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90 results for “virus detection”
Data from: Crop-associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection
To understand the eco-evolutionary significance of plant viruses in nature, we must (i) quantify the effects of infection on plant fitness and (ii) recognize that native plants are increasingly exposed to crop-associated viruses. Studies of perennials are particularly needed: most of our knowledge of plant-virus interactions is from annuals, yet long-lived species dominate landscapes. Here we used aster models for life-history analysis and longitudinal measures of plant virus status to evaluate multi-year consequences of crop virus infection in a native perennial. We used Barley yellow dwarf virus acquired from wheat to inoculate seedlings of Panicum virgatum L. (switchgrass), a North American prairie grass. We grew inoculated and mock-inoculated individuals of two ecotypes for 3 years in the field. We measured plant size, infection status and fitness components. Aster modelling provided integrated multi-year measures of fitness. Crop virus inoculation reduced multi-year native plant fitness by 30% over 2 years despite generally asymptomatic infection and evidence of resistance. This reduction was greater than predicted from individual fitness components or most size measures. Ecotypes differed in response, with the lowland ecotype experiencing higher apparent recovery from infection. Virus treatment in the upland ecotype delayed flowering phenology and reduced seed filling. Synthesis. Our use of field experimentation, surveys of plant infection status and aster modelling demonstrates a rigorous and broadly applicable approach for quantifying the effects of viruses and other microbes on multi-year plant fitness. We found that a crop virus had negative multi-year effects on native plant fitness even after infection was no longer detected. Viruses may have substantial effects on native vegetation with domestication of landscapes and agricultural expansion.
Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery
<p>This repository contains data and code used to analyze data for this manuscript: </p> <p><em>Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery</em></p>
Nanopore Sequencing of Double-Stranded RNA (dsRNA) for Plant Virus and Viroid Detection
<p>Thi file contain results of 24 grapevines leaf samples analyzed using dsRNA-MiSeq (Illumina Miseq) and dsRNAcD sequencing (ONT nanopore), that were used in the following article ''<strong>Nanopore Sequencing of Double-Stranded RNA (dsRNA) for Plant Virus and Viroid Detection'' </strong> submitted in Frontiers in Microbiology </p>
Pilot Study to Detect Zika Virus in Sperm
ClinicalTrials.gov study NCT02874456. IPD Sharing: NO. Countries: 1. Publications: 1.
COVID-19: Nasal and Salivary Detection of the SARS-CoV-2 Virus After Antiviral Mouthrinses
ClinicalTrials.gov study NCT04352959. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Detecting Respiratory Viruses in Upper and Lower Respiratory Tract Samples
ClinicalTrials.gov study NCT01597089. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Diagnostic Validation of Rapid Detection of the COVID-19 Causative Virus (SARS-CoV-2) in Saliva Samples by Mass Spectrometry
ClinicalTrials.gov study NCT04712175. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Pilot Study to Detect DENGUE Virus in Sperm
ClinicalTrials.gov study NCT03612609. IPD Sharing: NO. Countries: 1. Publications: 6.
Performance Evaluation of RealDetect™ COVID-19 RT-PCR Kit for the Detection of SARS-CoV-2 Virus
ClinicalTrials.gov study NCT04403672. IPD Sharing: NO. Countries: 1. Publications: 2.
Early Detection of Epstein-Barr Virus Related Disease.
ClinicalTrials.gov study NCT03546101. IPD Sharing: NO. Countries: 1. Publications: 1.
Pilot Study to Detect SARS-CoV-2 Virus in Sperm
ClinicalTrials.gov study NCT04584593. IPD Sharing: NO. Countries: 1. Publications: 4.
Data from: Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material
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Detection and genetic characterization of arboviruses and other viruses from mosquitoes collected in Southeastern and Central Senegal, October 2022
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Data from: Crop-associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection
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Data from: Label-free sensitive detection of influenza virus using PZT discs with a synthetic sialylglycopolymer receptor layer
We describe rapid, label-free detection of Influenza A viruses using the first radial mode of oscillations of lead zirconate titanate (PZT) piezoelectric disks with a 2-mm radius and 100-µm thickness fabricated from a piezoelectric membrane. The disks are modified with a synthetic sialylglycopolymer receptor layer,and the coated disks are inserted in a flowing virus suspension. Label-free detection of the virus is achieved by monitoring the disk radial mode resonance frequency shift. Piezo transducers with sialylglycopolymer sensor layers exhibited a long lifetime, a high sensitivity, and the possibility of regeneration. We demonstrate positive, label-free detection of Influenza A viruses at concentrations below 10^5 virus particles per millilitre. We show that label-free, selective, sensitive detection of Influenza viruses by home appliances is possible in principle.
Effectiveness of passive sampling for the detection and genetic characterization of human viruses in wastewater (Dataset 1)
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Effectiveness of passive sampling for the detection and genetic characterization of human viruses in wastewater (Dataset 2)
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Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection
<p>In the last decade, High-Throughput Sequencing (HTS) has revolutionized biology and medicine. This technology allows the sequencing of huge amount of DNA and RNA fragments at a very low price. In medicine, HTS tests for disease diagnostics are already brought into routine practice. However, the adoption in plant health diagnostics is still limited. One of the main bottlenecks is the lack of expertise and consensus on the standardization of the data analysis. The Plant Health Bioinformatic Network (PHBN) is an Euphresco project aiming to build a community network of bioinformaticians/computational biologists working in plant health. One of the main goals of the project is to develop reference datasets that can be used for validation of bioinformatics pipelines and for standardization purposes.</p> <p>Semi-artificial datasets have been created for this purpose (Datasets 1 to 10). They are composed of a "real" HTS dataset spiked with artificial viral reads. It will allow researchers to adjust their pipeline/parameters as good as possible to approximate the actual viral composition of the semi-artificial datasets. Each semi-artificial dataset allows to test one or several limitations that could prevent virus detection or a correct virus identification from HTS data (<i>i.e.</i> low viral concentration, new viral species, non-complete genome).</p> <p>Eight artificial datasets only composed of viral reads (no background data) have also been created (Datasets 11 to 18). Each dataset consists of a mix of several isolates from the same viral species showing different frequencies. The viral species were selected to be as divergent as possible. These datasets can be used to test haplotype reconstruction software, the goal being to reconstruct all the isolates present in a dataset.</p> <p><span>A GitLab repository (<a href="https://gitlab.com/ilvo/VIROMOCKchallenge">https://gitlab.com/ilvo/VIROMOCKchallenge</a>) is available and provides a complete description of the composition of each dataset, the methods used to create them and their goals.</span></p>
Detection and Characterisation of Varicella Zoster Virus From Dermal Lesions of Chickenpox-infected Patients
ClinicalTrials.gov study NCT00127608. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection
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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.