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8,565 results for “characterization”
Characterizing Novel Olfactory Receptors Expressed in the Murine Renal Cortex: Supplemental Table S1
<p><strong>Ligand screening of Olfr90, Olfr461, Olfr558, Olfr1034, and Olfr1396.</strong> The complete screening results of all compounds tested on all 5 murine ORs. Compounds were tested at 0.5 mM unless otherwise specified. “+” indicates robust statistically signification activation, while “–” indicates no response. ORs listed in the Classification column are siblings of tested ORs. The term “general” is used for compounds in our library that are commonly used to screen ORs, and “biofluids” refers to compounds listed in the Human Metabolome Database which are detected in biofluids such as blood, urine, etc.</p> <p> </p> <p> </p>
Bibliographic dataset characterizing studies that use online biodiversity databases
<p>This dataset includes bibliographic information for 501 papers that were published from 2010-April 2017 (time of search) and use online biodiversity databases for research purposes. Our overarching goal in this study is to determine how research uses of biodiversity data developed during a time of unprecedented growth of online data resources. We also determine uses with the highest number of citations, how online occurrence data are linked to other data types, and if/how data quality is addressed. Specifically, we address the following questions:</p> <p>1.) What primary biodiversity databases have been cited in published research, and which</p> <p> databases have been cited most often?</p> <p>2.) Is the biodiversity research community citing databases appropriately, and are</p> <p> the cited databases currently accessible online?</p> <p>3.) What are the most common uses, general taxa addressed, and data linkages, and how </p> <p> have they changed over time?</p> <p>4.) What uses have the highest impact, as measured through the mean number of citations</p> <p> per year?</p> <p>5.) Are certain uses applied more often for plants/invertebrates/vertebrates?</p> <p>6.) Are links to specific data types associated more often with particular uses?</p> <p>7.) How often are major data quality issues addressed?</p> <p>8.) What data quality issues tend to be addressed for the top uses? </p> <p>Relevant papers for this analysis include those that use online and openly accessible primary occurrence records, or those that add data to an online database. Google Scholar (GS) provides full-text indexing, which was important to identify data sources that often appear buried in the methods section of a paper. Our search was therefore restricted to GS. All authors discussed and agreed upon representative search terms, which were relatively broad to capture a variety of databases hosting primary occurrence records. The terms included: “species occurrence” database (8,800 results), “natural history collection” database (634 results), herbarium database (16,500 results), “biodiversity database” (3,350 results), “primary biodiversity data” database (483 results), “museum collection” database (4,480 results), “digital accessible information” database (10 results), and “digital accessible knowledge” database (52 results)--note that quotations are used as part of the search terms where specific phrases are needed in whole. We downloaded all records returned by each search (or the first 500 if there were more) into a Zotero reference management database. About one third of the 2500 papers in the final dataset were relevant. Three of the authors with specialized knowledge of the field characterized relevant papers using a standardized tagging protocol based on a series of key topics of interest. We developed a list of potential tags and descriptions for each topic, including: database(s) used, database accessibility, scale of study, region of study, taxa addressed, research use of data, other data types linked to species occurrence data, data quality issues addressed, authors, institutions, and funding sources. Each tagged paper was thoroughly checked by a second tagger.</p> <p>The final dataset of tagged papers allow us to quantify general areas of research made possible by the expansion of online species occurrence databases, and trends over time. Analyses of this data will be published in a separate quantitative review.</p>
"Marsh" database: characterization of the state of the necton in two depolderized zones of the Gironde estuary
<p>In the Gironde estuary, two accidentally de-polderized marshes have been the subject of biological monitoring (necton) since 2008: the Marais de Mortagne-sur-Gironde and the northern part of Île Nouvelle. The Mortagne-sur-Gironde marsh is located in the mesohalin sector of the Gironde estuary. With an area of 191 hectares, the marsh was dammed in 1966 and cultivated for more than 30 years. Its protective dike gave way during the December 1999 storm. Ile Nouvelle is located in the Oligaline Sector of the Gironde Estuary. The northern part of the island - an area of 141 hectares - has been depolderized during the passage of storm Xynthia in 2010, following the opening of a breach.<br> Biological monitoring (necton) was carried out in the Gironde estuary over the period 2008-2016 to test the hypothesis that the depoldisation of the estuarine shorelines makes it possible to recreate nursery and feeding areas for fish and fish. estuarine and coastal macrocrustaceans. This work was carried out by the National Institute for Research in Science and Technology for the Environment and Agriculture (Irstea), in partnership with the Conservatoire du Littoral, the Gironde Departmental Council and the Regional Council for Natural Areas ( CREN) of Poitou-Charentes.<br> The "Marsh" database includes all the surveys carried out throughout the study, between 2008 and 2016, and in particular samplings carried out within the necton.</p>
Characterizing Novel Olfactory Receptors Expressed in the Murine Renal Cortex: Supplemental Table S2
<p><strong>Olfactory receptors selected for study. </strong>Olfactory receptors (ORs) selected for study based on mapped reads in at least 7 out of 8 murine renal cortex samples. Murine samples are listed as A - M. Samples A - G were fed high fat diet, while samples I - M were fed control diet. (mm10) FPKM counts for ORs selected for study based on the GRCm30/mm10 genome build using previously published OR coordinates. ORs are listed using the "Olfr" gene names, as well as the "CUFFOR" names as determined by Ibarra-Soria X et al. (mm9) FPKM counts for ORs selected for study based on the NCBI37/mm9 genome build using established coordinates. ORs listed in green were identified and cloned from kidney RNA previously.</p> <p> </p> <p>Data accessible at NCBI GEO database, accession number GSE117249<br> https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117249</p>
Scattering matrices and integral scattering quantities of laboratory-characterized silicate and ice particles
<p>Mueller scattering matrices and integral scattering quantities of four different scattering particle shapes, two refractive indices, and various size parameters computed using ADDA (v1.2; Yurkin and Hoekstra, JQSRT 112, pp. 2234-2247, 2011). The file name consists of the particle shape designation (A-D), the refractive index designation ("m254" depicts a silicate-rich particle: m = 2.54 + 0.01i; "m178" depicts an ice-rich particle with impurities: m = 1.78 + 0.001i; both at microwave frequencies), and the volume-equivalent size parameter (spherical-volume-equivalent particle perimeter length per wavelength) ranging from 0.25 to 7-16 depending on the shape type. "CS" refers to Cross Sections, which includes the extinction cross section, the extinction efficiency, the absorption cross section, and the absorption efficiency. The cross sections assume a wavelength of 6.283185307. All Mueller scattering matrices are 4 x 4 matrices for 180 different scattering angles, and orientation-averaged over hundreds or thousands of orientations. The scattering matrix files include a descriptive header line. In the ADDA computations, the polarizability prescription is "Lattice dispersion relation" when |m| < 2 and "Filtered coupled dipoles" when |m| > 2. The Interaction term prescription is "Point dipoles" when |m| < 2 and "Filtered Green's tensor" when |m| > 2.</p> <p>The corresponding scatterer shape models are given in the files ending "dipoles_x12.out". ADDA uses scatterer shape models that have been discretized into equally-sized cubic voxels. The shape model files list the x, y, and z coordinates of each voxel. The shape models have been scaled to optimize computation times but ensuring that the number of dipoles per wavelength is greater than 10|m| for each size parameter. The given shape model fulfills this condition for a size parameter of 12. The particle shape models have been derived from atmospheric dust particles by scanning-electron microscopes (Lindqvist et al., Atmos. Chem. Phys. 14, 143-157, 2014).</p>
Datasets for 'Automated characterization of noise distributions in diffusion MRI data'
<p>Datasets we used for the manuscript 'Automated characterization of noise distributions in diffusion MRI data'.</p>
Proteomic characterization of human exhaled breath condensate.
<p>datasets from 3 studies, for In-depth proteomics characterization of exhaled breath condensate (EBC).</p> <p>1) Lacombe M. et al, 2018</p> <p>2) Muccilli V. et al, 2015</p> <p>3) Bredberg A. et al, 2012</p>
Characterization of heteroatom distributions in the polar fraction of North Sea oils using high-resolution mass spectrometry
<p>Supplementary data for <a href="https://doi.org/10.1016/j.petrol.2019.106563">10.1016/j.petrol.2019.106563</a></p> <p>Mass spectra were measured on a Q Exactive HF at 240k@200 m/z resolution in nanospray-ESI direct infusion using a Advion TriVersa NanoMate source. Broadband mass spectra were generated from SIM-segments using dimspy (https://github.com/computational-metabolomics/dimspy). Peaks were annotated using Formularity v.1.0.0 (10.1021/acs.analchem.7b03318) after internal calibration using a homologous CHN series (identified from preliminary KMD/KM plots). All plots were generated using python 3.6.6 and the plotly graphing library (https://plot.ly/python/).</p> <p> </p>
Research data supporting for "Characterization of recovery onset by subgrain and grain boundary migration in experimentally deformed polycrystalline olivine"
<p>Abstract: To apprehend plate tectonics and the dynamics of the lithosphere–asthenosphere boundary, composed principally of olivine, we need to understand the mechanisms that control plastic deformation of olivine in the relevant temperature domain. After more than 50 years of laboratory studies and investigations on natural rocks, the interplay of several key parameters (e.g. temperature, pressure, vacancy concentration, dislocation densities, grain size, strain rate) controlling polycrystalline olivine plasticity remains difficult to assess. Here, we study four olivine polycrystals, which have been deformed in axial compression under a confining pressure of 300MPa, at 1273 or 1473 K. Despite significant differences in mechanical properties (stress–strain curves), previous characterization by scanning (SEM) and transmission electron microscopy (TEM) did not reveal significant differences in dislocation microstructures which could explain these contrasted behaviours. We have undertaken automatic crystallographic orientation mapping (ACOM) analyses in TEM to increase the spatial resolution of characterization compared to previously obtained electron backscatter diffraction maps to further decipher the microstructures at nanoscale. With this novel technique applied to olivine, a noticeable difference in the onset of microstructural recovery has been identified between specimens deformed at 1273 and 1473 K. The microstructures of the olivine polycrystals deformed at 1473K exhibit numerous curved grain and subgrain boundaries, advocating for recovery by boundary migration. In contrast, the microstructures of the olivine polycrystals deformed at 1273K have significantly fewer subgrain boundaries and show more straight boundaries (i.e. closer to an equilibrium microstructure) than in the specimen deformed at 1473 K. Characterization by ACOM-TEM has permitted the identification of the onset of recovery, which is led by boundary migration even for very low macroscopic finite strains.</p> <p> </p>
Data and figures for Characterization of 30 ^{76}Ge enriched Broad Energy Ge detectors for GERDA Phase II
<p>Data and figures for Characterization of 30 <sup>76</sup>Ge enriched Broad Energy Ge detectors for GERDA Phase II</p>
Characterization of p53 family homologs in evolutionary remote branches of Holozoa
<p>Supplementary materials to article: Characterization of p53 family homologs in evolutionary remote branches of Holozoa</p> <p>The p53 family of transcription factors plays key roles in development, genome stability, senescence and tumor development, and p53 is the most important tumor suppressor protein in humans. Although intensively investigated for many years, its initial evolutionary history is not yet fully elucidated. Using bioinformatic and structure prediction methods on current databases containing newly-sequenced genomes and transcriptomes, we present a detailed characterization of p53 family homologs in remote members of the Holozoa group, in the unicellular clades Filasterea, Ichthyosporea and Corallochytrea. Moreover, we show that these newly characterized homologous sequences contain domains that can form structures with high similarity to the human p53 family DNA-binding domain, and some also show similarities to the oligomerization and SAM domains. The presence of these remote homologs demonstrates an ancient origin of the p53 protein family.</p>
Proteo-transcriptomic characterization of the venom from the endoparasitoid wasp Pimpla turionellae with aspects on its biology and evolution
<p>Within mega-diverse Hymenoptera non-aculeate parasitic wasps represent 75 % of all hymenopteran species. Their ovipositor dual-functionally injects venom and employs eggs into (endoparasitoids) or onto (ectoparasitoids) diverse host species. Few endoparasitoid wasps such as <em>Pimpla turionellae</em> paralyze the host and suppress its immune responses, such as encapsulation and melanization, to guarantee their offspring’s survival. In our proteo-transcriptomic analysis we shed new light on the venom biology of the endoparasitoid <em>Pimpla turionealle</em>.</p> <p>All additional data is made available here, such as the transcriptome assembly file, CDS prediction and all proteome data files including the raw data. All alignments to train HMMsearch and JACKHMMERsearch are stored here as well and the alignments of identified venom proteins (known and novel).</p> <p>The readme file gives further explanation/information.</p>
Figure 2 in Insect galls associated with Copaifera sabulicola J.A.S Costa & L.P Queiroz (Fabaceae): Characterization and new records
Figure 2 Gall morphotypes found on Copaifera sabulicola J.A.S Costa & L.P. Queiroz (Fabaceae) in Serra da Bandeira (Barreiras, Bahia, Brazil) from April 2015 to March 2016.
Figure 1 in Insect galls associated with Copaifera sabulicola J.A.S Costa & L.P Queiroz (Fabaceae): Characterization and new records
Figure 1 (A) Abundance and (B) frequency of gall morphotypes (%) found on Copaifera sabulicola J.A.S Costa & L.P. Queiroz (Fabaceae) in Serra da Bandeira (Barreiras, Bahia, Brazil) from April 2015 to March 2016.
Figure 3 in Molecular characterization and phylogenetic assessment of agricultural-related noctuids (Lepidoptera: Noctuidae) of South America
Figure 3 Continuation of phylogram in Fig. 2. The phylogenetic hypothesis of the Feltia + Agrotis clade based on a maximum likelihood analysis. Numbers given above branches are bootstrap values (>50%). GenBank accession numbers are provided for newly sequenced specimens.
Figure 2 in Molecular characterization and phylogenetic assessment of agricultural-related noctuids (Lepidoptera: Noctuidae) of South America
Figure 2 The phylogenetic relationships of the specimens sequenced and those mined from GenBank, based on a maximum likelihood analysis. Numbers given above branches are bootstrap values (>50%). The Feltia + Agrotis clade is shown in more detail in Fig. 3. GenBank accession numbers are provided for newly sequenced specimens.
Figs. 1–6 in Insect galls on Bauhinia cupulata (Fabaceae): morphotypes characterization and description of a new species of Schizomyia (Cecidomyiidae, Diptera)
Figs. 1–6. Different development stages of galls induced by Schizomyia barreirensis, sp. n. (1) First stage. (2) Second stage. (3) Third stage. (4) Fourth stage. (5) Fifth stage. (6) Last stage (gall cut open to show the larval chamber).
Figs. 19 and 20 in Insect galls on Bauhinia cupulata (Fabaceae): morphotypes characterization and description of a new species of Schizomyia (Cecidomyiidae, Diptera)
Figs. 19 and 20. Schizomyia barreirensis, sp. n. (19) Female, abdominal segments 7–8 (lateral view); (20) Ovipositor (ventral view). Scale bars in mm.
Fig. 3 in Development and morphological characterization of the immature stages of Tetrastichus giffardianus Silvestri (Hymenoptera: Eulophidae)
Fig. 3. Immature stages of Tetrastichus giffardianus. Egg (A); first-instar larva (B, C); second-instar larva (D); third-instar larva (E); pre-pupa (F); pupa at three different stages of melanization (G, H, I). Scale bar = 0.1 mm.
Figs. 13–18 in Insect galls on Bauhinia cupulata (Fabaceae): morphotypes characterization and description of a new species of Schizomyia (Cecidomyiidae, Diptera)
Figs. 13–18. Schizomyia barreirensis sp. n. (13) Male, head (frontal view); (14) Male, flagellomere 3; (15) Female, flagellomere 2; (16) Tarsal claws and empodium; (17) Male, abdominal segments 3–8 (lateral view); (18) Male, terminalia (dorsal view). Scale bars in mm.
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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.