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Dataset results
206 results for “Sampling & Detection”
Data from: Effects of distance on detectability of Arctic waterfowl using double-observer sampling during helicopter surveys
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eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals
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Nasopharyngeal swabs vs. saliva sampling for SARS-CoV-2 detection: A cross-sectional survey of acceptability for caregivers and children after experiencing both methods
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Data from: A method that accounts for differential detectability in mixed samples of long-term infections with applications to the case of Chronic Wasting Disease in cervids
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The Prevalence of 30 HPV genotypes detected by EUROArray HPV in cervical samples among unvaccinated women from Vojvodina province, Serbia
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Data from: Ground and stem sampling as potential detection tools for the wool of Adelges tsugae (Hemiptera: Adelgidae)
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Data from: Detection dog efficacy for collecting fecal samples from the critically endangered Cross River gorilla (Gorilla gorilla diehli) for genetic censusing
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Sampling of common eiders for the detection of Pasteurella multocida infection at Mitivik Island, Nunavut
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Supplementary material 4 from: Rusch JC, Mojžišová M, Strand DA, Svobodová J, Vrålstad T, Petrusek A (2020) Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe. NeoBiota 58: 1-32. https://doi.org/10.3897/neobiota.58.49358
Table S4
Supplementary material 2 from: Rusch JC, Mojžišová M, Strand DA, Svobodová J, Vrålstad T, Petrusek A (2020) Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe. NeoBiota 58: 1-32. https://doi.org/10.3897/neobiota.58.49358
Table S2
Supplementary material 3 from: Rusch JC, Mojžišová M, Strand DA, Svobodová J, Vrålstad T, Petrusek A (2020) Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe. NeoBiota 58: 1-32. https://doi.org/10.3897/neobiota.58.49358
Table S3
Supplementary material 1 from: Rusch JC, Mojžišová M, Strand DA, Svobodová J, Vrålstad T, Petrusek A (2020) Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe. NeoBiota 58: 1-32. https://doi.org/10.3897/neobiota.58.49358
Table S1
Noninvasive fecal sampling in Itatiaia National Park, Brazil: wild mammal identification and parasite detection
<p class="CAPA3"><b>Background</b>: Noninvasive collection of feces is a cost-effective strategy for monitoring free-living wild mammals. The aim of this study was to search for carnivore and artiodactyl species and investigate the gastrointestinal parasites in their feces, in Itatiaia National Park, Brazil.</p> <p class="CAPA3"><b>Methodology/Main Findings:</b> Between 2017 and 2018, feces from carnivores and artiodactyls were collected along trails in the park. Host species were identified from these feces through macroscopic and trichological examination and through molecular biology using mitochondrial gene fragments. To investigate parasites, the Faust, Lutz and modified Ritchie and Sheather techniques and enzyme immunoassays were used to detect <i>Cryptosporidium</i> sp. antigens. A total of 244 stools were collected in three regions of the park. The species identified were <i>C. brachyurus</i> (39.7%), <i>L. guttulus</i> (21.3%), <i>C. familiaris</i> (5.3%), <i>C. thous</i> (0.8%), <i>Puma</i> <i>yagouaroundi</i> (0.8%), <i>L. pardalis</i> (0.4%), <i>P</i>. <i>concolor</i> (0.4%) and <i>S. scrofa</i> (4.9%). The overall positivity for parasites was 81.1%. Helminths were more frequently detected in carnivore feces (70.9%), especially eggs of the family Ascarididae and <i>Toxocara</i> sp. Protozoa presented higher frequency in artiodactyl feces (87.1%), especially coproantigens of<i> Cryptosporidium</i> sp. This zoonotic protozoon was detected in eight mammal species, including one that may be invasive: animals from crossbreeding of domestic pig with wild boar. High values for parasite structural richness (R'), Shannon (H') and Simpson (D) parasite diversity indices were observed, especially in the feces of <i>C. brachyurus</i> (R' = 12, H' = 2.2761, D = 0.887). Significant differences in parasite diversity were observed between <i>C. brachyurus </i>and <i>C. familiaris</i>; and between <i>C. brachyurus</i> and <i>S. scrofa</i> (pooled t test = 0.01 and 0.03, respectively). The highest values for parasite similarity (Sorensen test ≥ 0.8) were found among species that are taxonomically close, such as <i>C. brachyurus</i> and <i>L. guttulus</i>.</p> <p class="CAPA3"><b>Conclusions/Significance</b>: This was the first parasitological survey on carnivore and artiodactyl feces collected noninvasively in Brazil. It enabled animal identification through correlations using three techniques and diagnosis of highly frequent parasite structures that can infect these animals.</p>
Data from: High-throughput adaptive sampling for whole-slide histopathology image analysis (HASHI) via convolutional neural networks: application to invasive breast cancer detection
Precise detection of invasive cancer on whole-slide images (WSI) is a critical first step in digital pathology tasks of diagnosis and grading. Convolutional neural network (CNN) is the most popular representation learning method for computer vision tasks, which have been successfully applied in digital pathology, including tumor and mitosis detection. However, CNNs are typically only tenable with relatively small image sizes (200x200 pixels). Only recently, Fully convolutional networks (FCN) are able to deal with larger image sizes (500x500 pixels) for semantic segmentation. Hence, the direct application of CNNs to WSI is not computationally feasible because for a WSI, a CNN would require billions or trillions of parameters. To alleviate this issue, this paper presents a novel method, High-throughput Adaptive Sampling for whole-slide Histopathology Image analysis (HASHI), which involves: i) a new efficient adaptive sampling method based on probability gradient and quasi-Monte Carlo sampling, and, ii) a powerful representation learning classifier based on CNNs. We applied HASHI to automated detection of invasive breast cancer on WSI. HASHI was trained and validated using three different data cohorts involving near 500 cases and then independently tested on 195 studies from The Cancer Genome Atlas. The results show that (1) the adaptive sampling method is an effective strategy to deal with WSI without compromising prediction accuracy by obtaining comparative results of a dense sampling (~6 million of samples in 24 hours) with far fewer samples (~2,000 samples in 1 minute), and (2) on an independent test dataset, HASHI is effective and robust to data from multiple sites, scanners, and platforms, achieving an average Dice coefficient of 76%.
Data from: The relative power of genome scans to detect local adaptation depends on sampling design and statistical method
Although genome scans have become a popular approach towards understanding the genetic basis of local adaptation, the field still does not have a firm grasp on how sampling design and demographic history affect the performance of genome scans on complex landscapes. To explore these issues, we compared 20 different sampling designs in equilibrium (i.e. island model and isolation by distance) and nonequilibrium (i.e. range expansion from one or two refugia) demographic histories in spatially heterogeneous environments. We simulated spatially complex landscapes, which allowed us to exploit local maxima and minima in the environment in 'pair' and 'transect' sampling strategies. We compared FST outlier and genetic–environment association (GEA) methods for each of two approaches that control for population structure: with a covariance matrix or with latent factors. We show that while the relative power of two methods in the same category (FST or GEA) depended largely on the number of individuals sampled, overall GEA tests had higher power in the island model and FST had higher power under isolation by distance. In the refugia models, however, these methods varied in their power to detect local adaptation at weakly selected loci. At weakly selected loci, paired sampling designs had equal or higher power than transect or random designs to detect local adaptation. Our results can inform sampling designs for studies of local adaptation and have important implications for the interpretation of genome scans based on landscape data.
Data from: A lateral flow immunochromatographic strip test for rapid detection of hexoestrol in fish samples
A lateral flow immunochromatographic test strip was developed for on-site rapid and sensitive detection of Hexoestrol (HES) residues in fish samples with colloidal gold labeled the anti-HES monoclonal antibody (mAb). The strip is composed of a sample pad, a conjugate reagent pad, an absorbent pad, and a test membrane containing a control line and a test line. The sensitivity (half inhibitory concentration, IC50) of the strip in the detection of fish extract samples was confirmed to be 1.86 μg/kg, and the limit detection (LOD) value was 0.62 μg/kg. For intra-assay and inter-assay reproducibility, recoveries of HES spiked samples were ranged from 86.3% to 92.3% and 85.8% to 93.4%, coefficients of variation were 2.91-4.64% and 4.24-5.17% respectively. High-performance liquid chromatography (HPLC) was employed to confirm the performance of the strip. The strip test only took less than 10 minutes, and thus provides a repaid method for on-site detection of HES residues.
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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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>
Balantioides coli in other zoonotic parasites detected in noninvasive fecal samples of artiodactyls with emphasis on the bioinvasive in a state park in Brazil
<p><strong>Background:</strong> Over the years the mammalian fauna, including artiodactyls, has been decreasing and changing due to the entry of bioinvaders into Conservation Units, highlighting, the free-living pig, <em>Sus scrofa</em>, also called feral pig or wild boar. As it is an exotic animal, it is relevant to analyze the gastrointestinal parasites, highlighting those with zoonotic potential that may be infecting these animals and native artiodactyls. To expand this information, this study aims to evaluate the gastrointestinal parasites of artiodactyls in fecal samples collected in the Pedra Selada State Park and in its buffer zones in Rio de Janeiro.</p> <p><strong>Methodology/Main Findings:</strong> Between 2020 and 2021, 101 fecal samples were collected with morphology compatible with artiodactyls in different areas of the Park. All collection points were georeferenced and plotted on maps. Part of the fecal material was submitted to identification of the host species by means of macroscopic and molecular analysis from PCR with primers that amplify the DNA fragment of the COI gene. The other part was submitted to parasite research by qualitative and quantitative coproparasitological techniques. The fecal samples that presented cysts of the Phylum Ciliophora were analyzed with primers that amplify a DNA fragment from the ITS1.5.8S.ITS2 region. Of the 101 samples collected, 72 (71.3%) were found in the covered areas of Pavão Valley, 24 (23.8%) in Grama Valley and 5 (4.9%) in Redondo Mountain. In general, it can be seen that the average length of stool varied very little. Regarding the average values of the weights, it can be seen that they varied a lot, highlighting a diversity of artiodactyls possibly associated with different age groups and sizes of the animals. Morphologically, the feces presented brownish coloration, were in the form of pellets, were rounded and slightly pointed, characteristics that are typically associated with the Order Artiodactyla. Regarding host identification through molecular analysis with the COI gene, 79 samples were identified as belonging to Sus scrofa and 2 as belonging to <em>Mazama gouazoubira</em>. In general, forms of protozoa are more evident than helminths. Protozoan cysts of the Phylum Ciliophora were the most detected forms of parasites, being present in 40 (39.6%) fecal samples. These structures were found only in the feces of Sus scrofa. In addition to these, other parasites were also identified in the feces of these animals, such as non-sporulated coccidian oocyst (2.9%), <em>Ascaris </em>spp. (1.8%), <em>Metrastrongylus </em>spp. (5.9%), strongylid eggs (3.9%), Trichuris spp. (3.9%), nematode larvae (7.9%) and taxonomically unidentified nematode egg (1%). Of the 40 samples in which cysts were detected, nucleotide sequences of protozoa of the Phylum Ciliophora originated from 26 can be interpreted, all of which are compatible with Balantioides coli. Of these, 13 were classified as genetic variant of type B0, one of type B1, 11 of type A0 and were only characterized as type A, not being fully framed in any of the pre-established subtypes.</p> <p><strong>Conclusions/Significance:</strong> It should be noted that parasites with zoonotic potential such as B. coli, highlighting the genetic variant of A0, were identified in the samples collected from Park and their buffer zones, this being the first study in Brazil that phylogenetically characterized this protozoan in free-living S. scrofa feces, placing this bioinvader as one of the reservoirs of this parasite.</p>
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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.