Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
206
datasets available to search
ShareScore release 0.9.0
Dataset results
206 results for “Sampling & Detection”
Data for the detection of the boreal chorus frog (Pseudacris maculata) using environmental DNA and call surveys at 180 ponds sampled in 2017-2018 in southeastern Québec, Canada
Open the record for dataset details and reuse information.
Data from: Rapid detection of subterranean fauna from passive sampling of groundwater eDNA
Open the record for dataset details and reuse information.
Data for: Development of a method for the measurement of human scent samples using comprehensive two-dimensional gas chromatography with mass detection
Open the record for dataset details and reuse information.
Demographic information and phthalate metabolite concentrations (µg/L) detected in bottlenose dolphins (Tursiops truncatus) urine sampled from Barataria Bay, LA during 2011-2023 and Sarasota Bay, FL during 2010-2019, 2022-2024
Open the record for dataset details and reuse information.
Leech-derived iDNA complements traditional surveying methods, enhancing species detections for rapid biodiversity sampling in the tropics
Open the record for dataset details and reuse information.
Data from: Detection of vertebrates from natural and artificial inland water bodies in a semi-arid habitat using eDNA from filtered, swept and sediment samples
Open the record for dataset details and reuse information.
Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations: data related to publication
<p>Data related to the following publication:</p> <p>"Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations"</p>
Data from: Spotting the pests of tomorrow - Sampling designs for detection of species associations with woody plants
Aim: Early warning against potentially harmful organisms of woody plant species can be achieved by sampling sentinel plants in exporting countries. However, it is unclear where sentinel plants can best be located, and how many samples are required and when and how often sampling optimally should take place for the adequate assessment of the biodiversity associated with the target plant species. We aimed to review spatial and temporal factors affecting associate biodiversity of single woody plant species and to develop guidance for the design of global biodiversity sampling studies. Location: Worldwide. Taxon: Insects and Fungi. Methods: Literature about factors affecting the diversity of insects and fungi in association with single plant species on global, regional, local and different temporal scales was reviewed. Case studies of insect and fungal diversity, primarily collected on single plant species, and the cost of collecting and analysing samples from locations around the world were analysed. Results: The review of the literature illustrated various factors affecting diversity, and the case studies allowed quantification of the relative impact of some spatial, temporal and financial aspects on captured biodiversity and, thus, illustrate the need to consider all possible factors that may affect the result of the sampling when deciding on a sampling design. Main conclusions: Our study illustrates the factors that should be considered when deciding on the location and timing of sampling for sentinel plants, which is important because of the trade-off between the number of samples and sampling locations needed to detect many of the species which may be potential pests, and the cost of (repeated) sampling in many locations. Decisions about the sampling design must be based on the objective of the sampling, but our recommendations apply irrespective of the targeted plant species or country.
Sampling of common eiders for the detection of Pasteurella multocida infection at Mitivik Island, Nunavut
<p>From 2007-2014, pre-breeding common eiders were captured in flight nets when arriving and flying over Mitivik Island, Nunavut, banded, sexed and measured. Cloacal and oral samples were collected for detection of current <i>Pasteurella multocida</i> infection, and blood samples were collected for detection of antibodies to this bacterium. For more details, see van Dijk et al. (2020) Herd immunity drives the epidemic fadeout of avian cholera in Arctic-nesting seabirds.</p>
Data from: How diverse is Mitopus morio? Integrative taxonomy detects cryptic species in a small-scale sample of a widespread harvestman
Mitopus morio is a widespread harvestman species occurring in most of Europe and in moderate and cold-moderate zones of Asia and North America. The species is characterized by extreme variability in body size and leg length. As leg length is correlated with habitat temperature, M. morio has been considered as an example of Allen's rule. Recently, observations for a single location in Tyrol, Austria, indicated the absence of mating between short- and long-legged individuals. This study examines for signs of putative cryptic species in M. morio using an integrative approach that combines mating trials, amplified fragment length polymorphism whole-genome scans, mitochondrial sequences and morphometrics. The mating trials did not corroborate the initial hypothesis of a reproductive barrier associated with leg size. Both types of genetic data revealed the existence of three distinct groups, in line with the mating results but largely unrelated to leg morphology and geographical origin of specimens. Morphometric characters supporting the findings of the other disciplines were identified using a supervised approach. We infer from all data together the existence of strongly diverged cryptic lineages among the analysed individuals, cautiously interpret them as three sympatric species and conclude that in these harvestmen Allen's rule applies at different levels. Due to the unexpected amount of differentiation found within a geographical scale very small compared with the distribution of M. morio, we suggest a thorough revision of the genus prior to formal taxonomic changes. Our case study underlines the general applicability of the integrative taxonomic protocol used and highlights the relevance of several rationales implemented in the protocol.
Data from: Detection of invasive mosquito vectors using environmental DNA (eDNA) from water samples
Repeated introductions and spread of invasive mosquito species (IMS) have been recorded on a large scale these last decades worldwide. In this context, members of the mosquito genus Aedes can present serious risks to public health as they have or may develop vector competence for various viral diseases. While the Tiger mosquito (Aedes albopictus) is a well-known vector for e.g. dengue and chikungunya viruses, the Asian bush mosquito (Ae. j. japonicus) and Ae. koreicus have shown vector competence in the field and the laboratory for a number of viruses including dengue, West Nile fever and Japanese encephalitis. Early detection and identification is therefore crucial for successful eradication or control strategies. Traditional specific identification and monitoring of different and/or cryptic life stages of the invasive Aedes species based on morphological grounds may lead to misidentifications, and are problematic when extensive surveillance is needed. In this study, we developed, tested and applied an environmental DNA (eDNA) approach for the detection of three IMS, based on water samples collected in the field in several European countries. We compared real-time quantitative PCR (qPCR) assays specific for these three species and an eDNA metabarcoding approach with traditional sampling, and discussed the advantages and limitations of these methods. Detection probabilities for eDNA-based approaches were in most of the specific comparisons higher than for traditional survey and the results were congruent between both molecular methods, confirming the reliability and efficiency of alternative eDNA-based techniques for the early and unambiguous detection and surveillance of invasive mosquito vectors. The ease of water sampling procedures in the eDNA approach tested here allows the development of large-scale monitoring and surveillance programs of IMS, especially using citizen science projects.
BactPrep: A user-friendly whole-genome sequencing analysis platform for the detection of homologous recombination and horizontal gene transfer in bacteria - Sample Dataset
<p>This is the dataset used as the sample dataset for the pipeline BactPrep. This dataset consists of 218 <em>Streptococcus pneumoniae</em> PMEN1 WGS assemblies collected from the year 1984 - 2008 from 22 unique countries globally. The raw sequencing data was originally published in the work: Rapid pneumococcal evolution in response to clinical interventions (doi: 10.1371/journal.ppat.1002745) under the bioproject PRJEB2085.</p> <p>We have assembled the raw sequences records with the following steps: 1) raw reads were first quality checked using fastQC 0.11.9; 2) adapters and low quality reads were removed using Trimmomatic 0.39 with parameter “ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”; 3) trimmed reads were error-corrected and assembled into WGS assemblies using SPAdes 3.15.0 with parameters "--careful --mismatch-correction”.</p>
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
From Microorganisms to Biosignatures: Subcritical Water Extraction as a Sample Preparation Technique for Future Life Detection Missions
<p>Data for all figures included in "From Microorganisms to Biosignatures: Subcritical Water Extraction as a Sample Preparation Technique for Future Life Detection Missions". Amino acid concentrations, enantiomeric excesses, and relative distributions for E. coli cells and B. subtilis spores after subcritical water extraction for 30 min at 200 °C using water and dilute acid.</p>
Nasopharyngeal swabs vs. saliva sampling for SARS-CoV-2 detection: A cross-sectional survey of acceptability for caregivers and children after experiencing both methods
<p><span>Background: </span><span>Saliva sampling is a promising alternative to nasopharyngeal swabs for SARS-CoV-2 testing, but acceptability data is lacking. We characterize the acceptability of saliva sampling and nasopharyngeal swabs for primary decision makers and their children after experiencing both testing modalities.</span></p> <p><span>Results: </span><span>48 participants and 48 primary decision makers completed the survey. Nasopharyngeal swab acceptability differed between scenarios, ranging 79% [95%CI: 66, 88] to 100% [95%CI: 95, 100]); saliva sampling acceptability was similar across scenarios, ranging 92% [95%CI: 82, 97]) to </span><span> </span><span>98% [95%CI: 89, 99]. 58% of youth described significant pain with nasopharyngeal swabbing, versus none with saliva sampling. 90% of children prefer saliva sampling. 66% of primary decision makers would prefer nasopharyngeal swabbing if it were 10% more sensitive.</span></p> <p><span>Conclusion: </span><span>Though youth prefer saliva sampling over nasopharyngeal swabs, primary decision makers present for testing remain highly accepting of both. Acceptance of nasopharyngeal swabs, however, varies with the testing indication and is influenced by perceived test accuracy. Understanding factors that influence sampling acceptance will inform more successful testing strategies.</span></p>
A synchronous spectrofluorometric technique for simultaneous detection of alfuzosin and tadalafil: Applied to tablets and spiked biological samples
<p>A facile, accurate, eco-friendly, and sensitive spectrofluorometric method was evolved to assay alfuzosin hydrochloride (AFH) and tadalafil (TDF) in different matrices. Such a co-administered combination is clinically used for the treatment of lower urinary tract symptoms. Both compounds are characterized by their native fluorescence spectra upon excitation at specific wavelengths. Their characteristic fluorescence spectra were utilized for sensitive assay of the studied analytes in tablets and human biological samples. The assay principle is based on first-order synchronous spectrofluorometric scan using Dλ = 60 nm in which AFH peaks were recorded at 366 nm. Meanwhile, TDF measurements were recorded at 293 nm in the same scans without overlap with AFH spectra. Recent analytical chemistry trends were implemented to lessen occupational and environmental perils, utilizing ethanol as a diluting solvent for method optimization and application. Linearity ranges were 5.0–90.0 and 10.0–100.0 ng. <span>mL⁻1</span> for AFH and TDF, respectively in their raw materials with average % recoveries of 100.44 % and 99.73 % in raw materials, 100.15 % and 100.20 % in spiked plasma, and 97.14 % and 99.99 % in spiked urine. The proposed method was successfully applied to Prostetrol® and Starkoprex® commercial tablets with no interference with common tablet additives.</p>
Applications of machine learning tools for ultra-sensitive detection of lipoarabinomannan with plasmonic grating biosensors in clinical samples of tuberculosis
Background <p>Tuberculosis is one of the top ten causes of death globally and the leading cause of death from a single infectious agent. Eradicating the Tuberculosis epidemic by 2030 is one of the top United Nations Sustainable Development Goals. Early diagnosis is essential to achieving this goal because it improves individual prognosis and reduces transmission rates of asymptomatic infected. We aim to support this goal by developing rapid and sensitive diagnostics using machine learning algorithms to minimize the need for expert intervention. </p> Methods and Findings <p>A single-molecule fluorescence immunosorbent assay was used to detect the Tuberculosis biomarker lipoarabinomannan from a set of twenty clinical patient samples and a control set of spiked human urine. Tuberculosis status was separately confirmed by GeneXpert MTB/RIF and cell culture. Two machine learning algorithms, an automatic and a semiautomatic model, were developed and trained by the calibrated lipoarabinomannan titration assay data and then tested against the ground truth patient data. The semiautomatic model differed from the automatic model by an expert review step in the former, which calibrated the lower threshold to determine single molecules from background noise. The semiautomatic model was found to provide 88.89% clinical sensitivity, while the automatic model resulted in 77.78% clinical sensitivity.</p> Conclusions <p>The semiautomatic model outperformed the automatic model in clinical sensitivity as a result of the expert intervention applied during calibration and both models vastly outperformed manual expert counting in terms of time-to-detection and completion of analysis. Meanwhile, the clinical sensitivity of the automatic model could be improved significantly with a larger training dataset. In short, semiautomatic, and automatic Gaussian Mixture Models have a place in supporting rapid detection of Tuberculosis in resource-limited settings without sacrificing clinical sensitivity.</p>
Dataset and code for 'Signal to Noise Ratio and Spectral Sampling Constraints on Olivine Detection and Compositional Determination in the Intermediate Infrared Region'
<p>Feature fitting code and spectra of olivine samples used in paper "<em>Signal to Noise Ratio and Spectral Sampling Constraints on Olivine Detection and Compositional Determination in the Intermediate Infrared Region: Applications in Planetary Sciences</em>"</p>
Dataset: Occupancy Detection, Tracking, and Estimation Using a Vertically Mounted Depth Sensor [Sample Dataset]
<p>[Sample Dataset File.]</p> <p>Occupancy detection, tracking, and estimation has a wide range of applications including improving building energy efficiency, safety, and security of the occupants. As depth sensors are getting cheaper, they offer a viable solution to estimate occupancy accurately in a non-privacy invasive manner. Even though there are publicly available depth datasets, they do not consider placing the sensor in the ceiling looking downwards to estimate occupancy. We deployed four Kinect for XBOX One in four CMU classrooms and conference rooms for a period of four weeks in 2017 and collected over 6 TB of depth data. We annotate this huge dataset by labelling bounding boxes around occupants and release the annotated dataset. </p>
Data from: Effects of distance on detectability of Arctic waterfowl using double-observer sampling during helicopter surveys
Aerial survey is an important, widely employed approach for estimating free‐ranging wildlife over large or inaccessible study areas. We studied how a distance covariate influenced probability of double‐observer detections for birds counted during a helicopter survey in Canada's central Arctic. Two observers, one behind the other but visually obscured from each other, counted birds in an incompletely shared field of view to a distance of 200 m. Each observer assigned detections to one of five 40‐m distance bins, guided by semi‐transparent marks on aircraft windows. Detections were recorded with distance bin, taxonomic group, wing‐flapping behavior, and group size. We compared two general model‐based estimation approaches pertinent to sampling wildlife under such situations. One was based on double‐observer methods without distance information, that provide sampling analogous to that required for mark–recapture (MR) estimation of detection probability, urn:x-wiley:20457758:media:ece34824:ece34824-math-0001, and group abundance, urn:x-wiley:20457758:media:ece34824:ece34824-math-0002, along a fixed‐width strip transect. The other method incorporated double‐observer MR with a categorical distance covariate (MRD). A priori, we were concerned that estimators from MR models were compromised by heterogeneity in urn:x-wiley:20457758:media:ece34824:ece34824-math-0003 due to un‐modeled distance information; that is, more distant birds are less likely to be detected by both observers, with the predicted effect that urn:x-wiley:20457758:media:ece34824:ece34824-math-0004 would be biased high, and urn:x-wiley:20457758:media:ece34824:ece34824-math-0005 biased low. We found that, despite increased complexity, MRD models (ΔAICc range: 0–16) fit data far better than MR models (ΔAICc range: 204–258). However, contrary to expectation, the more naïve MR estimators of urn:x-wiley:20457758:media:ece34824:ece34824-math-0006 were biased low in all cases, but only by 2%–5% in most cases. We suspect that this apparently anomalous finding was the result of specific limitations to, and trade‐offs in, visibility by observers on the survey platform used. While MR models provided acceptable point estimates of group abundance, their far higher stranded errors (0%–40%) compared to MRD estimates would compromise ability to detect temporal or spatial differences in abundance. Given improved precision of MRD models relative to MR models, and the possibility of bias when using MR methods from other survey platforms, we recommend avian ecologists use MRD protocols and estimation procedures when surveying Arctic bird populations.
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.