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665 results for “whole blood”
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>
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.
Growth, nutrient uptake, blood metabolites and bone properties in broilers consuming feed with mineral-enriched whole black soldier fly larvae
<p>Recycling critical minerals like phosphorus is essential for future circular agriculture. This study explored adding mineral-enriched black soldier fly larvae (BSFL), grown on substrates with sewage sludge recyclates (SSR), to broiler feed to reintroduce minerals from restricted waste streams into the nutrient cycle. Results showed that including 15% mineral-enriched BSFL in broiler diets for 42 days had no adverse effects on growth, nutrient intake, or bone condition, and maintained acceptable levels of heavy metals.</p>
Gene expression in monocytes, neutrophils and whole blood after stroke
<p>Dataset from:</p> <p>Carmona-Mora, P., Knepp, B., Jickling, G.C. <em>et al.</em> Monocyte, neutrophil, and whole blood transcriptome dynamics following ischemic stroke. <em>BMC Med</em> <strong>21</strong>, 65 (2023). https://doi.org/10.1186/s12916-023-02766-1</p> <p>All methods available in the publication above.</p> <p>Abstract</p> <p>Background After ischemic stroke (IS), peripheral leukocytes infiltrate the damaged region and modulate the response to injury. Peripheral blood cells display distinctive gene expression signatures post IS and these transcriptional programs reflect changes in immune responses to IS. Dissecting the temporal dynamics of gene expression after IS improves our understanding of immune and clotting responses at the molecular and cellular level that are involved in acute brain injury and may assist with time-targeted, cell-specific therapy.</p> <p>Methods The transcriptomic profiles from peripheral monocytes, neutrophils, and whole blood from 38 ischemic stroke patients and 18 controls were analyzed with RNAseq as a function of time and etiology after stroke. Differential expression analyses were performed at 0-24 h, 24-48 h, and >48 h following stroke.</p> <p>Results Unique patterns of temporal gene expression and pathways were distinguished for monocytes, neutrophils and whole blood with enrichment of interleukin signaling pathways for different timepoints and stroke etiologies. Compared to control subjects, gene expression was generally up-regulated in neutrophils and generally down- regulated in monocytes over all times for cardioembolic, large vessel and small vessel strokes. Self-Organizing Maps identified gene clusters with similar trajectories of gene expression over time for different stroke causes and sample types. Weighted Gene Co- expression Network Analyses identified modules of co-expressed genes that significantly varied with time after stroke and included hub genes of immunoglobulin genes in whole blood.</p> <p>Conclusions Altogether, the identified genes and pathways are critical for understanding how the immune and clotting systems change over time after stroke. This study identifies potential time- and cell-specific biomarkers and treatment targets.</p> <p>clinical_parameters_MON.txt: Clinical parameters from cohort used from monocyte samples.</p> <p>clinical_parameters_NEU.txt: Clinical parameters from cohort used from neutrophil samples.</p> <p>clinical_parameters_WB.txt: Clinical parameters from cohort used from whole blood samples.</p> <p>MON_gene_counts_filtered-WGCNA.txt: Filtered counts of each annotated gene from monocyte samples, cohort used for WGCNA analyses, (TPM normalized, non-log, filtered features where maximum <=40 reads were excluded).</p> <p>NEU_gene_counts_filtered-WGCNA.txt: Filtered counts of each annotated gene from neutrophil samples, cohort used for WGCNA analyses, (TPM normalized, non-log, filtered features where maximum <=40 reads were excluded).</p> <p>WB_gene_counts_filtered-WGCNA.txt: Filtered counts of each annotated gene from whole blood samples, cohort used for WGCNA analyses, (TPM normalized, non-log, filtered features where maximum <=80 reads were excluded).</p> <p>MON_gene_raw_counts.txt: raw counts for cohort used of monocyte samples.</p> <p>NEU_gene_raw_counts.txt: raw counts for cohort used of neutrophil samples.</p> <p>WB_gene_raw_counts.txt: raw counts for cohort used of whole blood samples.</p> <p>MON_Time_Course_filtered_normalized_counts_ready.txt: matrix counts of each annotated gene used for differential expression analyses of time points in monocyte samples. (TPM normalized, filtered features where maximum <=30 reads were excluded).</p> <p>NEU_Time_Course_filtered_normalized_counts_ready.txt: matrix counts of each annotated gene used for differential expression analyses of time points in neutrophil samples. (TPM normalized, filtered features where maximum <=30 reads were excluded).</p> <p>WB_Time_Course_filtered_normalized_counts_ready.txt: matrix counts of each annotated gene used for differential expression analyses of time points in whole blood samples. (TPM normalized, filtered features where maximum <=30 reads were excluded).</p> <p> </p> <p>All methods to generate the above files are available in the publication:</p> <p>Carmona-Mora, P., Knepp, B., Jickling, G.C. <em>et al.</em> Monocyte, neutrophil, and whole blood transcriptome dynamics following ischemic stroke. <em>BMC Med</em> <strong>21</strong>, 65 (2023). https://doi.org/10.1186/s12916-023-02766-1</p> <p> </p>
Whole blood RNA-seq demonstrates an increased host immune response in individuals with cystic fibrosis who develop nontuberculous mycobacterial pulmonary disease
<p><strong>Background </strong></p> <p>Individuals with cystic fibrosis have an elevated lifetime risk of colonization, infection, and disease caused by nontuberculous mycobacteria. A prior study involving non-cystic fibrosis individuals reported a gene expression signature associated with susceptibility to nontuberculous mycobacteria pulmonary disease (NTM-PD). In this study, we determined whether people living with cystic fibrosis who progress to NTM-PD have a gene expression pattern similar to the one seen in the non-cystic fibrosis population. <strong> </strong></p> <p><strong>Methods</strong></p> <p>We evaluated whole blood transcriptomics using bulk RNA-seq in a cohort of cystic fibrosis patients with samples collected closest in timing to the first isolation of nontuberculous mycobacteria. The study population included patients who did (n = 12) and did not (n = 30) develop NTM-PD following the first mycobacterial growth. Progression to NTM-PD was defined by a consensus of two expert clinicians based on reviewing clinical, microbiological, and radiological information. Differential gene expression was determined by DESeq2.</p> <p><strong>Results</strong></p> <p>No differences in demographics or composition of white blood cell populations between groups were identified at baseline. Out of 213 genes associated with NTM-PD in the non-CF population, only two were significantly different in our cystic fibrosis NTM-PD cohort. Gene set enrichment analysis of the differential expression results showed that CF individuals who developed NTM-PD had higher expression levels of genes involved in the interferon (α and γ), tumor necrosis factor, and IL6-STAT3-JAK pathways. <strong> </strong></p> <p><strong>Conclusion</strong></p> <p>In contrast to the non-cystic fibrosis population, the gene expression signature of patients with cystic fibrosis who develop NTM-PD is characterized by increased innate immune responses.</p>
Whole Blood Platelet Aggregation in Chronic Kidney Disease Patients on Aspirin Study
ClinicalTrials.gov study NCT01768637. IPD Sharing: YES. Countries: 1. Publications: 2.
Whole blood RNA-seq demonstrates an increased host immune response in individuals with cystic fibrosis who develop nontuberculous mycobacterial pulmonary disease
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Data from: Whole blood transcriptional profiles and the pathogenesis of tuberculous meningitis
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Beta-hydroxybutyrate ketone concentrations via ketometer and colorimetric assay in Steller sea lion whole blood and plasma
<p>We evaluated the Precision Xtra™ ketometer during a larger study categorizing free-ranging Steller sea lion (<em>Eumetopias jubatus</em>; SSL) pup fasting status, necessitating identification of plasma β-hydroxybutyrate concentrations ([β-HBA]) around a < and ≥0.3 mmol/L threshold. Whole blood samples mixed with sodium heparin (NaHep) or ethylenediaminetetraacetic acid liquid anticoagulants were tested <10 minutes after collection (n=14; triplicate technical replicates). Plasma (stored at -80°C, NaHep, <em>Thaw1</em>) measured via our laboratory's <em>Reference Assay </em>(Sigma Aldrich, St. Louis, MO, Kit #MAK041) served as the standard [β-HBA] for ketometer comparisons. Our observed β-HBA range (0.0–1.6 mmol/L), consistent with published [β-HBA] of free-ranging Otariid pups, represented the lower 20% of the ketometer's range (0.0–8.0 mmol/L). The maximal coefficient of variation (%CV) of ketometer technical replicates was 9.1% (NaHep, whole blood). The majority of ketometer technical replicate sets (84%, including all matrices, anticoagulants, and thawings) were identical (CV=0%). We found linear relationships and agreement of ketometer [β-HBA] between whole blood preserved with different anticoagulants and between whole blood and plasma (<em>Thaw1</em>) measurements. The ketometer produced results with linearity to the <em>Reference Assay</em> for both whole blood and plasma (<em>Thaw1</em>). We identified a non-linear relationship between plasma at <em>Thaw1</em> and <em>Thaw2</em> (tested four months apart, NaHep), as only samples with higher SSL [B-HBA] decreased in concentration, and all others remained the same. With respect to categorizing SSL pup fasting, the ketometer % Accuracy, %Sensitivity, and %Specificity for samples with <em>Reference Assay</em> β-HBA <0.2 and >0.4 mmol/L were 100%. We adopted a modified procedure: plasma samples with mean ketometer concentrations ±0.1 mmol/L of 0.3 mmol/L β-HBA were re-evaluated using the <em>Reference Assay</em>, improving measurement precision from tenths (ketometer) to thousandths (assay) mmol/L. The Precision Xtra™ ketometer was valuable to our application, over the range of [β-HBA] observed in SSL pup plasma and whole blood samples.</p>
Whole-transcriptome sequencing identifies neuroinflammation, metabolism and blood-brain barrier related processes in the hippocampus of aged mice during perioperative period
<p><span><strong>Aim</strong>:</span><span> Perioperative neurocognitive disorders (PND) occur frequently after surgery and anesthesia, especially in aged patients. Previous studies have shown multiple PND related mechanisms in the hippocampus, however, their relationships remain unclear. Meanwhile, the perioperative neuropathological processes are sophisticated and changeable, single period study could not reveal the accurate mechanisms. Thus, multiperiod whole-transcriptome study is necessary to elucidate the gene expression patterns during perioperative period.</span></p> <p><span><strong>Methods</strong>: </span><span>Aged</span><span> C57BL/6 mice were subjected to exploratory laparotomy under sevoflurane anesthesia. Whole-transcriptome sequencing (RNA-seq analysis) was performed on the hippocampi from control condition (Con), 30 minutes (Day0), 2 days (Day2) and 7 days (Day7) after surgery. Gene Ontology</span><span>/Kyoto Encyclopedia of Genes and Genomes analyses,</span><span> quantitative Real-Time PCR, immunofluorescence and fear conditioning test were also performed to elucidate the pathological processes and modulation networks during the period.</span></p> <p><span><strong>Results</strong>: </span><span>Through RNA-seq analysis, 328, 3597 and 4179 differentially expressed genes (DEGs) were screened out in intraoperative period (Day0 vs Con), early postoperative period (Day2 vs Day0) and late postoperative period (Day7 vs Day2). The involved GO biological processes were divided into 9 categories, and positive-regulated processes were more than negative-regulated ones. Seventy-four transcription factors were highlighted. The potential synaptic and neuroinflammatory pathways were constructed for Neurotransmitter, Synapse and Neuronal alteration categories with 9 DEGs (<em>Htr1a, Rims1, Ezh2,</em> etc.). The metabolic and mitochondrial pathways were constructed for Metabolism, Oxidative stress and Biological rhythm categories with 9 DEGs (<em>Gpld1, Sirt1, Cry2, </em>etc.). The blood-brain barrier and neurotoxicity related pathways were constructed for Blood-brain barrier, Neurotoxicity and Cognitive function categories with 10 DEGs (<em>Mmp2, Itpr1, Nrf1, </em>etc.).</span></p> <p><span><strong>Conclusion</strong>:</span><span> The results revealed gene expression patterns and modulation networks in the aged hippocampus during perioperative period, which provide insights into overall mechanisms and potential therapeutic targets for prevention and treatment of perioperative central nervous system diseases, such as PND, from the genetic level.</span></p>
Inferring whole-organism metabolic rate from red blood cells in birds
<p>Metabolic rate is a key ecological variable that quantifies the energy expenditure needed to fuel almost all biological processes in an organism. Metabolic rates are typically measured at the whole-organism level (woMR) with protocols that can elicit stress responses due to handling and confinement, potentially biasing resulting data. Improved, non-stressful methodology would be especially valuable for measures of field metabolic rate, which quantifies the energy expenditure of free-living individuals. Recently, techniques to measure cellular metabolic rate (cMR) in mitochondria of blood cells have become available, suggesting that blood-based cMR can be a proxy of organismal aerobic performance. Aerobic metabolism actually takes place in the mitochondria. Quantifying cMR from blood samples offers several advantages such as direct estimates of metabolism and minimized disturbance of individuals. To our knowledge, the hypothesis that blood-based cMR correlates with woMR has not yet been directly tested.</p> <p>We measured cMR in red blood cells of captive great tits (<i>Parus major</i>), first during their morning activity period and second after subjecting them to a 2.5 h day-time respirometry protocol to quantify woMR. We predicted cMR to decrease as individuals transitioned from an active to a resting state. In the two blood samples we also assessed circulating corticosterone concentrations to determine the perceived disturbance of individuals. From respirometry traces we extracted initial and final woMR measures to test for a predicted positive correlation with cMR measures, while accounting for corticosterone concentrations.</p> <p>Indeed, cMR declined from the first to the second measurement. Furthermore, woMR and cMR were positively related in individuals that had relatively low corticosterone concentrations and displayed little locomotor activity throughout respirometry. By contrast, woMR and cMR covaried negatively in birds that increased corticosterone concentrations and activity levels substantially.</p> <p>Our results show that red blood cell cMR represents a proxy for woMR when birds do not display signs of stress, i.e. either before increases in hormonal or behavioral parameters have occurred or after they have abated. This method represents a valuable tool for obtaining metabolic data repeatedly and in free-living individuals. Our findings also highlight the importance of accounting for individual stress responses when measuring metabolic rate at any level.</p> <p>Metabolic rate is a key ecological variable that quantifies the energy expenditure needed to fuel almost all biological processes in an organism. Metabolic rates are typically measured at the whole-organism level (woMR) with protocols that can elicit stress responses due to handling and confinement, potentially biasing resulting data. Improved, non-stressful methodology would be especially valuable for measures of field metabolic rate, which quantifies the energy expenditure of free-living individuals. Recently, techniques to measure cellular metabolic rate (cMR) in mitochondria of blood cells have become available, suggesting that blood-based cMR can be a proxy of organismal aerobic performance. Aerobic metabolism actually takes place in the mitochondria. Quantifying cMR from blood samples offers several advantages such as direct estimates of metabolism and minimized disturbance of individuals. To our knowledge, the hypothesis that blood-based cMR correlates with woMR has not yet been directly tested.</p> <p>We measured cMR in red blood cells of captive great tits (<i>Parus major</i>), first during their morning activity period and second after subjecting them to a 2.5 h day-time respirometry protocol to quantify woMR. We predicted cMR to decrease as individuals transitioned from an active to a resting state. In the two blood samples we also assessed circulating corticosterone concentrations to determine the perceived disturbance of individuals. From respirometry traces we extracted initial and final woMR measures to test for a predicted positive correlation with cMR measures, while accounting for corticosterone concentrations.</p> <p>Indeed, cMR declined from the first to the second measurement. Furthermore, woMR and cMR were positively related in individuals that had relatively low corticosterone concentrations and displayed little locomotor activity throughout respirometry. By contrast, woMR and cMR covaried negatively in birds that increased corticosterone concentrations and activity levels substantially.</p> <p>Our results show that red blood cell cMR represents a proxy for woMR when birds do not display signs of stress, i.e. either before increases in hormonal or behavioral parameters have occurred or after they have abated. This method represents a valuable tool for obtaining metabolic data repeatedly and in free-living individuals. Our findings also highlight the importance of accounting for individual stress responses when measuring metabolic rate at any level.</p>
Data from: Pathogen reduction of monkeypox virus in plasma and whole blood using riboflavin and UV light
<p>Background</p> <p>Monkeypox virus has recently emerged from endemic foci in Africa and, to date, several hundred human infections have been reported from at least 16 non-African countries. The detection of virus in skin lesions, blood, semen, and saliva of infected patients with monkeypox infections raises the potential for disease transmission via routes that have not been previously documented, including by blood and plasma transfusions. Methods for protecting the blood supply against the threats of newly emerging disease agents exist and include Pathogen Reduction Technologies (PRT) which utilize photochemical treatment processes to inactivate pathogens in blood while preserving the integrity of plasma and cellular components. Such methods have been employed broadly for over 15 years, but effectiveness of these methods under routine use conditions against monkeypox virus has not been reported.</p> <p>Results</p> <p>The levels of spiked virus present in whole blood and plasma samples exceeded 103 infectious particles per dose, corresponding to greater than 105 DNA copies per mL. Treatment of whole blood and plasma units under standard operating procedures for the Mirasol PRT System resulted in complete inactivation of infectivity to the limits of detection. This is equivalent to a reduction of ≥ 2.86 +/- 0.73 log10 pfu/mL of infectivity in whole blood and ≥ 3.47 +/-0.19 log10 pfu/mL of infectivity in plasma under standard operating conditions for those products. </p> <p>Conclusion</p> <p>Based on this data and corresponding studies on infectivity in patients with monkeypox infections, use of Mirasol PRT would be expected to significantly reduce the risk of transfusion transmission of monkeypox.</p>
Low-Titer O Positive Whole Blood Versus Component Therapy for Emergent Transfusion in Trauma Patients
ClinicalTrials.gov study NCT05081063. IPD Sharing: NO. Countries: 1. Publications: 6.
Clinical and Biological Efficacy of Mirasol-treated Fresh Whole Blood for the Prevention of Transfusion-transmitted Malaria
ClinicalTrials.gov study NCT02118428. IPD Sharing: Not stated. Countries: 1. Publications: 1.
SWiFT Canada (Study of Whole Blood in Frontline Trauma)
ClinicalTrials.gov study NCT06495294. IPD Sharing: YES. Countries: 1. Publications: 1.
Pragmatic Prehospital Group O Whole Blood Early Resuscitation Trial
ClinicalTrials.gov study NCT03477006. IPD Sharing: NO. Countries: 1. Publications: 2.
Early Whole Blood in Patients Requiring Transfusion After Major Trauma
ClinicalTrials.gov study NCT01227005. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Data from: Pathogen reduction of monkeypox virus in plasma and whole blood using riboflavin and UV light
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Whole mount 3D imaged adipose tissue demonstrating sympathetic neurons and blood vessels during cold exposure and thermoneutrality
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Whole-transcriptome sequencing identifies neuroinflammation, metabolism and blood-brain barrier related processes in the hippocampus of aged mice during perioperative period
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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.