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206 results for “Sampling & Detection”
Benign samples used in article "DeepDetectNet vs RLAttackNet: An Adversarial Method to Improve Deep Learning-based Static Malware Detection Model"
<p>This repository contains all benign samples used in article "DeepDetectNet vs RLAttackNet: An Adversarial Method to Improve Deep Learning-based Static Malware Detection Model". It is safe to download these samples.</p>
Data from: Spatial and temporal patterns of environmental DNA detection to inform sampling protocols in lentic and lotic systems.
<p>The development of efficient sampling protocols for the capture of environmental DNA (eDNA) could greatly help improve accuracy of occupancy monitoring for species that are difficult to detect. However, the process of developing a protocol in situ is complicated for rare species by the fact that animal locations are often unknown. We tested sampling designs in lake and stream systems to determine the most effective eDNA sampling protocols for two rare species: the Sierra Nevada yellow-legged frog (<i>Rana sierrae</i>) and the foothill yellow-legged frog (<i>R. boylii</i>). We varied water volume, spatial sampling, and seasonal timing in lakes and streams; in lakes we also tested multiple filter types. We found that filtering 2 L versus 1 L increased the odds of detection in streams 5.42X (95% CI: 3.2-9.19X) in our protocol, from a probability of 0.51 to 0.85 per technical replicate. Lake sample volumes were limited by filter clogging and we found no effect of volume or filter type. Sampling later in the season increased the odds of detection in streams by 1.96X for every 30 days (95% CI: 1.3 - 2.97X) but there was no effect for lakes. Spatial autocorrelation of the quantity of yellow-legged frog eDNA captured in streams between 100 and 200 m, indicating that sampling at close intervals is important.</p>
BRAMS Radio Spectrograms and Spectrogram Samples for Automatic Detection of Meteor Echoes
<p>The files in this dataset are based of radio recordings taped by BRAMS (Belgian RAdio Meteor Stations), the Belgian meteor detection network.</p> <p>Included in the dataset are the original BRAMS radio recordings (stored as .wav audio files), the spectrogram data for each radio recording (stored as .csv files) and the meteor and non-meteor samples extracted from the radio spectrograms (stored as .csv files).</p> <p>It should be noted that the the spectrogram data was sampled using a sliding window of size 30x20 pixels and the samples extracted in this manner were further processed by calculating the vertical average of each column in the 30x20 matrixes. The result of this sampling procedure is a set of data vectors containing the average power of the signal found in the original 30x20 spectrogram sample.</p>
Datasets associated with the manuscript "Differential detection workflows for multi-sample single-cell RNA-seq data"
<p>In this Zenodo repository, we share the data that is required to reproduce all the analyses from our publication "Differential detection workflows for multi-sample single-cell RNA-seq data".</p> <p>This repository includes all* input data, intermediate results and final outputs that are represented in our manuscript. For a more elaborate description of the data, we refer to the companion GitHub. https://github.com/statOmics/DD_benchmarks for the benchmarks and https://github.com/statOmics/DD_cases for the case studies, respectively.</p>
Leech-derived iDNA complements traditional surveying methods, enhancing species detections for rapid biodiversity sampling in the tropics
<p>Deforestation, exploitation, and other drivers of biodiversity loss in Madagascar leave its highly endangered and predominantly endemic wildlife at risk of extinction. Decreasing biodiversity threatens to compromise ecosystem functions and vital services provided to people. New, economical, and diverse methods of biodiversity monitoring can help to establish reliable baseline and long-term records of species richness. Metabarcoding with invertebrate-derived DNA (iDNA) has emerged as a promising new biosurveillance tool. An unexpected wet forest fragment tucked in the dry cliffs of Madagascar's southcentral plateau, the Ivohibory Protected Area (IPA), hosts a unique mosaic of species diversity, featuring both dry and wet forest species. Recently elevated to protected status, the IPA has been surveyed for flora and fauna with a range of inventory methods over three years and six expeditions (2016, 2017, & 2019). We collected 1,451 leeches over 12 days from the IPA to supplement known species richness and to compare results against current records. With iDNA, we pooled tissues, and isolated, and amplified bloodmeal DNA with five sets of primers. We detected 20 species of which four are species of frogs previously undetected and three of which are previously unknown to exist in this region. iDNA surveys can provide complementary data to traditional surveying methods like camera traps, line transects, and bioacoustic methods.</p>
Raw data from "AC transport detection of magnetic transitions in small and granular samples"
<p>Raw data supporting the submitted manuscript "AC transport detection of magnetic transitions in small and granular samples". Additional information avaliable upon request.</p>
Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies
<p>Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large – volume eDNA sampler with in situ filtration, capable of taking up to 12 samples per deployment. We conducted three deployments of our sampler on the robotic vehicle <em>Mesobot</em> in the Flower Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico and collected samples from 20 to 400 m depth. We compared the large volume (~40 – 60 liters) samples collected by <em>Mesobot</em> with small volume (~2 liters) samples collected using the conventional CTD rosette – mounted Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which detects a broad range of invertebrate taxa, and found that while both methods detected biodiversity changes associated with depth, our large volume samples detected approximately 66% more taxa than the CTD small volume samples. We found that the fraction of the eDNA signal originating from metazoans relative to the total eDNA signal decreased with sampling depth, indicating that larger volume samples may be especially important for detecting metazoans in mesopelagic and deep ocean environments. We also noted substantial variability in biological replicates from both the large volume <em>Mesobot</em> and small volume CTD sample sets. Both of the sample sets also identified taxa that the other did not – although the number of unique taxa associated with the <em>Mesobot</em> samples was almost four times larger than those from the CTD samples. Large volume eDNA sampling with in situ filtration, particularly when coupled with robotic platforms, has great potential for marine biodiversity surveys, and we discuss practical methodological and sampling considerations for future applications.</p>
Data for: Development of a method for the measurement of human scent samples using comprehensive two-dimensional gas chromatography with mass detection
<p>This dataset was used for development of a method for the measurement of human scent samples using comprehensive two-dimensional gas chromatography with mass detection [<a href="https://doi.org/10.1016/j.forsciint.2016.09.011">https://doi.org/10.1016/j.forsciint.2016.09.011</a>].</p> <p>The dataset contains chromatograms of a model mixture of human scent and chromatograms of the human scent of one volunteer measured on different column setups. Each sample was processed in ChromaToF(version 4.72.0.0) by LECO corp. The processing step was executed at the signal-to-noise (SN) ratio levels 100, 300, and 500 (human scent samples chromatograms).</p>
Sample Dataset for Automated Detection of Cheating Codes
<p><span>This project includes a resampled dataset and statistical code for analyzing various subcategories of cheating codes. The dataset is derived from an initial collection of SQL queries from HackerRank (</span><span><a href="../record/8199741">https://zenodo.org/record/8199741</a></span><span>). Originally, the dataset contained 5,767,890 correct codes and only 1,992 cheating codes. To address the issue of data imbalance, we implemented a resampling strategy to achieve a more balanced data distribution. Specifically, undersampling techniques were used to reduce the number of correct codes while retaining all cheating codes. From 22 programming problems, we randomly selected 20,000 correct codes from each problem. This approach aimed to balance data representation across different problem types, enhancing the model’s adaptability and generalization. After resampling, the dataset consisted of 440,000 correct codes and 1,992 cheating codes.</span></p>
Sampled sentence pairs from SemEval-2020 Task 1: Unsupervised Lexical Semantic Change Detection
<p>Each dataset consists of samples, containing two sentences with positions of one of the given target words. In every sample, first sentence is taken from corpus1 and second from corpus2. Initial sentences were taken from https://www.ims.uni-stuttgart.de/en/research/resources/corpora/sem-eval-ulscd/. </p>
Data from: Detection of the endangered European weather loach (Misgurnus fossilis) via water and sediment samples: testing multiple eDNA workflows.
<p>The European weather loach (<i>Misgurnus fossilis</i>) is classified as highly endangered in several countries of Central Europe. Populations of <i>M. fossilis</i> are predominantly found in ditches with low water levels and thick sludge layers and are thus hard to detect using conventional fishing methods. Therefore, environmental DNA (eDNA) monitoring appears particularly relevant for this species. In previous studies, <i>M. fossilis</i> was surveyed following eDNA water sampling protocols, which were not optimized for this species. Therefore, we created two full factorial study designs to test six different eDNA workflows for sediment samples and twelve different workflows for water samples. We used qPCR to compare the Threshold cycle (Ct) values of the different workflows, which indicate the target DNA amount in the sample, and spectrophotometry to quantify and compare the total DNA amount inside the samples. We analyzed 96 water samples and 48 sediment samples from a pond with a known population of <i>M. fossilis</i>. We tested several method combinations for long-term sample preservation, DNA capture and DNA extraction. Additionally, we analyzed the DNA yield of samples from a ditch with a natural <i>M. fossilis</i> population monthly over one year to determine the optimal sampling period. Our results showed that the long-term water preservation method commonly used for eDNA surveys of <i>M. fossilis </i>did not lead to optimal DNA yields, and we present a valid long-term sample preservation alternative. A cost-efficient high salt DNA extraction led to the highest target DNA yields and can be used for sediment and water samples. Furthermore, we were able to show that in a natural habitat of <i>M. fossilis</i>, total and target eDNA were higher between June and September, which implies that this period is favorable for eDNA sampling. Our results will help to improve the reliability of future eDNA surveys of <i>M. fossilis</i>.</p>
NPIP: A Comprehensive Analysis Pipeline for Rapid Pathogen Detection in Clinical Samples Based on Nanopore Sequencing
<p>Background: Rapid and accurate pathogen detection is important for effective control of infectious diseases. However, traditional pathogen culture methods have a very long detection time, as well as high rates of false-positive and false-negative results. Third generation sequencing (TGS) technology brings the new possibility of being used as a pathogen detection method. However, the practicability of a pathogen detection report based on TGS is still lacking. There is also a lack of professional and accurate report interpretation.</p> <p>Results: Here, we report on the development of a pathogen detection and analysis tool (NPIP) based on third generation nanopore sequencing technology. We also prove the practicability of nanopore sequencing and NPIP analysis tools in emergency and clinical pathogen detection by demonstrating its use in a practical case.</p> <p>Conclusions: This platform provides an effective, convenient, and fast analysis tool for clinicians and public health personnel to more successfully apply TGS in pathogen detection.</p>
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
<p>The boreal chorus frog (<em>Pseudacris maculata</em>) is at risk of extinction in parts of its range in Canada. Our objectives were to quantify the influence of local and landscape characteristics on the occurrence of the species in wetlands in southern Québec. We hypothesized that site occupancy depends on local characteristics and landscape characteristics contributing to site connectivity. We developed an environmental DNA (eDNA) method to detect the species and compared the detection probability of this method to traditional call surveys. We collected water samples at a total of 180 sites (90 in 2017, 110 in 2018), whereas we surveyed a subset of 63 sites using both eDNA and call surveys in 2018. Site occupancy varied across years, but was higher in sites where the species had been previously detected during the last 12 years by other studies. Site occupancy did not vary with other local and landscape characteristics, in part due to an apparent decrease in the number of sites occupied by the species since the last 12 years. Detection probability via eDNA (0.81; 95% CI: [0.31; 0.98]) did not differ from that of call surveys (0.62; 95% CI: [0.25; 0.89]). To identify the optimal sampling period for the boreal chorus frog, future studies should estimate the detection probability of eDNA during the breeding season and the larval development period of the species.</p>
Detection of SARS-CoV-2 variants by genomic analysis of wastewater ampliconic samples (Galaxy Training Material)
<p>The tutorial aims to train how to run workflows to analyze lineages abundances in SAR-CoV-2 wastewater ampliconic samples. (https://training.galaxyproject.org/training-material/)</p>
Detection of SARS-CoV-2 variants by genomic analysis of wastewater metatranscriptomic samples (Galaxy Training Material)
<p>The tutorial aims to train how to run workflows to analyze lineages abundances in SAR-CoV-2 wastewater metatranscriptomic samples. (https://training.galaxyproject.org/training-material/)</p>
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
<p>Climate warming will impact the sustainability of arid and semi-arid zone environments so we need to understand the influence of changes in arid lands on vertebrate populations. However, biomonitoring and biodiversity assessment in arid environments can be prohibitively time-consuming, expensive, and logistically challenging due to their often remote and inhospitable nature. Sampling of environmental DNA (eDNA) coupled with high-throughput sequencing is an emerging biodiversity assessment method. Here we explore the application of eDNA metabarcoding and various sampling approaches to estimate vertebrate richness and assemblage at human-constructed and natural water sources in a semi-arid region of Western Australia. Three sampling methods: sediment samples, filtering through a membrane with a pump, and membrane sweeping in the water body, were compared using two eDNA metabarcoding assays, 12S-V5 and 16smam, for 120 eDNA samples collected from four gnammas (gnamma: Australian Indigenous Noongar language term – granite rock pools) and four cattle troughs in the Great Western Woodlands, Western Australia. We detected higher vertebrate richness in samples from cattle troughs and found differences between assemblages detected in gnammas (more birds and amphibians) and cattle troughs (more mammals, including feral taxa). Total vertebrate richness was not different between swept and filtered samples, but all sampling methods yielded different assemblages. Our findings indicate that eDNA surveys in arid lands will benefit from collecting multiple samples at multiple water sources to avoid underestimating vertebrate richness. The high concentration of eDNA in small, isolated water bodies permits the use of sweep sampling which simplifies sample collection, processing, and storage, particularly when assessing vertebrate biodiversity across large spatial scales.</p>
Tornado Detection From Full-Resolution Polarimetric Weather Radar Data (SAMPLE)
<p>This dataset contains a small sample of the tornado dataset described in the talk "A Tornado Detection Algorithm using Deep Neural Networks, Full-Resolution Polarimetric Weather Radar Data, and Explainable AI" presented at the 40th Conference on Radar Meteorology on Aug 31st 2023.</p> <p>The files contained in this data represent approximately 1% of the full dataset that will be released upon final publication.</p> <p>For questions please contact</p> <p>James.Kurdzo@ll.mit.edu and mark.veillette@ll.mit.edu</p>
Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies
Open the record for dataset details and reuse information.
Data from: Spatial and temporal patterns of environmental DNA detection to inform sampling protocols in lentic and lotic systems
Open the record for dataset details and reuse information.
Data from: Detection of the endangered European weather loach (Misgurnus fossilis) via water and sediment samples: testing multiple eDNA workflows.
Open the record for dataset details and reuse information.
ScienceDex guides
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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.