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Dataset results
123 results for “Target detection”
Data from: Quantitative ornithology with a commercial marine radar: standard-target calibration, target detection and tracking, and measurement of echoes from individuals and flocks
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Data from: Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing
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Data from: D quantification of tumor vasculature in lymphoma xenografts in NOD/SCID mice allows to detect differences among vascular-targeted therapies
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Data from: Identifying targets of selection in mosaic genomes with machine learning: applications in Anopheles gambiae for detecting sites within locally adapted chromosomal inversions
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Data from: Fusobacterium nucleatum and Bacteroides fragilis detection in colorectal tumours: optimal target site and correlation with total bacterial load
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Selection and exploitation of prevalent, tandemly repeated genomic targets for improved real-time PCR-based detection of Wuchereria bancrofti and Plasmodium falciparum in mosquitoes
<p><b>Background</b></p> <p>Optimization of polymerase chain reaction (PCR)-based diagnostics requires the careful selection of molecular targets that are both highly repetitive and pathogen-specific. Advances in both next-generation sequencing (NGS) technologies and bioinformatics-based analysis tools are facilitating this selection process, informing target choices and reducing labor. Once developed, such assays provide disease control and elimination programs with an additional set of tools capable of evaluating and monitoring intervention successes. The importance of such tools is heightened as intervention efforts approach their endpoints, as accurate and complete information is an essential component of the informed decision-making process. As global efforts for the control and elimination of both lymphatic filariasis and malaria continue to make significant gains, the benefits of diagnostics with improved analytical and clinical/field-based sensitivities and specificities will become increasingly apparent.</p> <p><b>Methodology/Principal Findings </b></p> <p>Coupling Illumina-based NGS with informatics approaches, we have successfully identified the tandemly repeated elements in both the <i>Wuchereria bancrofti </i>and <i>Plasmodium falciparum </i>genomes of putatively greatest copy number. Utilizing these sequences as quantitative real-time PCR (qPCR)-based targets, we have developed assays capable of exploiting the most abundant tandem repeats for both organisms. For the detection of <i>P. falciparum</i>, analysis and development resulted in an assay with improved analytical and field-based sensitivity vs. an established ribosomal sequence-targeting assay. Surprisingly, analysis of the <i>W. bancrofti </i>genome predicted a ribosomal sequence to be the genome's most abundant tandem repeat. While resulting cycle quantification values comparing a qPCR assay targeting this ribosomal sequence and a commonly targeted repetitive DNA sequence from the literature supported our finding that this ribosomal sequence was the most prevalent tandemly repeated target in the <i>W. bancrofti </i>genome, the resulting assay did not significantly improve detection sensitivity in conjunction with field sample testing. </p> <p><b>Conclusions/Significance </b></p> <p>Examination of pathogen genomes facilitates the development of PCR-based diagnostics targeting the most abundant and specific genomic elements. While in some instances currently available tools may deliver equal or superior performance, systematic analysis of potential targets provides confidence that the selected assays represent the most advantageous options available and that informed assay selection is occurring in the context of a particular study's objectives.</p>
Sample site coordinates, environmental data, number of copies of target DNA/ul for each sample and limit of detection plot
<p>Human activities in coastal areas are accelerating ecosystem changes at an unprecedented pace, resulting in habitat loss, hydrological modifications, and predatory species declines. Understanding how these changes potentially cascade across marine and freshwater ecosystems requires knowing how mobile euryhaline species link these seemingly-disparate systems. As upper trophic level predators, bull sharks (<i>Carcharhinus leucas</i>) play a crucial role in marine and freshwater ecosystem health. Telemetry studies in Mobile Bay, Alabama suggest that bull sharks extensively use the northern portions of the bay, an estuarine-freshwater interface known as the Mobile-Tensaw Delta. To assess whether bull sharks use freshwater habitats in this region, environmental DNA surveys were conducted during the dry summer and wet winter seasons in 2018. In each season, 5 x<span> 1</span> L water samples were collected at each of 21 sites: five sites in Mobile Bay, six sites in the Mobile-Tensaw Delta, and ten sites throughout the Mobile-Tombigbee and Tensaw-Alabama Rivers. Water samples were vacuum-filtered, DNA extractions were performed on the particulate, and DNA extracts were analyzed with Droplet Digital™ Polymerase Chain Reaction using species-specific primers and an internal probe to amplify a 237-base pair fragment of the mitochondrial NADH dehydrogenase subunit 2 gene in bull sharks. One water sample collected during the summer in the Alabama River met the criteria for a positive detection, thereby confirming the presence of bull shark DNA. While preliminary, this finding suggests that bull sharks use less urbanized, riverine habitats up to 120 km upriver during Alabama's dry summer season.</p>
Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water
<ol> <li>The early detection of invasive non-native species (INNS) <span><span>is important for informing management actions</span></span>. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS – particularly during the early stages of an invasion. </li> <li>Here, we compared the use of traditional kick-net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR, and passive detection via metabarcoding with conserved primers) for detection of quagga mussel, <i>Dreissena rostriformis bugensis;</i> a high priority INNS, along a density gradient on the River Wraysbury, UK. </li> <li>All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples, and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor. </li> <li> <i>Synthesis and application.</i> All three molecular approaches were more sensitive than traditional kick-net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community, and consequently impacts of INNS. </li> </ol>
Supplementary material 2 from: Villacorta-Rath C, Lach L, Andrade-Rodriguez N, Burrows D, Gleeson D, Trujillo-González A (2023) Invasive terrestrial invertebrate detection in water and soil using a targeted eDNA approach. NeoBiota 83: 71-89. https://doi.org/10.3897/neobiota.83.98898
Additional qPCR results
Supplementary material 1 from: Villacorta-Rath C, Lach L, Andrade-Rodriguez N, Burrows D, Gleeson D, Trujillo-González A (2023) Invasive terrestrial invertebrate detection in water and soil using a targeted eDNA approach. NeoBiota 83: 71-89. https://doi.org/10.3897/neobiota.83.98898
Invasive terrestrial invertebrate detection in water and soil using a targeted eDNA approach
DETECT-Diabetes Cardiovascular Risk-Evaluation: Targets and Essential Data for Commitment of Treatment
ClinicalTrials.gov study NCT01076608. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Comparative Analysis of Transperineal Versus Transrectal Approaches for MRI-Targeted Biopsy of the Prostate for the Detection and Characterization of Prostate Cancer
ClinicalTrials.gov study NCT03366792. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Detection of Pathogen and Antibiotic Resistance Genes by Targeted Next-Generation Sequencing in ICU Patients.
ClinicalTrials.gov study NCT06157372. IPD Sharing: NO. Countries: 0. Publications: 6.
Data from: Validation of targeted next-generation sequencing for RAS mutation detection in FFPE colorectal cancer tissues: comparison with Sanger sequencing and ARMS-Scorpion real-time PCR
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Selection and exploitation of prevalent, tandemly repeated genomic targets for improved real-time PCR-based detection of Wuchereria bancrofti and Plasmodium falciparum in mosquitoes
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Data from: Background complexity and the detectability of camouflaged targets by birds and humans
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Sample site coordinates, environmental data, number of copies of target DNA/ul for each sample and limit of detection plot
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Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water
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Data from: The effect of a multi-target protocol on cetacean detection and abundance estimation in aerial surveys
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The mitochondrial-targeted peptide therapeutic elamipretide improves cardiac and skeletal muscle function during aging without detectable changes in tissue epigenetic or transcriptomic age [RNA-seq]
GEO Series GSE280699. Mus musculus. 78 samples. Type: Expression profiling by high throughput sequencing.
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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.