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”
Data from: Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in Campanulid angiosperms
The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lineages, which could lead to errors in estimating transition rates and the associated inference of ancestral states. Here we develop and implement a new method for identifying different rates of evolution in a binary character along different branches of a phylogeny. We illustrate this approach by exploring the evolution of growth habit in Campanulidae, a flowering plant clade containing some 35,000 species. The distribution of woody versus herbaceous species calls into question the use of traditional models of binary character evolution. The recognition and accommodation of changes in the rate of growth form evolution in different lineages demonstrates, for the first time, a robust picture of growth form evolution across a very large, very old, and very widespread flowering plant clade.
Data from: Identifying multiple coral reef regimes and their drivers across the Hawaiian archipelago
Loss of coral reef resilience can lead to dramatic changes in benthic structure, often called regime shifts, which significantly alter ecosystem processes and functioning. In the face of global change and increasing direct human impacts, there is an urgent need to anticipate and prevent undesirable regime shifts and, conversely, to reverse shifts in already degraded reef systems. Such challenges require a better understanding of the human and natural drivers that support or undermine different reef regimes. The Hawaiian archipelago extends across a wide gradient of natural and anthropogenic conditions and provides us a unique opportunity to investigate the relationships between multiple reef regimes, their dynamics and potential drivers. We applied a combination of exploratory ordination methods and inferential statistics to one of the most comprehensive coral reef datasets available in order to detect, visualize and define potential multiple ecosystem regimes. This study demonstrates the existence of three distinct reef regimes dominated by hard corals, turf algae or macroalgae. Results from boosted regression trees show nonlinear patterns among predictors that help to explain the occurrence of these regimes, and highlight herbivore biomass as the key driver in addition to effluent, latitude and depth.
Data from: Genetic mapping of molar size relations identifies inhibitory locus for third molars in mice
Molar size in Mammals shows considerable disparity and exhibits variation similar to that predicted by the Inhibitory Cascade model. The importance of such developmental systems in favoring evolutionary trajectories is also underlined by the fact that this model can predict macroevolutionary patterns. Using backcross mice, we mapped QTL for molar sizes controlling for their sequential development. Genetic controls for upper and lower molars appear somewhat similar, and regions containing genes implied in dental defects drive this variation. We mapped three relationship QTLs (rQTL) modifying the control of the mesial molars on the focal third molar. These regions overlap Shh, Sostdc1 and Fst genes, which have pervasive roles in development and should be buffered against new variation. It has theoretically been shown that rQTL produces new variation channeled in the direction of adaptive changes. Our results provide evidence that evolutionary/disease patterns of tooth size variation could result from such a non-random generating process.
Data from: Genetic analysis identifies the missing parchment of New Zealand's founding document, The Treaty of Waitangi.
Genetic analyses provide a powerful tool with which to identify the biological components of historical objects. Te Tiriti o Waitangi | The Treaty of Waitangi is New Zealand's founding document, intended to be a partnership between the indigenous Māori and the British Crown. Here we focus on an archived piece of blank parchment that has been proposed to be the missing portion of the lower parchment of the Waitangi Sheet of the Treaty. However, its physical dimensions and characteristics are not consistent with this hypothesis. We perform genetic analyses on the parchment membranes of the Treaty, plus the blank piece of parchment. We find that all three parchments were made from ewes and that the blank parchment is highly likely to be a portion cut from the lower membrane of the Waitangi Sheet because they share identical whole mitochondrial genomes, including an unusual heteroplasmic site. We suggest that the differences in size and characteristics between the two pieces of parchment may have resulted from the Treaty's exposure to water in the early 20th century and the subsequent repair work, light exposure during exhibition or the later conservation treatments in the 1970s and 80s. The blank piece of parchment will be valuable for comparison tests to study the effects of earlier treatments and to monitor the effects of long-term display on the Treaty.
Data from: Resequencing of common bean identifies regions of inter-gene pool introgression and provides comprehensive resources for molecular breeding
Common bean is the most important grain legume for human consumption and a main nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to P. vulgaris, P. acutifolius, and P. coccineus were sequenced by whole-genome sequencing (WGS), identifying more than 40 million genomic variants. Evaluation of nuclear DNA content and analysis of copy number variation revealed important differences in genomic content not only between P. vulgaris and two other domesticated Phaseolus species, but also within P. vulgaris, affecting hundreds of protein-coding genomic regions. A large number of inter-gene-pool introgressions were identified. Furthermore, interspecific introgressions for disease resistance in breeding lines were mapped. Evaluation of newly developed SNP markers within previously discovered QTL for common bacterial blight and angular leaf spot provide improved specificity to tag sources of resistance to these diseases. We expect that this dataset will provide a deeper molecular understanding of breeding germplasm and deliver molecular tools for germplasm development, aiming to increase the efficiency of bean breeding programs.
Using nominal group technique among resident physicians to identify key attributes of a burnout prevention program
<p>Purpose:<b> </b>To identify preferred burnout interventions within a resident physician population, utilizing the Nominal Group Technique. The results will be used to design a discrete choice experiment study to inform the development of resident burnout prevention programs.</p> <p>Methods:<b> </b>Three resident focus groups met (10-14 participants/group) to prioritize a list of 23 factors for burnout prevention programs. The Nominal Group Technique consisted of three steps: an individual, confidential ranking of the 23 factors by importance from 1 to 23, a group discussion of each attribute, including a group review of the rankings, and an opportunity to alter the original ranking across participants.</p> <p>Results:<b> </b>The total number of residents (36) were a representative sample of specialty, year of residency, and sex. There was strong agreement about the most highly rated attributes which grouped naturally into themes of autonomy, meaning, competency and relatedness. There was also disagreement on several of the attributes that is likely due to the differences in residency specialty and subsequently rotation requirements.</p> <p>Conclusion:<b> </b>This study identified the need to address multiple organizational factors that may lead to physician burnout. There is a clear need for complex interventions that target systemic and program level factors rather than focus on individual interventions. These results may help residency program directors understand the specific attributes of a burnout prevention program valued by residents. Aligning burnout interventions with resident preferences could improve the efficacy of burnout prevention programs by improving adoption of, and satisfaction with, these programs.</p>
Data from: Reconstruction of genetically identified neurons imaged by serial-section electron microscopy
Resolving patterns of synaptic connectivity in neural circuits currently requires serial section electron microscopy. However, complete circuit reconstruction is prohibitively slow and may not be necessary for many purposes such as comparing neuronal structure and connectivity among multiple animals. Here, we present an alternative strategy, targeted reconstruction of specific neuronal types. We used viral vectors to deliver peroxidase derivatives, which catalyze production of an electron-dense tracer, to genetically identified neurons, and developed a protocol that enhances the electron-density of the labeled cells and while retaining quality of the ultrastructure. The high contrast of the marked neurons enabled two innovations that dramatically speed data acquisition: targeted high-resolution reimaging of regions selected from rapidly-acquired lower resolution reconstruction, and an unsupervised segmentation algorithm. This pipeline reduces imaging and reconstruction times by at least two orders of magnitude, facilitating directed inquiry of circuit motifs.
Supplementary material 1 from: Hardisty AR, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2021) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7: e67379. https://doi.org/10.3897/rio.7.e67379
The type specimen for Holorchis Castex; a case example
Figure 3 from: Hardisty AR, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2021) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7: e67379. https://doi.org/10.3897/rio.7.e67379
Figure 3 Governance, operations, financing and architecture (GOFA) together delivering sustainability.
Figure 2 from: Hardisty AR, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2021) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7: e67379. https://doi.org/10.3897/rio.7.e67379
Figure 2 Scoring of PID scheme optionsKey: MPA = Multi-Primary Administrator, RA = Registration Agency.
Figure 1 from: Hardisty AR, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2021) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7: e67379. https://doi.org/10.3897/rio.7.e67379
Figure 1 Digitally transforming collections science with Digital Specimens and persistent identifiers (PID).
Supplementary material 2 from: Hardisty AR, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2021) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7: e67379. https://doi.org/10.3897/rio.7.e67379
Estimates of numbers of PIDs needed
Supplementary material 4 from: Hardisty AR, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2021) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7: e67379. https://doi.org/10.3897/rio.7.e67379
Dimensions appraisal of the options
Data from: Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage
We surveyed the iron nutrition-responsive transcriptome of Chlamydomonas reinhardtii using RNA-Seq methodology. Presumed primary targets were identified in comparisons between visually asymptomatic iron-deficient versus iron-replete cells. This includes the known components of high-affinity iron uptake as well as candidates for distributive iron transport in C. reinhardtii. Comparison of growth-inhibited iron-limited versus iron-replete cells revealed changes in the expression of genes in chloroplastic oxidative stress response pathways, among hundreds of other genes. The output from the transcriptome was validated at multiple levels: by quantitative RT-PCR for assessing the data analysis pipeline, by quantitative proteomics for assessing the impact of changes in RNA abundance on the proteome, and by cross-species comparison for identifying conserved or universal response pathways. In addition, we assessed the functional importance of three target genes, VITAMIN C 2 (VTC2), MONODEHYDROASCORBATE REDUCTASE 1 (MDAR1), and CONSERVED IN THE GREEN LINEAGE AND DIATOMS 27 (CGLD27), by biochemistry or reverse genetics. VTC2 and MDAR1, which are key enzymes in de novo ascorbate synthesis and ascorbate recycling, respectively, are likely responsible for the 10-fold increase in ascorbate content of iron-limited cells. CGLD27/At5g67370 is a highly conserved, presumed chloroplast-localized pioneer protein and is important for growth of Arabidopsis thaliana in low iron.
Analysis code and additional data associated with the manuscript entitled 'Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion'
<p>This dataset is associated with the research manuscript entitled ‘<em>Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion</em>’ (https://www.biorxiv.org/content/10.1101/754002v2).</p> <p>The folder ‘<strong>Zenodo_Saxena_etal_2021_AdditionalData_AnalysisCode</strong>’ contains:</p> <p>> Analysis code used for jerboas-mouse differential RNASeq analysis (<strong>saxena_Interspecies_DESEQ2_analysis.R</strong>).</p> <p>> A folder <strong>Mus_Jac_gtfDir</strong> with two gtf annotation files for 1:1 orthologs in Mouse (musAnno4_1To1Orthologs) and Jerboa (jerboaAnno4_1To1Orthologs) genomes generated with CESAR. This folder also contains two files with mouse or jerboa gene lengths in non-overlapping exons of each gene in the 1:1 orthologous GTF annotations (suffixed "*_exon_lengths_per_gene.txt"). A supporting R library required to run the analysis is provided in this folder (saxena_shared_library_v2.R).</p> <p>>A <strong>STAR_countsDir</strong> folder with STAR generated GeneCounts for mouse and jerboa samples (suffixed "*_SR50"). Subfolders contain metatarsal (MT) and Radius/ulna (RU) STAR Genecounts used in the primary (“*_n=3") and independent validation ("*_n=2") analyses.</p> <p>> A pdf file with <strong>Additional Figures 1 and 2</strong>. Fig 1 shows RNAScope <em>in situs </em>for <em>Galnt17</em> in jerboa and mouse postnatal day 5 cartilages. Fig 2 shows DESeq2 generated MA-plot for jerboa-mouse metatarsal comparisons (n=3).</p> <p>> <strong>Additional Data Tables_1to3</strong> with DESeq2 differential expression results for all of the 17,464 mouse and jerboa orthologs in the primary (n=3, Table1) and independent validation (n=2, Table2) analyses. r-log transformed gene counts for 17,464 mouse and jerboa 1:1 orthologs in metatarsal samples (n=3, Table3).</p>
Figure 1 in A contribution to the knowledge of fly fauna in the Kingdom of Saudi Arabia: new country records and an account of flies identified from Rawdhats, Riyadh Region, with biogeographical remarks (Insecta: Diptera)
Figure 1. Map of Kingdom of Saudi Arabia showing the collecting localities.
Figure 10 in Can hair width and scale pattern and direction of dorsal scapular mammalian hair be a relatively simple means to identify species?
Figure 10. Boxplot of 30 guard hair widths for each species including quartile ranges.
Patterns of niche contraction identify vital refuge areas for declining mammals
<p><i>Aim</i></p> <p>Investigation of realised niche contraction in declining species can help us understand how and where threats are being either mediated or tolerated across landscapes. It also provides insights into species' sensitivity to environmental change that are unable to be identified through analysis of declines in range size or abundance alone. Here, we apply the recently proposed 'niche reduction hypothesis' to investigate relationships between trends in niche breadth and geographic distribution of declining species.</p> <p><i>Location</i></p> <p>Northern Australia</p> <p><i>Methods</i></p> <p>We compare and contrast contemporary and historical datasets to examine the relationship between extent of occurrence (EOO) and realised niche hypervolume, and investigate changes in species' utilisation of environmental space through time via generalised linear modelling and bootstrapping of historical values. We also use the 'Maxent' algorithm to create and stack contemporary and historical ecological niche models (ENMs) and identify regions where resilience to threatening processes is maximised.</p> <p><i>Results</i></p> <p>We found larger mean reductions in niche hypervolume (39%) than EOO (30.5%), with little correlation (<i>r</i> = 0.07) between the two measures, suggesting that contraction of realised niche breadth can be largely independent of reduction in EOO. We also identified a general set of environmental conditions towards which species' realised niches contracted. <a name="_Hlk40866810">Comparison of stacked ENMs allowed us to identify regions of natural refuge </a>where environmental conditions are associated with increased species resilience to threats, and conversely, regions where habitat suitability has declined.</p> <p><i>Main conclusions</i></p> <p>Examining species declines from an ecological niche perspective provides a powerful tool for understanding how environmental conditions, biotic interactions, and species traits shape responses to local and global environmental changes. Quantifying reductions in niche breadth is crucial as contraction to a narrower subset of environmental space can reduce a species' ability to tolerate other threats and potentially lower adaptive capacity and genetic diversity, increasing extinction risk.</p>
Fig. 1 in DNA barcoding applied: identifying the larva of Merodon avidus (Diptera: Syrphidae)
Fig. 1. Molecular phylogenetic tree generated using the Maximum Likelihood criterion. Bootstrap support values are shown next to nodes.
FIGURE 47 in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURE 47. Known distribution of northern inland group species of Visma n. gen.
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.