I, S119P, and E157Q led to decreased susceptibility to elvitegravir but remained sensitive to dolutegravir and bictegravir.</p>
Antiviral Efficacy and Acceptability of Mouth Rinses for Inactivation of COVID-19
ClinicalTrials.gov study NCT04748783. IPD Sharing: YES. Countries: 1. Publications: 14.
Raw data for the article: Successful Use of Heterologous CMV-Reactive T Lymphocyte to Treat Severe Refractory Cytomegalovirus (CMV) Infection in a Liver Transplanted Patient: Correlation of the Host Antiviral Immune Reconstitution with CMV Viral Load and CMV miRNome
<p>Cytomegalovirus (CMV) infection is the most significant viral infection in hosts with compromised immune systems as solid organ transplant patients. Despite significant progress being made in the prevention of CMV disease in these patients, further therapeutic strategies for CMV disease and for the CMV reactivation prevention are needed. Here, we describe the outcome of the infusion of in vitro expanded CMV-reactive T-cells, taken from a healthy CMV-seropositive donor, in a liver-transplanted recipient with a refractory recurrent CMV. In this particular case, adoptive transfer of allogenic CMV-reactive T-lymphocytes resulted in the clearance of CMV infection and resolution of the pathological manifestations of the patient. In the study we also investigated circulating miRNAs, both cellular and viral, as potential biomarkers during the course of CMV infection. The results indicate that the infusion of allogenic CMV-reactive T-cells can be an effective strategy to treat CMV infection recurrence when the generation of autologous virus specific T cell clones is not possible.</p>
Bacterial homologs of innate eukaryotic antiviral defenses provide phage protection.
<p>Supplementary data regarding the 'Bacterial homologs of innate eukaryotic antiviral defenses provide phage protection' manuscript.</p><p> </p><p><strong>Abstract:</strong><br>Prokaryotes have evolved a multitude of defense systems to protect themselves from bacteriophage predation. Here, we discovered new phage defense systems related to innate antiviral genes from vertebrates and plants. Our search uncovered over 400 candidates from which eleven were selected and six novel phage defense systems validated. We identified a DNA replication helicase/nuclease 2 (Prometheus) which may act on transcription R-loops, an inositol-monophosphatase-like phage defense protein (Pan), and two ATPases from the NACHT family coupled to novel effectors NucS and SfsA (Nyx and Hypnos). In addition, a fused ubiquitin-like E1-E2-JAB protein combined with a putative MBL nuclease (6A-MBL) was found, and a novel member of the Thoeris family that contains four essential TIR domains with a putative effector SLOG domain (Thoeris type III). Collectively, these defense systems support the concept of deep evolutionary links and shared antiviral mechanisms between prokaryotes and eukaryotes.</p>
Supplement tables of Facilitating Antiviral Drug Discovery by Genetic and Evolutionary Knowledge
<p>Table S1: 36 human targets for approved antiviral drugs downloaded from Drugbank,</p> <p>Table S2: Supplementary information for Table 2,</p> <p>Table S3: Pockdrug druggability prediction results.</p>
SARS-CoV-2–host proteome interactions for antiviral drug discovery
<p>Images and datasets used in Fig 6 and corresponding supplementary material Image analysis was performed with Harmony 4.9 software (PerkinElmer) with feature extraction and linear classification of N-protein positive cells from the total population as presented in the PlateResults file. Prism files (GraphPad Software) include the calculations for curve fits of drug testing data (4PL logistic regression) as well as area under the curve (AUC) of the fitted curves..</p>
A genome-wide optical pooled screen reveals regulators of antiviral responses
<p>Supplementary Datasets for "A genome-wide optical pooled screen reveals regulators of antiviral responses"</p> <p><strong>Supplementary Dataset 1. </strong>Mean per-gene extracted features for all channels of genome-wide screen</p> <p><strong>Supplementary Dataset 2. </strong>Features from single cells in secondary antibody screen</p> <p><strong>Supplementary Dataset 3. </strong>Features from single cells in secondary reporter screen</p> <p><strong>Supplementary Dataset 4. </strong>IRF3 translocation scores from primary and secondary IRF3 antibody and IRF3 reporter screens (the latter upon both Sendai virus and VSV infection) and SeV intensity scores from secondary antibody screen.</p> <p><strong>Supplementary Dataset 5. </strong>Peroxisome and Sendai virus feature scores from genome-wide screen</p>
Data from: Rotavirus NSP1 subverts the antiviral oligoadenylate synthetase-RNase L pathway by inducing RNase L degradation
<div>The interferon (IFN)-inducible 2′,5′-oligoadenylate synthetase (OAS)-RNase L pathway plays a critical role in antiviral immunity. Group A rotaviruses, including the simian SA11 strain, inhibit this pathway through two activities: an E3-ligase related activity of NSP1 that degrades proteins necessary for IFN signaling, and a phosphodiesterase (PDE) activity of VP3 that hydrolyzes the RNase L-activator 2′,5′-oligoadenylate. Unexpectedly, we found that a recombinant (r) SA11 double mutant virus deficient in both activities (rSA11-VP3H797R-NSP1ΔC17) retained the ability to prevent RNase L activation. Mass spectrometry led to the discovery that NSP1 interacts with RNase L in rSA11-infected HT29 cells. This interaction was confirmed through copulldown assay of cells transiently expressing NSP1 and RNase L. Immunoblot analysis showed that infection with wild-type rSA11 virus, rSA11-VP3H797R-NSP1ΔC17 double mutant virus, or single mutant forms of the latter virus all resulted in the depletion of endogenous RNase L. The loss of RNase L was reversed by addition of the neddylation inhibitor MLN4924, but not the proteasome inhibitor MG132. Analysis of additional mutant forms of rSA11 showed that RNase L degradation no longer occurred when either the N-terminal RING domain of NSP1 was mutated or the C-terminal 98 amino acids of NSP1 were deleted. The C-terminal RNase L degradation domain is positioned upstream and is functionally independent of the NSP1 domain necessary for inhibiting IFN expression. Our studies reveal a new role for NSP1 and its E3-ligase related activity as an antagonist of RNase L and uncover a novel virus-mediated strategy of inhibiting the OAS-RNase L pathway.</div>
Evaluation of Safety, Tolerability, and Antiviral Activity of Chlorcyclizine HCl in Patients With Chronic Hepatitis C
ClinicalTrials.gov study NCT02118012. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Study to Evaluate the Safety, Tolerability, Pharmacokinetics, and Antiviral Activity of Multiple Doses of ABT-333 Alone and in Combination With Pegylated Interferon (pegIFN) and Ribavirin (RBV) in S
ClinicalTrials.gov study NCT00851890. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Safety and Efficacy of Sofosbuvir/Velpatasvir/Voxilaprevir and Sofosbuvir/Velpatasvir in Adults With Chronic HCV Infection Who Have Not Previously Received Treatment With Direct-Acting Antiviral Thera
ClinicalTrials.gov study NCT02607800. IPD Sharing: YES. Countries: 8. Publications: 1.
Study to Evaluate the Safety and Antiviral Activity of Remdesivir (GS-5734™) in Participants With Moderate Coronavirus Disease (COVID-19) Compared to Standard of Care Treatment
ClinicalTrials.gov study NCT04292730. IPD Sharing: YES. Countries: 15. Publications: 3.
Safety, Antiviral Activity, and Pharmacokinetics of GSK2336805 With Peginterferon and Ribavirin in Chronic Hepatitis C Subjects
ClinicalTrials.gov study NCT01439373. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Study to Determine the Safety and Effectiveness of Antiviral Combination Therapy to Treat Hepatitis C Virus (HCV) in Patients Who Have Previously Not Received the Standard of Care
ClinicalTrials.gov study NCT01359644. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Antiviral Activity of Peg-IFN-Alpha-2A in Chronic HIV-1 Infection
ClinicalTrials.gov study NCT00594880. IPD Sharing: Not stated. Countries: 1. Publications: 3.
A Study to Evaluate the Pharmacokinetics, Safety, Tolerability, and Antiviral Activity of Rilpivirine (TMC278) in Human Immunodeficiency Virus Infected Adolescents and Children Aged Greater Than or Eq
ClinicalTrials.gov study NCT00799864. IPD Sharing: Not stated. Countries: 8. Publications: 1.
Evaluating the Safety, Tolerability, Pharmacokinetics, and Antiviral Activity of the Monoclonal Antibody PGT121.414.LS Administered Alone and in Combination With VRC07-523LS Via Intravenous or Subcuta
ClinicalTrials.gov study NCT04212091. IPD Sharing: NO. Countries: 1. Publications: 1.
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.