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.
11,177
datasets available to search
ShareScore release 0.9.0
Dataset results
11,177 results for “identify”
List of studies on Covid-19 identified in PubMed and excluded from our systematic review
<p>In the course of our PubMed searches we identified and screened the title and abstract of a number of studies on Covid-19 that were finally excluded from our systematic review. </p> <p>This file will be updated regularly.</p>
Figure 3 in Reptile distribution may identify terrestrial islands for conservation: the Levant's 'Arava Valley as a model
Figure 3. The estimated proportions (± SE) of shared species (species occurring in both Israel and Jordan) among all the regions in the north and south studied areas. Groups with similar letters are not significantly different from each other.
Figure 2 in Reptile distribution may identify terrestrial islands for conservation: the Levant's 'Arava Valley as a model
Figure 2. Young male Gazella gazella acaciae Mendelssohn et al. (1997) from the 'Arava Valley, photographed for identification in January 1964 in the then Elat Zoo, Israel, 33 years before the taxon was recognized and described (photo: YL & N Werner).
Figure 1 in Reptile distribution may identify terrestrial islands for conservation: the Levant's 'Arava Valley as a model
Figure 1. Schematic map of Cisjordan, Transjordan and the 'Arava valley shared by them. The number of squamate taxa in an area is encircled in that area. The number of species shared by two areas is in the arc bridging them. In the middle of the southern complex is a bridge joining all three areas. (Technique inspired by figures 92 and 95 in Anderson 1968).
Data from: Host sex and age typically explain variation in parasitism of Rock Ptarmigan: implications for identifying determinants of exposure and susceptibility
<p>Measures of parasitism often differ between hosts. This variation is thought due in part to age or sex differences in exposure to parasites and/or susceptibility to parasitism. We assessed how often age or sex biases in parasitism were found using a large, multi-year (2006 – 2017) dataset of 12 parasite species of Icelandic Rock Ptarmigan (<em>Lagopus muta</em>). We found host traits (i.e. age and/or sex) accounted for significant variation in abundance of 11 of the 12 parasite species. We often found increased abundance among juvenile hosts, although significant adult biases were observed for three parasite species. Additionally, higher levels of parasitism by many species were observed for female hosts, contrary to frequent male biases in parasitism reported for other vertebrates. Abundance of six parasite species was best explained by interactions between host age and sex; some degree of decrease in abundance with host age was present for both male and female hosts for four of those parasite species. We consider various host and parasite traits that could account for observed singular and repeated patterns of age and/or sex biases in parasitism (e.g. age- and sex-related grouping behaviours, age-specific mortality in relation to parasitism, acquisition of greater immunity with age). This work provides a foundation for future studies investigating age-related differences in acquired immunity and age-specific parasite-mediated mortality for males and females, as well as studies on interactions between co-infecting parasite species.</p>
Data from: Simultaneous measurement of excitation-contraction coupling parameters identifies mechanisms underlying contractile responses of hiPSC-derived cardiomyocytes
Cardiomyocytes from human induced pluripotent stem cells (hiPSC-CMs) are increasingly recognized as valuable for determining the effects of drugs on ion channels but they do not always accurately predict contractile responses of the human heart. This is in part attributable to their immaturity but the sensitivity of measurement tools may also be limiting. Measuring action potential, calcium flux or contraction individually misses critical information that is captured when interrogating the complete excitation-contraction coupling cascade simultaneously. Here, we develop an hypothesis-based statistical algorithm that identifies mechanisms of action. We design and build a high-speed optical system to measure action potential, cytosolic calcium and contraction simultaneously using fluorescent sensors. These measurements are automatically processed, quantified and then assessed by the algorithm. Multiplexing these three critical physical features of hiPSC-CMs allows identification of all major drug classes affecting contractility with detection sensitivities higher than individual measurement of action potential, cytosolic calcium or contraction.
Preprocessing scripts and data for study: Identifying high-confidence capture Hi-C interactions using CHiCANE
<p>Preprocessing scripts and processed data from CHi-C libraries generated from breast cancer cells (T47-D) and Megakaryoctye cells (MK).</p>
Identifying Improvement Opportunities in Software Engineering Education at the Maranhão State: Listening to Voices from Academy and Industry
<p>The teaching of Software Engineering (SE) has become challenging due to the large amount of content taught and the constant evolution of the software industry, directly impacting the requirements necessary to apply for a position in the area of Information Technology (IT). In this context, it is clear that students of computer courses still find it difficult to know how to prepare for the job market, and Higher Education Institutions (HEIs) may have difficulties in aligning themselves with market expectations with their syllabus in SE. This paper aims to provide a holistic view of the teaching-learning process, involving the views of students, HEIs and IT companies in the context of the state of Maranhão; and to propose reflections on the current state of the education to complement the contents and methodologies applied in the classroom with the needs of the local industry. To do so, three activities were carried out: (1) mapping expectations and evaluating higher education from the students’ point of view; (2) analysis of higher education disciplines in higher education institutions in the state of Maranhão in Brazil; and (3) survey of expectations of the IT market considering the vacancies disclosed in relation to the SE area in the state of Maranhão. The results indicate a partial fulfillment of the demand regarding the taught topics related to SE from the local industry by the HEIs. In addition, there is a need to improve the teaching-learning methodological processes, focusing on practical activities and the learning of teamwork skills, in addition to knowledge in software development.</p>
A Lightweight Technique to Identify Equivalent Mutants
<p>Mutation analysis is a popular but costly approach to assess the quality of test suites. Equivalent mutants are useless and contribute to increase costs. We propose a lightweight technique to identify equivalent mutants by proving equivalences with Z3 in the context of weak mutation testing. To evaluate our approach, we apply our technique for 40 mutation targets (mutations of an expression or statement) and automatically identify 13 equivalent mutations for seven mutation targets. We manually confirm that the equivalent mutants detected by our technique are indeed equivalent. Moreover, we evaluate our approach in the context of strong mutation testing against mutants generated by MuJava for 5 projects. Our technique detects all equivalent mutants detected by TCE. The results of our technique can be useful to improve mutation testing tools by avoiding the application of 13 mutations for 7 mutation targets.</p>
An Approach to Identify and Classify State Machine Changes from Code Changes
<p>Vídeo de auxílio para apresentação do artigo: An Approach to Identify and Classify State Machine Changes from Code Changes</p>
Systems genetics in diversity outbred mice inform BMD GWAS and identify determinants of bone strength
<p>This data repository contains data in support of "Systems genetics in diversity outbred mice inform BMD GWAS and identify determinants of bone strength".</p> <p>The following data are included:</p> <ul> <li>Raw genotyping results using the GigaMUGA array for 619 Diversity Outbred mice (.txt files).</li> <li>Genotype probabilities as an Rdata file, calculated using R/qtl2 (pr_basic_cleaned.Rdata).</li> <li>Allele probabilities as an Rdata file, calculated using R/qtl2 (apr_basic_cleaned.Rdata).</li> <li>R/qtl2 cross files for QTL (cross_basic_cleaned.Rdata) and eQTL (cross_eqtl_REDO.Rdata) mapping. Cross files also include covariates (including PEER factors in cross_eqtl_REDO.Rdata).</li> </ul> <p>Supporting sequencing data can be found from the NCBI Gene Expression Omnibus database (GSE152708, GSE152806).</p> <p>For more information, please visit (https://github.com/basel-maher/DO_project).</p> <p>Contact: bma8ne AT virginia DOT edu</p> <p> </p>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Jocelyn Colella, <a href="https://orcid.org/0000-0003-2463-1029">https://orcid.org/0000-0003-2463-1029</a>. Claims were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Supplementary material for "Compounds with antiviral, anti-inflammatory and anticancer activity identified in wine via high resolution mass spectrometry and bioinformatics analyses"
<p>Wine contains a variety of molecules with potential beneficial effects on human health. Our aim was to examine the wine components with high-resolution mass spectrometry including high-resolution tandem mass spectrometry in two wine types made from grapes with or without the fungus <em>Botrytis cinerea</em>, or “noble rot.” For LC-MS/MS analysis, 12 wine samples (7 without and 5 with noble rotting) from 4 different wineries were used and wine components were identified and quantified. Results: 288 molecules were identified in the wines and the amount of 169 molecules was statistically significantly different between the two wine types. A database search was carried out to find the molecules, which were examined in functional studies so far, with high emphasis on molecules with antiviral, anti-inflammatory and anticancer activities. Conclusions: A comprehensive functional dataset related to identified wine components is also provided highlighting the importance of components with potential health benefits.</p>
The roles of data stewards in the data stewardship landscape identified in Denmark and the Netherlands
<p>The roles and stakeholders in the data stewardship landscape that were identified in Denmark and the Netherlands align very well as is shown in the Figure. </p> <p>References:<br> Danish project report: <strong> </strong>Wildgaard, L., Vlachos, E., Nondal, L., Larsen, A. V., & Svendsen, M. (2020, January 31). National Coordination of Data Steward Education in Denmark: Final report to the National Forum for Research Data Management (DM Forum) (Version 1). Zenodo. <a href="http://doi.org/10.5281/zenodo.3609516">http://doi.org/10.5281/zenodo.3609516</a><br> Dutch project report: Scholtens, S., Jetten, M., Böhmer, J., Staiger, Ch., Slouwerhof, I., Van der Geest, M. & Van Gelder, C.W.G.. (2019, October 3). Final report: Towards FAIR data steward as profession for the lifesciences. Report of a ZonMw funded collaborative approach built on existing expertise. Zenodo. <a href="http://doi.org/10.5281/zenodo.3474789">http://doi.org/10.5281/zenodo.3474789</a> <br> Dutch project report: Jetten, M. et al. Professionalising data stewardship in the Netherlands: competences, training and education - Dutch roadmap towards national implementation of FAIR data stewardship (to be published in 2021)</p>
Identifying conservation priorities in a defaunated tropical biodiversity hotspot
<p><b>Aim: </b>Unsustainable hunting is leading to widespread defaunation across the tropics. To mitigate against this threat with limited conservation resources, stakeholders must make decisions on where to focus anti-poaching activities. Identifying priority areas in a robust way allows decision-makers to target areas of conservation importance, therefore maximizing the impact of conservation interventions.</p> <p><b>Location: </b>Annamite mountains, Vietnam and Laos.</p> <p><b>Methods: </b>We conducted systematic landscape-scale surveys across five study sites (four protected areas, one unprotected area) using camera-trapping and leech-derived environmental DNA. We analyzed detections within a Bayesian multi-species occupancy framework to evaluate species responses to environmental and anthropogenic influences. Species responses were then used to predict occurrence to unsampled regions. We used predicted species richness maps and occurrence of endemic species to identify areas of conservation importance for targeted conservation interventions.</p> <p><b>Results: </b>Analyses showed that habitat-based covariates were uninformative. Our final model therefore incorporated three anthropogenic covariates as well as elevation, which reflects both ecological and anthropogenic factors. Conservation-priority species tended to found in areas that are more remote now or have been less accessible in the past, and at higher elevations. Predicted species richness was low and broadly similar across the sites, but slightly higher in the more remote site. Occupancy of the three endemic species showed a similar trend.</p> <p><b>Main conclusion: </b>Identifying spatial patterns of biodiversity in heavily-defaunated landscapes may require novel methodological and analytical approaches. Our results indicate to build robust prediction maps it is beneficial to sample over large spatial scales, use multiple detection methods to increase detections for rare species, include anthropogenic covariates that capture different aspects of hunting pressure, and analyze data within a Bayesian multi-species framework. Our models further suggest that more remote areas should be prioritized for anti-poaching efforts to prevent the loss of rare and endemic species.</p>
Data from: Transcriptomes of parents identify parenting strategies and sexual conflict in a subsocial beetle
Parenting in the burying beetle Nicrophorus vespilloides is complex and, unusually, the sex and number of parents that can be present is flexible. Such flexibility is expected to involve specialized behaviour by the two sexes under biparental conditions. Here, we show that offspring fare equally well regardless of the sex or number of parents present. Comparing transcriptomes, we find a largely overlapping set of differentially expressed genes in both uniparental and biparental females and in uniparental males including vitellogenin, associated with reproduction, and takeout, influencing sex-specific mating and feeding behaviour. Gene expression in biparental males is similar to that in non-caring states. Thus, being 'biparental' in N. vespilloides describes the family social organization rather than the number of directly parenting individuals. There was no specialization; instead, in biparental families, direct male parental care appears to be limited with female behaviour unchanged. This should lead to strong sexual conflict.
Data from: Molecular field analysis of trophic relationships in soil-dwelling invertebrates to identify mercury, lead and cadmium transmission through forest ecosystems
Contamination pathways in complex food chains in soil ecosystems can be difficult to elucidate. Molecular analysis of predator gut content can, however, rapidly reveal previously unidentified trophic interactions between invertebrates and thereby uncover pathways of pollutant spread. Here we measured concentrations of the toxic metals lead, cadmium and mercury in carabid beetle predators and their prey. Invertebrates were sampled at one control and four heavy metal polluted sites in order to reveal the impact of diet composition and seasonal variation in prey availability on metal burden in carabids and metal transfer pathways through forest ecosystems. This is the first report, to our knowledge, of carabid diet composition based on PCR analysis of gut contents at the forest community level, rather than in cultivated fields. Extensive screening using group- and species-specific primers revealed that carabids ate primarily earthworms and slugs, as well as smaller numbers of woodlice and springtails. Metal concentrations in carabids correlated with seasonal changes in diet. Mercury accumulated in beetle predators more than in their slug prey. Since earthworms, slugs and carabid beetles are the major prey of many birds and mammals, prey-predator transfer and associated toxicity are major risks at mercury-contaminated sites. Carabids may be useful bioindicators for assessing the impact of pollutants on soil ecosystems, as long as species and seasonal factors are taken into account.
Data from: Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae)
DNA barcoding is a technique to identity species by using standardized DNA sequences. In the present study, a total of 105 samples, representing 30 Parnassia species were collected to test the effectiveness of four proposed DNA barcodes (rbcL, matK, trnH-psbA and ITS) for species identification. Our results demonstrated that all four candidate DNA markers have a maximum level of primer universality and sequencing success. As single DNA marker, ITS region provided the highest species resolution with 86.7%, followed by trnH-psbA with 73.3%. The combination of the core barcode, matK + rbcL, gave the lowest species identification success (63.3%) among any combination of multiple markers, and was found unsuitable as DNA barcode for Parnassia. The combination of ITS + trnH-psbA achieved the highest species discrimination with 90.0% resolution (27 out of 30 sampled species), equal to the four-marker combination; ITS combined with matK, rbcL or matK + rbcL did not improve species discrimination. Therefore, matK and rbcL should not be used as DNA barcode for species identification of Parnassia. Based on the overall performance, the combination of ITS + trnH-psbA, is proposed as the most suitable DNA barcode for identifying Parnassia species. DNA barcoding is a useful technique to providing a reliable and effective mean for the discrimination of Parnassia species, and in combination with morphology based taxonomy can be a robust approach for tackling taxonomically complex groups. In the light of our findings, we found among the three species not identified a possible cryptic speciation event in Parnassia.
Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses
Switchgrass is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving not only simple additive marker effects but also interactions with genetic backgrounds, e.g., ecotypes, or synergies with other markers. We analyzed plant height, carbon content, nitrogen content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotype. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, but also 83,290 markers for marker-by-ecotype interactions and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected based on marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for carbon content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected based on pairwise marker correlations. Furthermore, one marker-by-ecotype interaction and one pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits in switchgrass. Moreover, they exemplified the importance of interactive effects for the depiction of genetic bases, and illustrated the usefulness of preselection of marker pairs for identifying pairwise marker interactions in association testing.
Data from: Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters
Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified Fragment Length Polymorphisms (AFLP) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff between culling all but the lowest-error loci to minimize overall genotyping error versus the potential for increasing population genetic signal by retaining more loci. Here, we used AFLPs to compare population structure in co-distributed broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris) oyster species. Using existing methods for almost entirely automated marker selection and scoring, genotyping error tradeoffs were evaluated by comparing results across a nested series of datasets with mean mismatch errors of 0, 1, 2, 3, 4 and >4%. Artifactual population structure was diagnosed in high-error datasets and we assessed the low-error point at which expected population substructure signal was lost. In both species we identified substructure patterns deemed to be inaccurate at error rates {less than or equal to}2% and >4%. In the species comparison, the optimum datasets showed higher gene flow for the brooding oyster with more oceanic salinity tolerances. AFLP tradeoffs may differ among studies, but our results suggest that important signal may be lost in the pursuit of 'acceptable' error levels and our procedures provide a general method for empirically exploring these tradeoffs.
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.