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1,102 results for “human use”
A targeted metabolomics-based assay using human induced pluripotent stem cell-derived cardiomyocytes identifies structural and functional cardiotoxicity potential
<p>Implementing screening assays that identify functional and structural cardiotoxicity earlier in the drug development pipeline has the potential to improve safety and the cost and time required to bring new drugs to market. In this study, a metabolic biomarker-based assay was developed that predicts the cardiotoxicity potential of a drug based on changes in the metabolism and viability of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM). Assay development and testing was conducted in two phases: (1) biomarker identification and (2) targeted assay development. In the first phase, metabolomic data from hiPSC-CM spent media following exposure to 66 drugs was used to identify biomarkers that identified both functional and structural cardiotoxicants. Four metabolites that represent different metabolic pathways (arachidonic acid, lactic acid, 2'-deoxycytidine, and thymidine) were identified as indicators of cardiotoxicity. In phase two, a targeted, exposure-based biomarker assay was developed that measured these metabolites and hiPSC-CM viability across an eight-point concentration curve. Metabolite-specific predictive thresholds for identifying the cardiotoxicity potential of a drug were established and optimized for balanced accuracy or sensitivity. When predictive thresholds were optimized for balanced accuracy, the assay predicted the cardiotoxicity potential of 81 drugs with 86% balanced accuracy, 83% sensitivity, and 90% specificity. Alternatively, optimizing the thresholds for sensitivity yields a balanced accuracy of 85%, 90% sensitivity, and 79% specificity. This new hiPSC-CM-based assay provides a paradigm that can identify structural and functional cardiotoxic drugs that could be used in conjunction with other endpoints to provide a more comprehensive evaluation of a drug's cardiotoxicity potential.</p>
HUMANE: Qualitative data on REVEAL use case implementation
<p>Data regarding the REVEAL use case implementation were gathered through two focus groups from journalists.</p>
ChromBERT: Uncovering Chromatin State Motifs in the Human Genome using a BERT-based Approach
<ol> <li>Pretrain data and results for: <ul> <li>Promoter regions for all genes in 127 different cell lines in ROADMAP </li> <li>CRM (<em>cis</em>-regulatory module) regions longer than 2k bps in 127 different cell lines in ROADMAP</li> <li>Whole genome regions without continuous low signal state ("O") in 4-mer</li> </ul> </li> <li>Fine-tuning data and result for: <ul> <li>[Classification] Promoter regions of high-expressed genes (from RPKM>10 to RPKM>50) compared to not expressed genes (RPKM=0) or low-expressed genes (RPKM>0) with the directory names:<br> <ul> <li>not_n_rpkm0 : RPKM=0 vs. RPKM>0</li> <li>not_n_rpkm10 : RPKM=0 vs. RPKM>10</li> <li>not_n_rpkm20 : RPKM=0 vs. RPKM>20 </li> <li>not_n_rpkm30 : RPKM=0 vs. RPKM>30 </li> <li>not_n_rpkm50 : RPKM=0 vs. RPKM>50 </li> <li>rpkm0_n_rpkm10 : RPKM>0 vs. RPKM>10 </li> <li>rpkm0_n_rpkm20 : RPKM>0 vs. RPKM>20 </li> <li>rpkm0_n_rpkm30 : RPKM>0 vs. RPKM>30 </li> <li>rpkm0_n_rpkm50 : RPKM>0 vs. RPKM>50 </li> <li>rpkm10_n_rpkm20 : RPKM>10 vs. RPKM>20 </li> <li>rpkm10_n_rpkm30 : RPKM>10 vs. RPKM>30 </li> <li>rpkm10_n_rpkm50 : RPKM>10 vs. RPKM>50 </li> <li>rpkm20_n_rpkm30 : RPKM>20 vs. RPKM>30 </li> <li>rpkm20_n_rpkm50 : RPKM>20 vs. RPKM>50 </li> <li>rpkm30_n_rpkm50 : RPKM>30 vs. RPKM>50 </li> </ul> </li> <li>[Regression] Quantitative gene expression prediction for promoter regions</li> <li>CRM regions longer than 2k bps compared to non-CRM regions</li> </ul> </li> </ol>
Data, Metadata, R-codes and R data files for publication "Comparative ungulate diversity and biomass change with human use and drought: implications for community stability and protected area prioritization in African savannas" by Bartzke et al. in Ecology and Evolution
<p>These files contain data and metadata for modeling ungulate diversity and biomass in the Maasai Mara ecosystem in Kenya in the drought year of 1999 and a year with normal rainfall, 2002. The files also contain R codes and R data files.</p> <p>Metadata.pdf: Metadata for files "mc_333m.csv" and "mc_1km.csv"</p> <p>mc_333m.csv: A data file for 333-meter-by-333-meter sub-blocks.</p> <p>prepare_data.r: R code to impute missing vegetation records in 333-meter-by-333-meter subblocks and summarize the data over 1-kilometer-by-1-kilometer blocks for analysis.</p> <p>krige_vegetation.RData: An R data file containing the imputed vegetation records.</p> <p>mc_1km.csv: A data file for 1-kilometer-by-1-kilometer blocks for analysis.</p> <p>mc_1km.r: R code for modeling ungulate diversity and biomass; mc_1km_mod.RData: An R data file for loading the ungulate diversity and biomass models.</p> <p>mc_1km.RData: An R data file containing model predictions of ungulate diversity and biomass.</p> <p>mc_1km_plots.r: R code for plotting model predictions of ungulate diversity and biomass.</p> <p>MMNR_boundary.shp: A shapefile of the Maasai Mara National Reserve boundary in Kenya and associated files. These files are used for plotting the predictions of ungulate diversity and biomass.</p> <p>MMNR_border.zip: A shapefile and associated files for the Maasai Mara National Reserve border with Tanzania. These files are also used for plotting predictions of ungulate diversity and biomass.</p>
Raw Data and Scripts used in Regulation of single-cell heterogeneity of capsular polysaccharide synthesis in a human gut symbiont
<p>Raw data used in this publication. Single-cell analysis of promoter inversions reveals differential inversion rates as a determinant of bacterial population heterogeneity.</p> <p> </p> <p>Libx.zip contains raw sequencing reads</p> <p>scripts.zip contains code for analysis of reads and growth curve data</p> <p>SequencingRawDataFilesIndex.xls contains a description of all the raw data in each libx.zip.</p>
Supplementary material 1 from: Sosa-López JR, Díaz Bernal NN, Padilla E, Briones-Salas M (2023) Analysis of the effects of habitat characteristics, human disturbance and prey on felids presence using long-term community monitoring information. Nature Conservation 53: 279-295. https://doi.org/10.3897/natureconservation.53.104135
Sampling sites and dates on which the camera-traps were installed and Generalized linear mixed models (GLMM) for Puma, Bobcat and Margay
Banking dataset used for cloud computing and comparison with Human
<p>Banking dataset used for cloud computing </p>
DATA SET: Near-infrared diffuse optical characterization of human thyroid using ultrasound-guided hybrid time-domain and diffuse correlation spectroscopies
<p>This repository contains the data sets of the article:</p> <p>P. Fernández Esteberena et al. (2024). Near-infrared diffuse optical characterization of human thyroid using ultrasound-guided hybrid time-domain and diffuse correlation spectroscopies. <em>Biomedical Optics Express</em>. <a href="https://doi.org/10.1364/BOE.538141">https://doi.org/10.1364/BOE.538141</a></p>
Virtual Screening and Testing of GSK-3 Kinase Inhibitors Using human SH-SY5Y Neuronal cells Expressing Tau Folding Reporter and Mouse Hippocampal Primary Neuron Culture Under Tau Cytotoxicity
<p>Supplementary Figure S1. for IJMS</p>
Marginal imprint of human land use upon fire history in a mire-dominated boreal landscape of the Veps Highland, North-West Russia
<p>Spatially explicit reconstructions of fire activity in European boreal forests are rare, limiting our understanding of factors driving vegetation dynamics in this part of the boreal domain. We have developed a spatially explicit dendrochronological reconstruction of a fire regime in a mire-dominated landscape of the Veps Nature Park (North-West Russia) over the 1580-2000 CE period.</p> <p>We dated 74 fire years using 164 fire-scarred living and dead Scots pine (Pinus sylvestris L.) trees collected on 31 sites. The historical fire cycle was 91.4 years (90% confidence intervals, CI 66.2–137.6 years) over the 1580–1720 period, decreasing to 35.9 (CI 28.1–47.6 years) between 1730 and 1770, and then increasing again to 122.7 years (CI 91.0–178.0 years) over the 1780–2000 period. The reconstructed forest fire history featured a number of patterns clearly deviating from the trends documented in previous Northern European reconstructions. The most striking feature was the absence of a period with increased fire activity during the 1600s, a pattern widely observed in Fennoscandia and in Russian Karelia. We noted, however, a higher fire activity period between 1730 and 1780, resulting from the increase in early season fires.</p> <p>Land-use history of the area did not appear to have an effect on historical fire dynamics. The current FC in the Veps Highland is close to the estimates reported for the pre-industrial colonisation period in Fennoscandia, which suggests that the area's forests currently maintain their close-to-natural fire regime.</p>
Impacts on food web properties of island invertebrate communities vary between different human land uses
<p><span>Human land use is of growing concern for island ecosystems. Besides direct impacts on biodiversity, land uses can alter the functioning and structure of ecosystems. Central to this are impacts on food webs. The release of additional nutrients from human origin, habitat homogenization, or environmental filtering due to human land use can change the diet of individual consumer species (i.e., their trophic niches) and the distribution and overlap of trophic niches within a food web. However, it remains largely unclear whether the effects on food web properties vary between the different and predominant human land uses present on islands. Here, we investigated the impact of two dominant human land uses on small oceanic islands (i.e., urban and tourism development) and tested if and how different land uses on islands affect food web structure. To disentangle human land uses, we investigated islands, which were either privately owned by a tourist facility (i.e., exclusively tourism land use) or experienced urban development from the local population (i.e., urban land use), or remained uninhabited, serving as reference sites free of direct land use. Using stable isotope analysis, we show that isotope signature, trophic (isotopic) niches, and overall food web properties of the investigated island invertebrate communities were significantly changed under both land use regimes. While trophic diversity was reduced and trophic niche widths increased under tourism land use, the investigated food webs showed reduced trophic diversity at the food web base and a more uneven trophic niche distribution under urban land use. In summary, these findings show that different human land uses can have contrasting impacts on oceanic island food webs. As oceanic islands experience rapidly growing human land conversion, our results indicate that they may also face increasing yet unpredictable long-term changes in food web dynamics.</span></p>
Verifying the Conformance of Human Behavior Using Hybrid Models - Synthetic Event Logs
<p>Synthetic event logs used in the evaluation of the approach for the verification of conformance checking of human behavior, using hybrid process models.</p>
Large-scale human tissue analysis identifies Uroplakin 3B as a useful diagnostic marker for mesothelioma and normal meso-thelial cells
<p><strong>Supplement Figure 1:</strong> IHC validation by comparison of antibodies. Using MSVA-736M, an apical membranous Upk3b positivity is seen in mesothelial cells covering an appendix (A), amnion cells of a placenta (B), and umbrella cells of the renal pelvis urothelium (C), while staining is absent in adrenal gland (D). Using clone C362, a similar membranous staining is seen in mesothelial cells of the appendix (E), amnion cells (F), and urothelial umbrella cells (G) despite of a higher level of background staining. Clone C362 results in a significant nuclear staining of adrenocortical cells (H) which was not seen by MSVA-736M.</p>
Efficient gene expression in human stem cell derived-cortical organoids using adeno associated virus
<p><strong>Supplementary figure 6. Neuronal network activity in human cortical organoid</strong>. Videos of AAV-mediated expression of the calcium indicator jGCaMP7 under the human synapsin promoter for control (aCSF), glutamate, gabazine and TTX treated cortical organoids.</p>
Humans flexibly use visual priors to optimize their haptic exploratory behaviour
<p>datasets of the first, second and third experiment</p> <p>for each subject, there is one .raw file and one folder containing the .trj movement data files of each trial.</p> <p>the .trj files contain the variables (columns left to right): time in ms, x, y, z, force, velocity, position (-1 not on stim, 0 left, 1 right), inStimPos (-1 not, 0 outerstim, 1 innerstim)</p> <p>the .raw files contain the variables (columns left to right): block nr, trial nr, randomization nr, stimulus orientation, visual quality, startstim (0 left 1 right), ref stim, comp stim (always < ref), chosenStim, force. in exp2&3, ref stim and comp stim have the numbers 1xx for the "hard" block and 2xx for the "easy" block.</p>
Supplementary Movies (Humans use Predictive Gaze Strategies to Target Waypoints During Steering)
<p>Supplementary movies for the article Humans use Predictive Gaze Strategies to Target Waypoints During Steering</p>
Perspectives of ammunition users on the use of lead ammunition and its potential impacts on wildlife and humans
<p>Views of UK ammunition users about lead ammunition were statistically analysed using Q-methodology. Each participant was asked to rank, in order of agreement, 56 opinion statements about the topic. The dataset therefore includes information on:</p> <p>1. The participant ID (all participants were anonymous)</p> <p>2. The individual scores given to each statement by the participant, where -5 relates to statements most strongly disagreed with and +5 relates to statements most agreed with. There were a fixed number of statements along the scale.</p> <p>A pyramid shaped grip (know as an array) was used for the sorting exercise as it requires participants to rank statements in a forced quasi-normal distribution. See Figure S1 (Supplementary Materials).</p> <p> </p>
A global land-use data cube 1992-2020 based on the Human Appropriation of Net Primary Production: Dataset 3
<p>This dataset is part of the LUIcube, a global dataset on land-use at 30 arcsecond spatial resolution. The LUIcube includes information on area, the change in NPP due to land conversions (HANPP<sub>luc</sub>), the harvested NPP (including losses, HANPP<sub>harv</sub>), and the NPP remaining in ecosystems after harvest (NPP<sub>eco</sub>) for 32 land-use classes in annual time-steps from 1992 to 2020. A detailed description of the LUIcube is available in the accompanying publication.</p> <p>The layers of land-use areas are provided in square kilometers (km²) per grid cell. All NPP flows are provided in tC/yr per grid cell. Adding HANPP<sub>harv</sub> to NPP<sub>eco</sub> results in the actual NPP available before harvest (NPP<sub>act</sub>=NPP<sub>eco</sub>+HANPP<sub>harv</sub>), and adding HANPP<sub>luc</sub> to NPP<sub>act</sub> results in the potential NPP available in the hypothetical absence of land use (NPP<sub>pot</sub>=NPP<sub>act</sub>+HANPP<sub>luc</sub>) for the given land-use class. Area-intensive values (in gC/m²/yr) can be calculated by dividing the NPP flows by the area of the respective land-use class per grid cell. HANPP in % of NPP<sub>pot</sub> can be calculated by summing up HANPP<sub>harv</sub> and HANPP<sub>luc</sub> and dividing it by NPP<sub>pot</sub>. Areas and NPP flows of land-use classes can be aggregated to calculate their overall HANPP.</p> <p>This Zenodo repository provides data on following land-use classes: grazing land with (almost) no trees (GL-notrees); cropland used for production of other fibres (CL-OFIB); fallow cropland areas (CL-FALL)</p>
Supplementary Materials for Discovery of Hub Genes and Construction of Competitive Endogenous RNA Network in Human Cytomegalovirus Infection Using Computational and Bioinformatics Tools
<p><span>Table S1: List of targeted genes by 41 differentially expressed microRNAs (DEMs) agreed in Targetscan and miRDB; Table S2: Significant biological process (BP) of 144 genes associated with Human Cytomegalovirus (HCMV); Table S3: Significant cellular components (CC) of 144 genes associated with HCMV; Table S4: Enriched molecular function (MF) of 144 genes associated with HCMV; Table S5: Pathways significantly affected by 144 genes in HCMV; Figure S1: Number of interactions for each gene in protein-protein interaction (PPI) network.</span></p>
CAMI2 Challenge - Human Microbiome Project Toy Database - sample 19 - regenerated using recent RefSeq representative genomes
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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.