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12,749 results for “Blood”
A new in vitro blood flow model for the realistic evaluation of antimicrobial surfaces
<p>Dataset to the publication</p> <p>A new <em>in vitro</em> blood flow model for the realistic evaluation of antimicrobial surfaces</p> <p>Juliane Valtin, Stephan Behrens, André Ruland, Florian Schmieder, Frank Sonntag, Lars D. Renner, Manfred F. Maitz, Carsten Werner</p> <p><em>Adv. Healthcare Mater.</em> 2023, 2301300. <a href="https://doi.org/10.1002/adhm.202301300">https://doi.org/10.1002/adhm.202301300</a></p>
Supplemental data for: Mapping lifestyle factors in blood glucose variability in adolescents with Type 1 Diabetes Mellitus- A pilot study
<div> <p>The dataset was used in the paper “Mapping lifestyle factors in blood glucose variability in adolescents with Type 1 Diabetes Mellitus- A pilot study”. The article is currently under review for publication. DOI to be inserted.</p> </div> <div> <p>A data-in-brief article is to be published to give in-depth information about the data collected to improve reproducibility "Dataset for: Lifestyle Factors and Blood Glucose Variability in Adolescents with Type 1 Diabetes Mellitus". DOI to be inserted. </p> <p> </p> <p>The aim of the study was to assess whether adolescents with T1D in Ireland meet current nutrition and physical activity (PA) guidelines and to explore the impact of nutrition and PA on glycaemic variability (GV). The dataset includes continuous glucose monitoring (CGM) data, dietary intake records, and PA metrics, providing a comprehensive view of the participants' glucose levels and associated lifestyle behaviours.</p> </div>
Data and codes for 'A Bayesian Approach to Blood Rheological Uncertainties in Aortic Hemodynamics'
<p>This submission is supplementary material in the form of data and codes used in and for the manuscript 'A Bayesian Approach to Blood Rheological Uncertainties in Aortic Hemodynamics' submitted to the International Journal of Numerical Methods in Biomedical Engineering (currently under review).</p>
2D Cardiac black-blood TSE MR raw data
<p>Raw data in ismrmrd format obtained with a 2D black-blood TSE sequence on a 3T Siemens Verio scanner in three different orientations. This data is used as test data for the comparison of different open-source image reconstruction packages provided here: <a href="https://github.com/ckolbPTB/OpenSourceMrRecon">OpenSourceMrRecon</a></p>
Comparison of blood parameters for brachycephalic and non-brachycephalic dogs
<p>Cranial and upper-airway anatomy of short-nosed flat-faced brachycephalic dogs predisposes brachycephalic obstructive airway syndrome (BOAS). Periodic apnoea, increased inspiratory resistance and inability to thermoregulate effectively are characteristic for BOAS, but internationally accepted objective markers of BOAS severity are missing. The objective of this study was to compare the blood parameters between non-brachycephalic (NC) and brachycephalic (BC) dogs exploring the possibility to develop a blood test for BOAS. We evaluated blood biochemistry, complete blood cell counts, red blood cell (RBC) indices, reticulocyte counts, a blood-born marker of intermittent hypoxia (glutathione, NO production), RBC hydration, deformability, and blood markers of metabolic changes and stress between BC (n = 18) and NC (meso- and dolichocephalic, n = 22) dogs. Reticulocyte counts and the abundance of middle-fluorescence immature reticulocytes were significantly higher in BC dogs compared to NC dogs. BC dogs had significantly more NO-derived NO<sub>2</sub><sup>-</sup>/NO<sub>3</sub><sup>- </sup>in plasma than NC dogs. RBCs of BC dogs were shedding significantly more membrane as follows from the intensity of Eosin maleimide staining and had significantly higher mean corpuscular hemoglobin concentration than NC dogs. Intracellular reduced glutathione content in RBCs of BC dogs was significantly lower, while plasma lactate was significantly higher in BC dogs compared to NC dogs. Plasma cholesterol and triglyceride were significantly lower and cortisol was significantly higher in BC dogs compared to NC dogs. Eosinophil counts were significantly lower and the neutrophil-to-lymphocyte ratio was significantly higher in BC dogs compared to NC dogs. Taken together, our findings suggest that brachycephalic phenotype in dogs is associated with stress at the level of blood cells and systemically, with oxidation and emotional stress. The parameters identified within this study should be further investigated for their potential as objective indicators for BOAS.</p>
Opioid medication use and blood DNA methylation: epigenome-wide association meta-analysis
<p>We conducted the first large-scale epigenome-wide meta-analysis of blood DNA methylation and recent use of opioid medications. There were five participating studies (10,842 individuals; 9,886 European ancestry and 956 African ancestry participants) including four that used the newer Illumina EPIC/850K array and one that used the older Illumina 450K array. We identified novel loci differentially methylated in relation to opioid medication use.</p>
Datasets for "Targeted insertion and reporter transgene activity at a gene safe harbor of the human blood fluke, Schistosoma mansoni"
<p>To identify sites that could serve as potential genomic safe harbours (GSHs) for transgene integration, we conducted a genome-wide bioinformatic search based on established, widely accepted criteria, along with newly introduced criteria (below), that would satisfy benign and stable gene expression. </p> <p>At the outset, we identified <strong>euchromatic</strong> regions in all developmental stages of <em>S. mansoni </em>to avoid silencing genes to be integrated upon CRISPR/Cas manipulation. With these criteria, we enriched for regions that were, (i) close to peaks of H3K4me3, a histone modification that is associated with euchromatin and transcription start sites, (ii) regions that did not include H3K27me3, a histone modification that is associated with heterochromatin, (iii) regions of open euchromatin accessible to Tn5 integration, in an Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) providing a positive display of integration events, and (iv) given that HIV-1 integrates preferentially into euchromatin in human cell lines, we used sites of HIV proviral integration known from <em>S. mansoni</em> to likewise support predictions of euchromatic regions.</p> <p>Examination of the draft genome of <em>S. mansoni</em> in Worm Base Parasite, version 7 (WormBase Parasite) identified 6,884 regions with enrichment of H3K4me3 in the absence of H3K27me3 in available developmental stages (H3K4me3 not K3K27me3). In mature, adult schistosomes, we found consistently 10,533 ATAC positive regions. There were 4,027 ATAC regions that overlapped with H3K4me3 but not K3K27me3, and 2,915 genes overlapped with (ATAC and H3K4me3 not H3K27me3). Forty-two unambiguous HIV integration sites were identified, and eight genes were ≤ 11 kb upstream or downstream from these integration sites. Repeats were masked with RepeatMasker V4.1.0 using a specific repeat library produced with RepeatModeler2 V2.0.1 and stored as a GFF file.</p> <p>To identify intergenic GSH, we located 10,149 intergenic regions. There were 9,985 regions beyond 2 kb upstream and 8,837 regions outside long non-coding-RNA (lncRNA), which were intersected to 95,587 unique intergenic regions outside 2 kb and lncRNA of ≥100 bp. Two hundred regions were identified intersecting with merged ATAC H3K4me3 signal. Four of these were situated ≤ 11 kb distance from HIV integration sites. </p> <p>Made at George Washington University, Justus Liebig University Giessen, Khon Kaen University, Naresuan University, Aberystwyth University, Schistosomiasis Resource Center, IHPE. </p>
Curated GWAS summary statistics on African ancestry on 19 blood count traits and glycemic traits (hg38)
<p>Genome wide curated summary statistics on 19 blood count traits and glycemic traits</p> <p>File format is the inittable format intended to be used with the Joint Analysis of Summary Statistics (JASS), which allows to perform multi-trait GWAS:</p> <p>https://gitlab.pasteur.fr/statistical-genetics/jass</p> <p>GWAS of hematological traits originate from Chen et al paper and were downloaded from the GWAS Catalog (<a href="https://www.ebi.ac.uk/gwas/publications/32888493#study_panel">https://www.ebi.ac.uk/gwas/publications/32888493#study_panel</a>). GWAS of glycemic traits come from the <a href="https://www.zotero.org/google-docs/?S1MIfx">(18)</a> study downloadable from GWAS Catalog (<a href="https://www.ebi.ac.uk/gwas/publications/34059833">https://www.ebi.ac.uk/gwas/publications/34059833</a>).</p> <p> </p>
Curated GWAS summary statistics on East Asian ancestry on 19 blood count traits and glycemic traits
<p>Genome wide curated summary statistics on 19 blood count traits and glycemic traits</p> <p>File format is the inittable format intended to be used with the Joint Analysis of Summary Statistics (JASS), which allows to perform multi-trait GWAS:</p> <p>https://gitlab.pasteur.fr/statistical-genetics/jass</p> <p>GWAS of hematological traits originate from Chen et al paper and were downloaded from the GWAS Catalog (<a href="https://www.ebi.ac.uk/gwas/publications/32888493#study_panel">https://www.ebi.ac.uk/gwas/publications/32888493#study_panel</a>). GWAS of glycemic traits come from the <a href="https://www.zotero.org/google-docs/?S1MIfx">(18)</a> study downloadable from GWAS Catalog (<a href="https://www.ebi.ac.uk/gwas/publications/34059833">https://www.ebi.ac.uk/gwas/publications/34059833</a>).</p> <p>Full description of the method used to derive this dataset can be found in </p>
Bird plumage brightness scores and blood parasite prevalence values of North American passerine species
<p>Dataset with bird plumage brightness scores and blood parasite prevalence values for 114 North American passerine host species. One file contains the data table. One file contains a table with descriptions of the columns in the data table.</p> <p>Note: These data were reconstructed from files used in Read & Harvey 1989 (<a href="https://doi.org/10.1038/339618a0">https://doi.org/10.1038/339618a0</a>) with column headings inferred with the help of Read 1991 (<a href="https://doi.org/10.1086/285225">https://doi.org/10.1086/285225</a>).</p>
Measurement of Absolute Retinal Blood Flow Using a Laser Doppler Velocimeter Combined with Adaptive Optics
<p><strong>Purpose</strong>: Development and validation of an absolute laser Doppler velocimeter (LDV) based on an adaptive optical fundus camera which provides simultaneously high definition images of the fundus vessels and absolute maximal red blood cells (RBCs) velocity in order to calculate the absolute retinal blood flow.\newline<br> <strong>Methods</strong>: This new absolute laser Doppler velocimeter is combined with the adaptive optics fundus camera (rtx1, Imagine Eyes$^\copyright$,Orsay, France) outside its optical wavefront correction path. A 4 seconds recording includes 40 images, each synchronized with two Doppler shift power spectra. Image analysis provides the vessel diameter close to the probing beam and the velocity of the RBCs in the vessels are extracted from the Doppler spectral analysis. Combination of those values gives an average of the absolute retinal blood flow. An in vitro experiment consisting of latex microspheres flowing in water through a glass-capillary to simulate a blood vessel and in vivo measurements on six healthy humans were done to assess the device.\newline<br> <strong>Results</strong>: In the in vitro experiment, the calculated flow varied between 1.75µl/min and 25.9µl/min and was highly correlated (r<sup>2</sup>= 0.995) with the imposed flow by a syringe pump.<br> In the in vivo experiment, the error between the flow in the parent vessel and the sum of the flow in the daughter vessels was between -11% and 36% (mean±sd 5.7±18.5%). Retinal blood flow in the main temporal retinal veins of healthy subjects varied between 0.9 µL/min and 13.2µL/min.</p> <p><strong>Conclusion</strong>: This adaptive optics LDV prototype (aoLDV) allows the measurement of absolute retinal blood flow derived from the retinal vessel diameter and the maximum RBCs velocity in that vessel.</p>
Standard Distributions of Blood Tests for Public Use
<p>This dataset is the distribution parameters obtained by approximating the distribution of blood test values taken from inpatients in a Japanese hospital by a lognormal distribution or an exponential distribution. </p> <p>The parameters P1, P2 and P3 of the lognormal distribution are used in the following equation.<br> P1*exp(-(ln(x/P2)/P3)^2)</p> <p>The parameters P1 and P2 of the exponential distribution are used in the following.<br> P1*exp(-P2*x)</p> <p>This file is CSV with UTF-8 charset, and the columns are as follows.</p> <p>---<br> Test name<br> Test name in Japanese<br> Unit of the value<br> Distribution type (LogNormal or Exp)<br> P1<br> P2<br> P3<br> P1 Error(1sigma)<br> P2 Error(1sigma)<br> P3 Error(1sigma)<br> Number of data points used to make this distribution<br> Bin width used to make the distribution<br> ---</p> <p>Any researchers can use this dataset without privacy issues.<br> CC BY-NC 4.0<br> </p>
Dataset: Whole blood count, used in: "AIDeveloper: deep learning image classification in life science and beyond"
<p>Real-time deformability cytometry (RT-DC) data of whole blood measurements.<br> Data was used to train and validate a neural net to perform a blood count based on brightfield images of RT-DC.</p> <p>01_Model: Contains the final model as well as an AIDeveloper meta-file that allows to reproduce the training procedure. The metafile preciesely defines which dataset was used for training and which for validation as well as all parameters that were set in AIDeveloper.</p> <p>The following folders contain data that was used for training (and validation):</p> <ul> <li>Cambr</li> <li>KIK</li> <li>20190306_DextranBlood_AI_DataSet</li> <li>Gs_Blood_Train</li> </ul> <p>Testing data is stored on figshare:<br> https://figshare.com/articles/Krater_et_al_2020_Data_zip/9902636</p>
Fig. 3 in Croton calcareus: a new species of dragon's blood (Euphorbiaceae) from dry forest in the state of Chiapas, Mexico
Fig. 3. Image of one of the paratypes of Croton calcareus Riina & Mateo-Ram. sp. nov. (Cabrera and Cabrera 7870, MEXU), previously indentified as C. xalapensis Kunth, to show the variation in leaf shape and indumentum density. It also shows immature fruits (younger than those in the type specimens).
Full summary statistics of mixQTL for GTEx v8 Whole_Blood
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Fecal and Blood Metabolites of Pigs
<p>The experimental design of the animal study and the sanitary challenge model used have been described by Van der Meer et al. (2020). Pigs were divided into high sanitary condition (HSC) or to low sanitary condition (LSC), for details please see the original publication by Van der Meer et al. (2020). At the dissection day, three pigs per room were euthanized to collect blood and digesta samples for further analysis. We used colon digesta and blood samples from pigs in this study that received a diet with a basal amino acid (AA) ratios (indicated as “diet AA-B” in the paper of van der Meer et al. 2020) and a protein content of CP 168 g/kg; LSC (n=18) and HSC (n=18). </p> <p>These samples were analyzed by Nuclear Magnetic Resonance (NMR) and by Triple Quad Mass Spectrometry (TQMS). The details of these laboratory analysis are described in the journal article entitled "Sanitary conditions affect the colonic microbiome and the colonic and systemic metabolome of female pigs" (doi: will update accordingly). The data uploaded here are by the format of the Joint Committee on Atomic and Molecular Physical Data (JCAMP). Moreover the metadata file shows the link between the samples and their corresponding group, i.e. HSC or LSC, and other characteristics.</p>
Data from: Blockade of dengue virus transmission from viremic blood to Aedes aegypti mosquitoes using human monoclonal antibodies
Background <p class="CxSpFirst">Dengue is the most prevalent arboviral disease of humans. Virus neutralizing antibodies are likely to be critical for clinical immunity after vaccination or natural infection. A number of human monoclonal antibodies (mAbs) have previously been characterized as able to neutralize the infectivity of dengue virus (DENV) for mammalian cells in cell-culture systems.</p> <p class="CxSpLast"> </p> Methodology/Principle findings <p class="CxSpFirst">We tested the capacity of 12 human mAbs, each of which had previously been shown to neutralize DENV in cell-culture systems, to abrogate the infectiousness of dengue patient viremic blood for mosquitoes. Seven of the twelve mAbs (1F4, 14c10, 2D22, 1L12, 5J7, 747(4)B7, 753(3)C10), almost all of which target quaternary epitopes, inhibited DENV infection of <i>Ae. aegypti</i>. The mAbs 14c10, 747(4)B7 and 753(3)C10 could all inhibit transmission of DENV in low microgram per mL concentrations. An Fc-disabled variant of 14c10 was as potent as its parent mAb.</p> <p class="CxSpLast"> </p> Conclusions/Significance <p class="CxSpFirst">The results demonstrate that mAbs can neutralize infectious DENV derived from infected human cells, in the matrix of human blood. Coupled with previous evidence of their ability to prevent DENV infection of mammalian cells, such mAbs could be considered attractive antibody classes to elicit with dengue vaccines, or alternatively, for consideration as therapeutic candidates.</p>
Immune repertoire profiling reveals that clonally expanded B and T cells infiltrating diseased human kidneys can also be tracked in the blood
<p>Recent advances in high-throughput sequencing allow for the competitive analysis of the human B and T cell immune repertoire. In this study we compared Immunoglobulin and T cell receptor repertoires of lymphocytes found in kidney and blood samples of 10 patients with various renal diseases based on next-generation sequencing data.</p>
Validation data set for automatic blood vessel segmentation in colorectal cancer histology (IHC)
<p><strong>Content</strong></p> <p>This data set contains 100 histological image patches of 1000 * 1000 px size. The samples were immunostained for CD34 (3,3'-Diaminobenzidine, DAB [brown]) with hematoxylin (blue) counterstain.</p> <p>Furthermore, the data set contains a table of blood vessel counts in each image by three blinded observers as well as an automatic count with a method based on the following paper:</p> <p>Kather, Jakob Nikolas et al. "Continuous Representation Of Tumor Microvessel Density And Detection Of Angiogenic Hotspots In Histological Whole-Slide Images". <em>Oncotarget</em> 6.22 (2015): 19163-19176. http://dx.doi.org/10.18632/oncotarget.4383</p> <p><strong>Image format</strong></p> <p>All images are RGB, 0.50 µm per pixel, digitized with an Aperio ScanScope (Aperio/Leica biosystems), magnification 20x. Histological samples are fully anonymized images of formalin-fixed paraffin-embedded human colorectal adenocarcinomas (primary tumors and liver metastases) from our pathology archive (Institute of Pathology, University Medical Center Mannheim, Heidelberg University, Mannheim, Germany).</p> <p><strong>Ethics statement</strong></p> <p>All experiments were approved by the institutional ethics board (medical ethics board II, University Medical Center Mannheim, Heidelberg University, Germany; approval 2015-868R-MA). The institutional ethics board waived the need for informed consent for this retrospective analysis of anonymized samples. All experiments were carried out in accordance with the Declaration of Helsinki.</p> <p><strong>Contact</strong></p> <p>For questions, please contact:<br> Dr. Jakob Nikolas Kather<br> http://orcid.org/0000-0002-3730-5348<br> ResearcherID: D-4279-2015</p>
Averaged results of blood flow simulations with discrete RBC tracking for microvascular networks
<p>The dataset contains the results for blood flow simulations in 3 cerebral micorvascular networks.The microvascular networks are from the mouse parietal cortex (Blinder et al., 2013) and embedded in a tissue volume of approximately 1 cubic mm. For the blood flow simulations we used a numercial model with discrete tracking of RBCs which is described in Schmid et al., 2017.</p> <p>For each network the following data are provided:<br> - Microvascular network with averaged flow and pressure field, as well as averaged values for the distribution and motion of red blood cells (RBCs).<br> - RBC trajectories describing the motion of individual RBCs through the microvascular networks.<br> - The data is stored as a graph, i.e. vertices connected by edges.<br> - Details regarding the simulation parameters can be found in Schmid et al., 2017.<br> - Data format (pickle - files containing python dictonairies).<br> <br> <strong>Microvascular networks:</strong><br> <strong>edgesDict.pkl:</strong> dictionary with edge related data (dictionary keys: flow [um^3/ms], diameter [um], tuple [-], httBC [-], nkind [-], length [um], htt [-], nRBC [-], diameters [um], points [um])<br> <strong>verticesDict.pkl:</strong> dictionary with vertex related data (dictionary keys: pressure [mmHg], coordinates [um], pBC [mmHg])</p> <p>Additional comments on dictionary keys:<br> - pBC: pressure boundary conditions. 'None' for internal nodes. Assigned based on the hierarchical boundary conditions approach (see Schmid et al. 2017 for details)<br> - tuple: connectivity of graph, tuple of vertices<br> - httBC: tube hematocrit boundary conditions. 'None' for internal nodes. Constant value assigned.<br> - nkind: integere to describe the vessel type. 0: pial artery, 1: pial venule, 2: descending arteriole, 3: ascending venule, 4: capillaries, 5: unknown<br> - htt: tube hematocrit<br> - nRBC: number of red blood cells<br> - points: list of tortuous vessel coordinates per edge<br> - diameters: local diameter measurements associated to the 'points' key.</p> <p><br> <strong>RBC trajectories:</strong><br> <strong>RBC_trajectories.pkl: </strong>dictonary for each RBC with relevant tracking data (dictionary key: RBC index). The relavant tracking data per RBC is stored in another dictionary with the following keys: edges, lengths, times, pressure, nkindsMod, RBCleft</p> <p>Additional comments on dictionary keys per RBC:<br> - RBCleft: bool to indicate that RBC left the computational domain<br> - edges: edge indices through which the RBC moves on its way through the vasculature<br> - pressure: pressure [mmHg] values at the nodes along the RBC trajectory<br> - times: time [ms] the RBC spends in the respective edge segment<br> - nkindsMod: nkind at the nodes along the RBC trajectory <br> - lengths: cummulative length travelled [um]</p>
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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.