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2,212 results for “virality”
Viral Communication: Trajectories of Experience through the Pandemic - A Qualitative Longitudinal Dataset
<p>Here, we present a dataset collected within a longitudinal interview study that has been conducted as part of a larger project (i.e., Viral Communication), exploring (changing) public attitudes and behaviours through the course of the pandemic in Germany. From a nationally representative survey, forty participants were purposively sampled on the basis of gender, age and socioeconomic status for the interviews. Each participant was interviewed three times within a 10 month time frame (between December 2020 and September 2021), with the exception of two dropouts from the study. The semi-structured interviews were developed to further elaborate on some of the responses in the survey instrument and to provide additional insights into topics and controversies surrounding the Covid-19 pandemic in Germany, such as information/misinformation, trust/distrust, compliance, vaccination, and conspiracy beliefs. </p> <ul> <li>Interviews Phase I (December 2020): 40 Interviews</li> <li>Interviews Phase II (April 2021): 38 Interviews</li> <li>Interviews Phase III (September 2021): 38 Interviews</li> </ul>
Assessment of hepatitis B viral lymphotrophism using deep curation
<p><strong><span>Background</span></strong><span><strong>:</strong> The replicative forms of the hepatitis B virus (HBV) is found in several types of white blood cells within the host defense system. To determine the dimensionality of the extrahepatic manifestation of HBV in host white blood cells, it is important to understand the complete biology of its pathogenesis and lymphotropic nature.</span></p> <p><strong><span>Methods</span></strong><span><strong>: </strong>Deep curation of the literature from the PubMed database pertaining to the HBV manifestation in the human host white blood cells was conducted and then manually filtered to determine the behavioral trend of the virus within the human white blood cells.</span></p> <p><strong><span>Results</span></strong><span><strong>:</strong> The curation of 198 research articles identified 28 genes, 92 proteins, and 20 Peripheral Blood Mononuclear cells involved in HBV pathogenesis, while 20 immune cells were found to be permissive for the viral penetration and replication. The presence of the replicative forms of HBV in the host immune cells led to the further elucidation of 28 genes and 92 proteins that interact with one or more viral genes and proteins.</span></p> <p><strong><span>Conclusions</span></strong><span><strong>:</strong> A multi-dimensional analysis using deep curation identified a possible lymphotropic character of HBV. Moreover, there are certain pathways that could aid in the propagation of viral infection by using immune cells to its advantage. Thus, instead of eliminating HBV, the immune system may contribute to the population expansion of the virus.</span></p>
TikTok dataset - Current affairs on TikTok. Virality and entertainment for digital natives
<p>Tiktok network graph with 5,638 nodes and 318,986 unique links, representing up to 790,599 weighted links between labels, using Gephi network analysis software.</p> <p>Source of:</p> <p>Peña-Fernández, Simón, Larrondo-Ureta, Ainara, & Morales-i-Gras, Jordi. (2022). Current affairs on TikTok. Virality and entertainment for digital natives. Profesional De La Información, 31(1), 1–12. <a href="https://doi.org/10.5281/zenodo.5962655">https://doi.org/10.5281/zenodo.5962655</a></p> <p>Abstract:</p> <p>Since its appearance in 2018, TikTok has become one of the most popular social media platforms among digital natives because of its algorithm-based engagement strategies, a policy of public accounts, and a simple, colorful, and intuitive content interface. As happened in the past with other platforms such as Facebook, Twitter, and Instagram, various media are currently seeking ways to adapt to TikTok and its particular characteristics to attract a younger audience less accustomed to the consumption of journalistic material. Against this background, the aim of this study is to identify the presence of the media and journalists on TikTok, measure the virality and engagement of the content they generate, describe the communities created around them, and identify the presence of journalistic use of these accounts. For this, 23,174 videos from 143 accounts belonging to media from 25 countries were analyzed. The results indicate that, in general, the presence and impact of the media in this social network are low and that most of their content is oriented towards the creation of user communities based on viral content and entertainment. However, albeit with a lesser presence, one can also identify accounts and messages that adapt their content to the specific characteristics of TikTok. Their virality and engagement figures illustrate that there is indeed a niche for current affairs on this social network.</p> <p> </p>
Single-cell transcriptome analysis of the in vivo response to viral infection in the cave nectar bat Eonycteris spelaea
<p>Bats are reservoir hosts of many zoonotic viruses with pandemic potential in humans. Here, we<br> utilized single-cell transcriptome sequencing (scRNA-seq) to provide detailed comparative<br> analyses of the immune repertoire and the transcriptional responses in the bat lungs upon in<br> vivo infection with a double-stranded RNA virus, Pteropine orthoreovirus PRV3M. Neutrophils<br> were observed to have basally high IDO1 expression, uniquely amongst mammals currently<br> profiled by scRNA-seq. NK/T cells were the most abundant immune cell type in lung tissue, and<br> included three distinct CD8 + effector T cell populations delineated by the differential expression<br> of KLRB1, GFRA2 and DPP4. We identified NK/T clusters which up-regulated genes involved in<br> T-cell activation and effector function early after viral infection. Alveolar macrophages and<br> classical monocytes were key drivers of antiviral interferon signaling. Infection also resulted in<br> the expansion of a CSF1R + population expressing collagen-like genes, which became the<br> predominant myeloid cell type after infection. This work uncovers novel features relevant to viral<br> disease tolerance in bats, lays a foundation for future in vivo and in vitro experimental<br> investigations, and serves as a key resource for comparative immunology studies across bats<br> and other mammals.</p> <p> </p> <p>This upload is the transcriptome fasta file used for alignment for the dataset.</p>
Viral mimicry response is associated with clinical outcome in pleural mesothelioma
<p>Raw data supporting the manuscript</p>
Antarctic Rock Viral Catalog
<p>Viral catalog associated with:<br> <br> Highly diverse and unknown viruses may enhance Antarctic endoliths adaptability<br> <br> Analysis, code, intermediate and supporting files are archived here: <a href="https://zenodo.org/record/7374327">https://zenodo.org/record/7374327</a><br> <br> While this archive contains:<br> <strong>(1) predicted_viral_sequences.fa.gz </strong>- compressed fasta file of all 101,085 predicted viral sequences<br> <strong>(2) vOTUs.fa.gz </strong>- compressed fasta file of all 76,985 95% similarity vOTUs<br> <strong>(3) vOTU_info.csv </strong>- csv containing metadata associated with each viral sequence and linking viral sequences to vOTUs</p>
Viral tweets with fakenews on 2016 US election day
<p>Collection of tweets related to the 2016 US election that went viral during the election day (Nov 8th). Viral tweets are those that achieved the 1000-retweet threshold duing the collection period.</p> <p>We queried Twitter's streaming API using the hashtags #MyVote2016, #ElectionDay, #electionnight, and the user handles @realDonaldTrump and @HillaryClinton.</p> <p>Tweets have been labelled as containing fake news or not by one expert. A fake news is one the following:</p> <p>Serious fabrication<br> Large-scale hoaxes<br> Jokes taken at face value<br> Slanted reporting of real facts<br> Stories where the 'truth' is contentious</p>
Fakenews on 2016 US elections viral tweets (November 2016 - March 2017)
<p>Collection of tweets related to the 2016 US election that went viral between election day (Nov 8th) and March 2017. Viral tweets are those that achieved the 1000-retweet threshold during the collection period. We queried Twitter's streaming API using the hashtags <em>#MyVote2016</em>, <em>#ElectionDay</em>, <em>#electionnight</em>, and the user handles <em>@realDonaldTrump</em> and<em> @HillaryClinton</em>.</p> <p>Tweets have been labelled as containing fake news or not by two sets of people. A fake news is one the following:</p> <ul> <li>Serious fabrication</li> <li>Large-scale hoaxes</li> <li>Jokes taken at face value</li> <li>Slanted reporting of real facts</li> <li>Stories where the 'truth' is contentious</li> </ul>
Metabolic enzymes moonlight as selective autophagy receptors to protect plants against viral-induced cellular damage
<p>The dataset contains all the original raw files for the following study:</p> <p><strong>Metabolic enzymes moonlight as selective autophagy receptors </strong><strong>to protect plants against viral-induced cellular damage</strong></p> <p>Marion Clavel<sup>1,2,*</sup>, Anita Bianchi<sup>1</sup>, Roksolana Kobylinska<sup>1</sup>, Roan Groh<sup>1,3</sup>, Juncai Ma<sup>4</sup>, Ranjith K. Papareddy<sup>1</sup>, Nenad Grujic<sup>1</sup>, Lorenzo Picchianti<sup>1,3</sup>, Ethan Stewart<sup>5</sup>, Michael Schutzbier<sup>1</sup>, Karel Stejskal<sup>1</sup>, Juan Carlos de la Concepcion<sup>1</sup>, Victor Sanchez de Medina Hernandez<sup>1,3</sup>, Yoav Voichek<sup>1</sup>, Pieter Clauw<sup>1</sup><strong>, </strong>Joanna Gunis<sup>1</sup>, Gerhard Durnberger<sup>1</sup>, Jens Christian Muelders<sup>2</sup>, Annett Grimm<sup>2</sup>, Arthur Sedivy<sup>5</sup>, Mathieu Erhardt<sup>6</sup>, Victoria Vyboishchikov<sup>1</sup>, Peng Gao<sup>1</sup>, Esther Lechner<sup>6</sup>, Emilie Vantard<sup>6</sup>, Jakub Jez<sup>5</sup>, Elisabeth Roitinger<sup>1</sup>, Pascal Genschik<sup>6</sup>, Byung-Ho Kang<sup>4</sup>, Yasin Dagdas<sup>1,*</sup></p> <p><strong> </strong></p> <p><strong>Affiliations</strong></p> <p><sup>1</sup>Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.</p> <p><sup>2</sup>Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany</p> <p><sup>3</sup>Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna, Austria</p> <p><sup>4</sup>School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China</p> <p><sup>5</sup>Vienna Biocenter Core Facilities (VBCF), Vienna, Austria</p> <p><sup>6</sup>Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France</p> <p> </p> <p>*Correspondence: Marion Clavel (marion.clavel@mpimp-golm.mpg.de),</p> <p> Yasin Dagdas (yasin.dagdas@gmi.oeaw.ac.at)</p> <p><strong> </strong></p> <p><strong>Abstract</strong></p> <p>RNA viruses co-opt the host endomembrane system and organelles to build replication complexes for infection. How the host responds to these membrane perturbations is poorly understood. Here, we explore the autophagic response of <em>Arabidopsis thaliana</em> to three viruses that hijack different cellular compartments. Autophagy is significantly induced within systemically infected tissues, its disruption rendering plants highly sensitive to infection. Contrary to being an antiviral defense mechanism as previously suggested, quantitative analyses of the viral loads established autophagy as a tolerance pathway. Further analysis of one of these viruses, the Turnip Crinkle Virus (TCV) that hijack mitochondria, showed that despite perturbing mitochondrial integrity, TCV does not trigger a typical mitophagy response. Instead, TCV and Turnip yellow mosaic virus (TYMV) infection activates a distinct selective autophagy mechanism, where oligomeric metabolic enzymes moonlight as selective autophagy receptors and degrade key executors of defense and cell death such as EDS1. Altogether, our study reveals an autophagy-regulated metabolic rheostat that gauges cellular integrity during viral infection and degrades cell death executors to avoid catastrophic amplification of immune signaling.</p> <p> </p> <p>One archive corresponds to one main or supplemental figure.</p>
Comprehensive large-scale datasets for 26 viral families for fine-tuning BERT-infect models
<p>These datasets were constructed in the paper "Hidden Challenges in Evaluating Spillover Risk of Zoonotic Viruses using Machine Learning Models" (doi: https://doi.org/10.1101/2024.04.25.591033). The details were also described in the git-hub (https://github.com/Junna-Kawasaki/BERT-infect_2024).</p> <ul> <li>The compressed files, such as ${virus}.tar.xz, contain fasta and genbank files.</li> </ul>
Long-term wastewater monitoring of SARS-CoV-2 viral loads and variants at the major international passenger hub Amsterdam Schiphol Airport: a valuable addition to COVID-19 surveillance
<p>Datasets used for the manuscript: <em>Long-term wastewater monitoring of SARS-CoV-2 viral loads and variants at the major international passenger hub Amsterdam Schiphol Airport: a valuable addition to COVID-19 surveillance</em></p> <p><em>pandemic_daily_passenger_counts.tsv</em>: An overview of daily passenger arrival counts at Amsterdam Schiphol Airport per continent of origin during the study period 16-02-2020 - 04-09-2022</p> <p><em>pre-pandemic_daily_passenger_averages.tsv: </em>An overview of mean daily passenger arrival counts at Amsterdam Schiphol Airport in the pre-pandemic period 2017-2019.</p> <p><em>viral_load_data.tsv: </em>Sample metadata (sample identifier, sampling date, flow, average # particles per ml, and flow-corrected viral-load) for samples taken at the wastewater treatment plant of Amsterdam Schiphol Airport.</p> <p><em>wastewater_variant_frequencies.tsv: </em>SARS-CoV-2 lineage estimates in samples taken at the wastewater treatment plant of Amsterdam Schiphol Airport, analyzed using whole-genome tiled amplicon sequencing.</p> <p> </p> <p> </p> <p> </p>
Viral diversity and co-evolutionary dynamics across the ant phylogeny
<p>This repository contains the alignment file and phylogeny of every viral clade assessed in this study. The viral phylogenies are in Newick format as well as a pdf and contain bootstrap values greater than 50. The alignment files are in PHYLIP format. Additionally, this repository contains nucleotide sequences of every viral sequence identified in this study and it is entitled: "final_viruses_contigs.fasta" in fasta format. </p>
Epidemiologic data relating to age and gender specific HIV viral suppression in Rakai, Uganda, 2013-2019
<div> <p>This repository contains the data for the analyses presented in the paper "<span><span>Age and gender profiles of HIV infection burden and viraemia: novel metrics for HIV epidemic control in African populations with high antiretroviral therapy coverage</span></span>", soon available as a preprint. </p> <p>We thank all contributors, program staff, and participants to the Rakai Community Cohort Study.</p> <p>We also extend our gratitude to the <a href="https://doi.org/10.14469/hpc/2232">Imperial College Research Computing Service</a> for providing the computational resources to perform this study. Additionally, we thank the Office of Cyberinfrastructure and Computational Biology at the <a href="https://www.niaid.nih.gov/">National Institute for Allergy and Infectious Diseases</a> for data management support; and Zulip for sponsoring team communications through the Zulip Cloud Standard chat app. </p> <p>All analysis code is available from <a href="https://github.com/MLGlobalHealth/longi_viral_loads">https://github.com/MLGlobalHealth/longi_viral_loads</a>.</p> </div>
Fig. 1 in Refining the Occurrence of Viral Encephalopathy and Retinopathy, Photobacteriosis, and Vibriosis in Connection with Seawater Physicochemical Parameters: A Five-Year Case Study Abstract
Fig. 1: Study area.
SRR606249 spiked with fungal and viral Illumina reads at 1x, 10X, and 100X
<p>SRR606249 spiked with fungal and viral Illumina reads at 1x, 10X, and 100X using the ART simulator.</p> <p>See also: https://osf.io/dm938/ and https://dahak-metagenomics.github.io/</p> <p>Fungal and viral genomes used for computational spike-ins.<br> Kingdom Organism Accession Link<br> Fungus Candida albicans SC5314 NC_032089.1 https://www.ncbi.nlm.nih.gov/genome/?term=Candida+albicans<br> Fungus Cryptococcus neoformans var. grubii H99 NC_026745.1 https://www.ncbi.nlm.nih.gov/genome/?term=Cryptococcus+neoformans<br> Fungus Aspergillus fumigatus Af293 NC_007194.1 https://www.ncbi.nlm.nih.gov/genome/?term=Aspergillus+fumigatus<br> Fungus Histoplasma capsulatum NAm1 NW_001813913.1 https://www.ncbi.nlm.nih.gov/genome/?term=Histoplasma+capsulatum<br> Virus Human immunodeficiency virus 1 NC_001802.1 https://www.ncbi.nlm.nih.gov/genome/10319<br> Virus Influenza A virus (A/New York/392/2004(H3N2)) NC_007373.1 https://www.ncbi.nlm.nih.gov/genome/10290<br> Virus Marburg virus - Musoke, Kenya, 1980 NC_001608.3 https://www.ncbi.nlm.nih.gov/genome/5314<br> Virus Ebola virus - Mayinga, Zaire, 1976 NC_002549.1 https://www.ncbi.nlm.nih.gov/assembly/GCF_000848505.1/</p>
Dataset S2 - Viral metagenomics in the clinical realm: lessons learned from a Swiss-wide ring trial
<p>Dataset S2. FASTQ datasets for increment 2.</p> <p>Supplemental material of article "Viral metagenomics in the clinical realm: lessons learned from a Swiss-wide ring trial".</p>
Dataset S1 - Viral metagenomics in the clinical realm: lessons learned from a Swiss-wide ring trial
<p>Dataset S1. SIB common database.</p> <p>Supplementary material from article "Viral metagenomics in the clinical realm: lessons learned from a Swiss-wide ring trial".</p>
Exploiting functional regions in the viral RNA genome as druggable entities
<p><span>XML files with normalized SHAPE reactivities are provided in SHAPE_react_rep1/2.react.xml; </span></p> <p><span>WIG files with Shannon entropies are provided in SHAPE_react_rep1/2.react.xml,</span></p> <p><span>and the full secondary structure are provided in PEDV_incell_secondary structure.ct</span></p>
Graphic Illustration of Rick White's Talk: Preventing the next viral pandemic via elucidation of mammalian reservoirs
<p><a href="https://lib.ku.edu/people/courtney-foat" target="_blank" rel="noopener">Courtney Foat</a>, Advisor for Strategic Initiatives & Organizational Engagement at the University of Kansas, graphically recorded this invited talk by Rick White at an NSF-supported Workshop: Digital Collections Data and Tracking Disease.</p>
Data from: Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions
1.Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. 2.Here we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype specific transmission pathways in a social carnivore. 3.We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIVPle) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIVPle molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father and/or mother offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype specific FIVPle co-occurrence networks and assessed what combination of social networks, spatial networks, or co-infection best structured the FIVPle network. 4.While social organization (i.e., pride) was an important component of FIVPle transmission pathways at all scales, we find that FIVPle subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIVPle transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype specific. 5.Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.
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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.