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1,940 results for “data sample”
Sample Data for ICDAR'24 MapText Competition
<p>Data set of 353 image tiles (2Kx2K) cropped from 31 historical maps taken from nine (9) atlases for the <a href="https://rrc.cvc.uab.es/?ch=28">ICDAR'24 Competition on Historical Map Text Detection, Recognition, and Linking</a>.</p> <p>Annotations (<code>sample.json</code>) and images (<code>sample/*.png</code> within <code>sample.zip</code>) follow the format described at the competition website and can be evaluated using the official <a href="https://github.com/icdar-maptext/evaluation">evaluation repository</a> script.</p> <p>The data set contains 34,882 words in 31,200 label phrase groups; annotations result from automatically merging two distinct prior manual annotations (<a href="https://doi.org/11084/19349">Boateng Asante et al. 2017</a> and <a href="https://doi.org/11084/23295">Ray et al. 2018</a>). As a result, all text on the maps has been marked, but—unlike the official competition data—the annotations likely contain false negatives among the grouping (meaning, some words that should be linked into groups are not), and some words may divided into separate annotations, even individual characters.</p>
Data from: Sampling origins and directions affect the minimum sampling area in forest plots
<p><span>The minimum sampling area (or minimum area), representing the smallest space </span>that reflects the species composition and characteristics of a plant community, is estimated using species-area relationships (SARs) for designing and managing biodiversity conservation. However, the sampling design's effect on the determination of the minimum area has rarely been systematically evaluated. In this study, we used tree census data from three forest dynamic plots of 25–60 ha in different climatic zones in China to calculate the minimum areas of woody plants in the plots and analyze the effects of species richness and topographic heterogeneity on the areas by changing sampling origins and directions. Our findings reveal that the estimated size of the minimum areas varied significantly with sampling origins and directions, with a difference of approximately 1.5–2 times in forest plots. Topographic heterogeneity affected the minimum area through changes in species composition, while species richness had only a weak impact. These results suggest the importance of considering the sampling origin and direction design when utilizing SARs to estimate the minimum area and species diversity in plant communities, which contributes to a better understanding of vegetation characteristics and the minimum area required for censuses in heterogeneous habitats.</p>
Evaluation data for: Adaptive sampling by citizen scientists improves species distribution model performance: a simulation study
<p>All of the evaluation data for the simulations in the paper: Adaptive sampling by citizen scientists improves species distribution model performance: a simulation study. We considered the impact of five adaptive sampling methods on the performance of species distribution models (SDMs), please see the paper for more information. Contained in this repository are the evaluation metrics (AUC, mean square error (MSE) and correlation) for SDMs before and after adaptive sampling has taken place. The MSE and correlation evaluation metrics were calculated against the true distributions of the species. These files are those with "combined_outputs" in the titles. The repository also contains the observations of all the species in the simulations both before and after adaptive sampling (the files with "all_observations" in the title.</p> <p>These datasets are to be used with the plotting and evaluation scripts in the GitHub repository associated with the paper.</p>
Data from: Are fecal samples an appropriate proxy for amphibian intestinal microbiota?
<p>The intestinal microbiota, an invisible organ supporting a host's survival, has essential roles in metabolism, immunity, growth, and development. Since intestinal microbiota influences a host's biology, application of such data to wildlife conservation has gained interest. There are standard protocols for studying the human intestinal microbiota, but no equivalent for wildlife. A major challenge is sampling the intestinal microbiota in an effective, unbiased way. Fecal samples are a popular proxy for intestinal microbiota because collection is non-invasive, convenient, and allows for longitudinal sampling. Yet, it is unclear whether the fecal microbiota is representative of the intestinal microbiota. In amphibians, research on sampling methodology is limited. In this study, we characterize and compare microbiota (small intestine, large intestine, feces) of two Hong Kong stream-dwelling frog species: Lesser Spiny Frog (<em>Quasipaa exilispinosa</em>), and Hong Kong Cascade Frog (<em>Amolops hongkongensis</em>). We found that both species have similar dominant phyla and families, but diverge in terms of the dominant genera. Next, we assess the performance of fecal microbiota in representing the intestinal microbiota in these two species. We found that (1) microbiota of small and large intestine differs significantly, (2) feces are not an appropriate proxy of both intestinal sections, and (3) a set of microbial taxa significantly differs between sample types. Our cautions equating fecal and intestinal microbiota. Sampling feces can avoid sacrifice of an animal, but researchers should avoid over-extrapolation and interpret results carefully.</p>
Bulk Carbon and Amino Acid nitrogen isotope data from Baltic cod (Gadus morhua) and European flounder (Platichthys flesus) muscle tissue samples from the western and central Baltic Sea
<p><span>Eutrophication, increased temperatures and stratification can lead <span>to massive, filamentous, N<sub>2</sub>-fixing cyanobacterial (FNC) blooms in coastal ecosystems with largely unresolved consequences for the mass and energy supply in pelagic and benthic food webs. Mesozooplankton adapt to not top-down controlled FNC blooms by switching diets from phytoplankton to microzooplankton, resulting in a directly quantifiable increase in its trophic position (TP) from 2.0 (herbivore) to as high as 3.0 (carnivore). If this process in mesozooplankton, we call trophic lengthening, was transferred up to higher trophic levels of a food web, a large loss of energy could result in massive declines of fish biomass. </span></span><span>We used compound-specific nitrogen stable isotope data of amino acids (CSIA) to estimate and compare </span><span>the nitrogen (N) sources and TPs of cod and flounder (mesopredators) from areas</span><span> </span><span>with influence of FNC blooms (central Baltic Sea) and without it (western Baltic Sea)</span><span>. We tested if FNC-caused </span><span>trophic lengthening in mesozooplankton is carried over to fish.</span><span> The TP of cod from the western Baltic, feeding mainly on decapods, was equal to the global mean value (4.1, secondary carnivore). Only cod from the central Baltic, mainly feeding on zooplanktivorous pelagics, had a higher TP (4.8, near-tertiary carnivore), indicating a strong carry-over effect of </span><span>FNC-</span><span>caused trophic lengthening from mesozooplankton. In contrast, the TP of molluscivorous flounder (3.2 ± 0.2 in both areas), associated with the benthic food web, was unaffected by trophic lengthening. This suggests that FNC blooms cause a large loss of energy in zooplanktivorous but not in molluscivorous mesopredators. If FNC blooms continue to detour energy at the base of the pelagic food web, the TP of cod will not return to global mean values and the fish stock not recover. Monitoring the TP of key species can identify fundamental changes in ecosystems and provide useful information for resource management.</span></p>
Data from: Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples
<p>Genetic tools for wildlife monitoring can provide valuable information on spatiotemporal population trends and connectivity, particularly in systems experiencing rapid environmental change. Though many DNA sequencing approaches still require high quality and quantity of DNA obtained from traditional sources (e.g. blood and tissue), rapid genotyping tools such as Genotyping-in-Thousands by sequencing (GT-seq) have improved our ability to make use of degraded and less concentrated DNA commonly obtained from non-invasive and archival samples. Here, we developed a multi-purpose GT-seq panel (307 single nucleotide polymorphisms) for a climate sentinel mammal (the American pika, <em>Ochotona princeps</em>) for use as a genetic tool for monitoring populations in the Canadian Rocky Mountains. We optimized the panel using contemporary tissue samples (n = 77) and subsequently applied it to archival tissue (n = 17) and contemporary fecal pellet samples (n = 129) to evaluate its effectiveness at identifying individuals and sex, estimating relatedness, and inferring population structure. The panel demonstrated high efficacy with contemporary and archival tissue samples (94.7% and 90.5% genotyping success, respectively) and negligible genotyping error (0.001% and 0.0%, respectively). Despite relatively high genotyping success for fecal pellet samples (79.7%), high genotyping error (28.4%) limited its power as a monitoring tool to assess genetic variation using non-invasive samples and highlighted the need for further optimization around sample and data collection.</p>
Original genotype data of 159 wheat samples
<p>This dataset contains all 55K SNP original genotype data from 159 wheat samples used in the study, including SNP site IDs, chromosomes and positions, allele information, and genotype information for each material at each SNP site.</p>
Data for umbrella sampling windows for polyleucine partitioning in thickness gradient
<p>Water removed from trajectories</p> <p>30 microseconds per window</p> <p>Martini 2.2</p> <p>https://www.biorxiv.org/content/10.1101/2024.02.02.578561v1.abstract</p>
Code & data of the paper "Data sampling via Active Learning in Cartesian Genetic Programming for Biomedical Data"
<p>Code & data of the paper "Data sampling via Active Learning in Cartesian Genetic Programming for Biomedical Data"</p> <p> </p>
Calibrated and uncalibrated projection data from the paper "Assessing observational constraints on future European climate in an out-of-sample framework"
<p>Individual uncalibrated and calibrated projections for each of the five methods (A-E) in the following folders:</p> <p>MethodA_proj/</p> <p>MethodB_proj/</p> <p>MethodC_proj/</p> <p>MethodD_proj/</p> <p>MethodE_proj/</p> <p> </p> <p>Also included are the out-of-sample data from the "pseudo-observations" (taken from CMIP6 models) used for the verification (see paper for full details):</p> <p>FUTUREverif/</p>
Pepper_Biomass Sample Data
<p>The data we have uploaded consists of partial sample data from the 'pepper_biomass' dataset. Due to reasons concerning intellectual property and personal privacy, we have chosen not to publicly disclose the complete dataset. However, interested parties may contact the corresponding author of the article to request access to the full dataset, provided that they make a reasonable academic inquiry.</p>
Data used in "Chemically specific sampling bias: the ratio of PM2.5 to surface AOD on average and peak days in the U.S."
<p>This dataset contains all relevant data used in the manuscript "Chemically specific sampling bias: the ratio of PM2.5 to surface AOD on average and peak days in the U.S." published in Environmental Science: Atmospheres.</p>
Data from: Disequilibrium oxygen isotope distribution among aqueously altered minerals in Ryugu asteroid returned samples
<p>Oxygen 3-isotope ratios of magnetite and carbonates in aqueously altered carbonaceous chondrites provide important clues to understanding the evolution of the fluid in the asteroidal parent bodies. We conducted oxygen 3-isotope analyses of magnetite, dolomite, and breunnerite in two sections of asteroid Ryugu returned samples, A0058 and C0002, using a secondary ion mass spectrometer (SIMS). Magnetite was analyzed by using a lower primary ion energy that reduced instrumental biases due to the crystal orientation effect. We found two groups of magnetite data identified from the SIMS pit morphologies: (1) higher δ<sup>18</sup>O (from 3‰ to 7‰) and ∆<sup>17</sup>O (~2‰) with porous SIMS pits mostly from spherulitic magnetite, and (2) lower δ<sup>18</sup>O (~ –3‰) and variable ∆<sup>17</sup>O (0-2‰) mostly from euhedral magnetite. Dolomite and breunnerite analyses were conducted using multi-collection Faraday cup detectors with precisions ≤0.3‰. The dependence of instrumental biases on carbonate compositions was corrected using two methods, using Fe and (Fe+Mn) contents, because Ryugu dolomite contains higher amounts of Mn than the terrestrial standard. Results of dolomite and breunnerite analyses show a narrow range of ∆<sup>17</sup>O; 0.0–0.3‰ for dolomite in A0058 and 0.2–0.8‰ for dolomite and breunnerite in C0002. The majority of breunnerite, including large ≥100 µm grains, show systematically lower δ<sup>18</sup>O (~21‰) than dolomite (25–30‰ and 23–27‰ depending on the instrumental bias corrections). The equilibrium temperatures between magnetite and dolomite from the coarse-grained lithology in A0058 are calculated to be 51±11˚C and 78±14˚C, depending on the instrumental bias correction scheme for dolomite; a reliable temperature estimate would require a Mn-bearing dolomite standard to evaluate the instrumental bias corrections, which is not currently available. These results indicate that oxygen isotope ratios of aqueous fluids in the Ryugu parent asteroid were isotopically heterogeneous, either spatially or temporally. Initial water ice accreted to the Ryugu parent body might have ∆<sup>17</sup>O >2‰ that was melted and interacted with anhydrous solids with the initial ∆<sup>17</sup>O <0‰. In the early stage of aqueous alteration, spherulitic magnetite and calcite formed from aqueous fluid with ∆<sup>17</sup>O ~2‰ that was produced by isotope exchange between water (∆<sup>17</sup>O >2‰) and anhydrous solids (∆<sup>17</sup>O <0‰). Dolomite and breunnerite along with some magnetite formed at a later stage of aqueous alteration under higher water-to-rock ratios and the oxygen isotope ratios were nearly at equilibrium between fluid and solid phases. Including literature data, δ<sup>18</sup>O of carbonates decreases in the order of calcite, dolomite, and breunnerite, suggesting that the temperature of alteration might have increased with the degree of aqueous alteration.</p>
Data for Sampling Real‐Time Atomic Dynamics in Metal Nanoparticles by Combining Experiments, Simulations, and Machine Learning
<div> <p>Even at low temperatures, metal nanoparticles (NPs) possess atomic dynamics that are key for their properties but challenging to elucidate. Recent experimental advances allow obtaining atomic‐resolution snapshots of the NPs in realistic regimes, but data acquisition limitations hinder the experimental reconstruction of the atomic dynamics present within them. Molecular simulations have the advantage that these allow directly tracking the motion of atoms over time. However, these typically start from ideal/perfect NP structures and, suffering from sampling limits, provide results that are often dependent on the initial/putative structure and remain purely indicative. Here, by combining state‐of‐the‐art experimental and computational approaches, how it is possible to tackle the limitations of both approaches and resolve the atomistic dynamics present in metal NPs in realistic conditions is demonstrated. Annular dark‐field scanning transmission electron microscopy enables the acquisition of ten high‐resolution images of an Au NP at intervals of 0.6 s. These are used to reconstruct atomistic 3D models of the real NP used to run ten independent molecular dynamics simulations. Machine learning analyses of the simulation trajectories allows resolving the real‐time atomic dynamics present within the NP. This provides a robust combined experimental/computational approach to characterize the structural dynamics of metal NPs in realistic conditions.</p> </div> <div></div>
Development and Implementation of a Tool for Data Capture @ Point of Sampling
<p><span>Poster presented at EFSA Symposium “Data Readiness for Artificial Intelligence”, held on 23-24 October 2024. </span></p> <p><span> </span><span>It describes the project “Development and Implementation of a Tool for Data Capture @ Point of Sampling” coordinated by the Portuguese Economic and Food Safety Authority (ASAE) with technical support from LIACC (Artificial Intelligence and Computer Science Laboratory, University of Porto), and involving two Danish organisations (Danish Veterinary and Food Administration and Technical University of Denmark) as end users of an application designed to enhance the harmonization and robustness of data collection processes. </span></p> <p><span> </span><span>The project is focused on two key areas: the further development of the mobile tool for data capture at the point of sampling in EFSA's SSD2 format, including SSD2 catalogue integration and translation into national languages, and the installation of this tool within partner entities across participating countries. </span></p> <p><span>The new system will incorporate validation features through the integration of the SSD2 data format and the FoodEx2 classification at the point of data creation.</span></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>
Data for 'Magmatic dikes in the Chang'E-6 sampling area'
<p>This dataset contains the codes, data, and scripts used to generate figures in the manuscript '<strong>Magmatic dikes in the Chang’E-6 sampling area</strong>' published in EPSL</p>
BioMates - WP1: Novel pyrolysis oil from non-food/feed biomass - Data sheet: Identifiers for samples and blends
<p>Ablative fast pyrolysis (AFP) is the first step in the BioMates-concept for producing bio-based intermediates (BioMates) with reliable properties from stalk-type biomass. These intermediates are designed for co-processing within conventional refineries. The H2020-project BioMates validates the process concept (<a href="http://www.biomates.eu">www.biomates.eu</a>).</p> <p>AFP produces bio-oil to be mildly hydrotreated towards said intermediates afterwards. This document provides identifiers for samples and blends produced in TRL4 via AFP from wheat-barley-straw and Miscanthus within the BioMates-project.</p>
A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 12
<p>We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 12 contains stitched image montages of thin sections (selected areas) through the lung of patients C04 and C07 which were acquired by scanning electron microscopy. The images show alveolae with various degree of epithelial damage.</p>
A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 11
<p>We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 11 contains a stitched image montage of a thin section (selected area) through the lung of patient C05 which was acquired by scanning electron microscopy. The image shows a lung area with a dissolved alveolar architecture and a massive type-2-cell hyperplasia.</p>
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.