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1,742 results for “activity data”
Complement activation induces excessive T cell cytotoxicity in severe COVID-19: Analysis of single cell data cohort 1 (Berlin).
<p>This repository contains the R Markdown files with the analysis of CyTOF and scRNA-seq data corresponding to cohort 1 (Berlin) analysed in Georg et al. 2021 "Complement activation induces excessive T cell cytotoxicity in severe COVID-19". Additionally, here we include the necessary CyTOF data to reproduce this analysis.</p> <p>CyTOF data:</p> <ul> <li>The debarcoded fcs files (before batch-correction) can be found in <a href="https://flowrepository.org/id/FR-FCM-Z4P5">https://flowrepository.org/id/FR-FCM-Z4P5</a>. \</li> <li>Here you can find the necessary data to reproduce the analysis (cytof_analysis.Rmd, cytof_analysis.html): <ul> <li>data_norm_all.csv: single-cell protein expression data (after batch-normalization and in linear scale).</li> <li>data_Tcells_annotated.csv: single-cell protein expression of gated T cells with cluster annotation.</li> <li>phenograph_CD4_k30.csv, phenograph_CD8_k30.csv, phenograph_TCRgd_k30.csv: output from Louvain Clustering computed with PhenoGraph (<a href="https://github.com/jacoblevine/PhenoGraph">https://github.com/jacoblevine/PhenoGraph</a>) per T cell compartment.</li> <li>clusterannotation.csv: annotation for each cluster and metacluster</li> </ul> </li> </ul> <p>scRNA-seq data:</p> <ul> <li>The raw data can be found in <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175450">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175450</a></li> <li>Other files to reproduce the analysis (scRNAseq_analysis_1preprocessing.Rmd, scRNAseq_analysis_2clustering.Rmd, scRNAseq_analysis_3convalescent.Rmd): <ul> <li><a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_Sawitzki_RECAST_09_2021.xlsx">scRNAseq_Sawitzki_RECAST_09_2021.xlsx</a>: Single-cell metadata.</li> <li>scRNAseq_samples.tsv: Samples metadata.</li> <li><a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_genelist_annotation.xlsx">scRNAseq_genelist_annotation.xlsx</a>: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175450">G</a>ene list for the annotation of T cells (Also in Mendeley, see Data and Code Availability).</li> <li><a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_GO_RESPONSE_TO_TYPE_I_INTERFERON.txt">scRNAseq_GO_RESPONSE_TO_TYPE_I_INTERFERON.txt</a>, <a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_GO_DEFENSE_RESPONSE_TO_VIRUS.txt">scRNAseq_GO_DEFENSE_RESPONSE_TO_VIRUS.txt</a>, , <a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_GO_T_CELL_MEDIATED_CYTOTOXICITY.txt">scRNAseq_GO_T_CELL_MEDIATED_CYTOTOXICITY.txt</a>: Gene lists for the signatures “Response to Type I Interferon” , “Defense Response to virus” and “Cytotoxicity” used for GSEA. (Also in Table S2).</li> <li><a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_traj18_trav10.txt">scRNAseq_traj18_trav10.txt</a>,<a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_trbv25.txt">scRNAseq_trbv25.txt</a>: sequences to determine the proportion of TRAV10-TRAJ18-TRBV25 pairing T cell clones across all T cell clusters.</li> </ul> </li> </ul>
Fruit-feeding butterfly community data analysed in "Recovery patterns in community composition of fruit-feeding butterflies following 26 years of active forest restoration"
<p>Community data of fruit-feeding butterflies collected from Kibale National Park, Uganda, in the periods 2011-2012 and 2020-2021 analysed in our paper Korkiatupa et al. 2023: "Recovery patterns in community composition of fruit-feeding butterflies following 26 years of active forest restoration" (<em>Ecosphere</em> <span>14</span>(<span>5</span>): e4514. <a href="https://doi.org/10.1002/ecs2.4514">https://doi.org/10.1002/ecs2.4514</a>).</p> <p>The table consists of two parts. First part shows counts of individuals of butterfly species in each study site. Second part shows the metadata: code of studysite, census (2011-2012/2020-2021), planting year (planting year or "Primary forest"), and coordinates (WGS 84 coordinate system).</p>
Publication & Supplementary data: Pro-health compounds and antioxidant activity of 65 potato cultivars
<p>Metadata (climatic conditions, list of varieties, field plan, etc.) and data (carotenoid content, vitamin C content, radical scavenging activity DPPH and FRAP, yellow index) related to the paper of Tatarowska et al., "The content of total carotenoids, vitamin C and antioxidant properties of 65 potato cultivars characterised under the European project ECOBREED" published in Int. J. Mol. Sci. 24 (2023), 11716.</p>
CollecTRI Data for Investigation of SETBP1 gene expression and transcription factor activity across human tissues
<p>Here we provide the human CollecTRI prior (accessed May 2023) for inference of TF activity across 31 GTEx tissues using multivariate linear modeling method decoupleR.<br> <br> The `human_prior_tri.csv` includes 1,178 unique TFs (referred to as the source) that target 6,627 unique genes (referred to as targets) to give us 42,595 interactions in the CollecTRI prior input. Interactions are represented as a + or - 1 (mor).</p>
Data from: MET receptor activation by stromal cells serves as promising target in melanoma brain metastases
<p>Supplementary tables to our recent manuscript: MET receptor activation by stromal cells serves as promising target in melanoma brain metastases</p>
High-frequency water temperature, chlorophyll fluorescence, wind speed, and photosynthetically active radiation data for 18 globally-distributed lakes 2008 - 2013
Abstract: This dataset was used in the analysis described in the manuscript by Rusak, J. A.J. Tanentzap, J.L. Klug, K. Rose, L.A. Winslow R. Smyth, E. Jennings, D. Pierson, S. Hendricks, A. Laas, E. Ryder, D. White, R. Adrian, L. Arvola, E. de Eyto, H. Feuchtmayr, M. Honti, V. Istanovics, I. Jones, C. McBride, S. Schmidt, G. Zhu. Wind and trophic status explain the temporal and spatial variability of chlorophyll in lakes. In review: Limnology and Oceanography Letters. The variation in chlorophyll fluorescence from 18 globally distributed lakes, was tested at monthly, daily and hourly scales in related to high-frequency measurements of wind, water temperature and radiation within lakes as well as lake productivity and morphometry among lakes. Overall, monthly variation in algal biomass was greater than that expressed at either daily or hourly scales but, combined, these latter time scales were equivalent to seasonal variation. Among lakes, algal biomass variation increased with trophic status while, within-lake variation increased with increasing wind speed variation. Together, our results suggest that predicted changes associated with a changing climate, as well as widespread ongoing cultural eutrophication, have the potential to substantially alter the variability of algal biomass and thus the predictability of the services it provides. This dataset includes the data used in the analysis described above.
Photosynthetically Active Radiation data taken with the Delta-T SunScan wand every 15 cm of 1m x 1m chamber flux and point frame plots as well as four remotely monitored canopies at the Toolik Field Station in AK, Summer 2012.
Within-canopy PAR was measured with a Delta-T SunScan wand every 15 cm from the ground to above the canopy under both direct and diffuse light. The data includes all outputs from the SunScan wand: time of measurement, spread of PAR sensors, total irradiance, total diffuse light, and individual outputs of 64-PAR sensors on the SunScan wand. These measurements were taken for 1m x 1m chamber flux (n=14) and point frame (n=19) plots as well as sites four montitored remotely by PAR sensors located above, within, and below shrub canopies. All plots were dominated either by tall Salix pulchra and Betula nana species and were located near the LTER shrub plots at Toolik Field Station , AK in the summer of 2012.
Photosynthetically active radiation (PAR) measurements, relative humidity, and temperature data logged every five minutes from Betula nana and Salix pulchra shrub canopies, summer of 2012 in vicinity of Toolik Lake, Alaska.
This file contains PAR , relative humidity, and temperature data logged every five minutes from within, below, and above Betula nana and Salix pulchra shrub canopies at two locations near Toolik Lake, Alaska during the summer of 2012. The location of the PAR sensor and dataloggers were co-located with the LTER shrub plots (block 1 and 2), also used for the chamber flux and point frame measurements taken this same year. There were two logging sites (block 1 and 2), each of which had five PAR sensors, two for each shrub canopy and one above, as well as three sensors to log relative humidity and temperature. Additional data about the daily instrument output from these sites can be found in the file "ShrubCanopy_DailyLogger".
Daily summaries of photosynthetically active radiation (PAR), relative humidity, and temperature data logged above, within, and below Betula nana and Salix pulchra shrub canopies during the summer of 2012 in vicinity of Toolik Lake, Alaska.
This file contains limited daily summaries of PAR, relative humidity, and temperature data monitored above, within, and below Betula nana and Salix pulchra shrub canopies at two locations near Toolik Lake, Alaska during the summer of 2012. The location of the PAR sensor and dataloggers were co-located with the LTER shrub plots (block 1 and 2), also used for the chamber flux and point frame measurements taken this same year. There were two logging sites (block 1 and 2), each of which had PAR five PAR sensors, two for each shrub canopy and one above, as well as three sensors to log relative humidity and temperature. This file contains maximum PAR, total daily PAR, and daily average temperature data, as well as intermittant maximum and minimum values for temperature and relative humidity. Data monitored every five minutes is available in the file "ShrubCanopy_InstantLogger".
Active Layer Depth Data for the BBC collapse scar for 2003 and 2004
This data set contains active layer depth measurements (cm) for a transect from the center of the BBC collapse scar (0 m) into the surrounding fire scar (30 m) of the Survey Line Fire (burned in June-July 2001). Data were collected using a 120m (and during 2004 a 205.5 m) permafrost probe at every visit to the site in 2003 and 2004. Three permafrost depth measurements were made within a 25cm radius at every point along the transect (0, 3, 6, 9, 12, 15, 18, 21, 24, 27, and 30 m on the east and west sides of the boardwalk and at 33 m on the west side only). This data set was collected to monitor the increase in active layer throughout the growing season to relate this to measured fluxes of CO2 and CH4 emissions from soils along the same transect. The data set was also used to monitor permafrost collapse at the margins of the BBC collapse scar.
Bonanza Creek moisture gradient physical data at BZBS: hourly temperature, moisture and photosynthetically active radiation.
This dataset contains the hourly output from temperature, moisture and PAR sensors at five unique vegetative sites at the Bonanza Creek moisture gradient. This data can be sorted and viewed by site, year, hour and depth of probe below surface. Data from each site within this transect will be update yearly. Start dates for the probes at each site vary depending on when they were installed.
Bonanza Creek moisture gradient physical data at BZWB: hourly temperature, moisture and photosynthetically active radiation.
This dataset contains the hourly output from temperature, moisture and PAR sensors at five unique vegetative sites at the Bonanza Creek moisture gradient. This data can be sorted and viewed by site, year, hour and depth of probe below surface. Data from each site within this transect will be update yearly. Start dates for the probes at each site vary depending on when they were installed.
Bonanza Creek moisture gradient physical data at BZTG: hourly temperature, moisture and photosynthetically active radiation.
This dataset contains the hourly output from temperature, moisture and PAR sensors at five unique vegetative sites at the Bonanza Creek moisture gradient. This data can be sorted and viewed by site, year, hour and depth of probe below surface. Data from each site within this transect will be update yearly. Start dates for the probes at each site vary depending on when they were installed.
Bonanza Creek moisture gradient physical data at BZEC: hourly temperature, moisture and photosynthetically active radiation.
This dataset contains the hourly output from temperature, moisture and PAR sensors at five unique vegetative sites at the Bonanza Creek moisture gradient. This data can be sorted and viewed by site, year, hour and depth of probe below surface. Data from each site within this transect will be update yearly. Start dates for the probes at each site vary depending on when they were installed.
Bonanza Creek moisture gradient physical data at BZDE: hourly temperature, moisture and photosynthetically active radiation.
This dataset contains the hourly output from temperature, moisture and PAR sensors at five unique vegetative sites at the Bonanza Creek moisture gradient. This data can be sorted and viewed by site, year, hour and depth of probe below surface. Data from each site within this transect will be update yearly. Start dates for the probes at each site vary depending on when they were installed.
Station data of passive and active fluorescence measurements of chlorophyll-a (Chl), phycoerythrin (PE), chromophoric dissolved organic matter (CDOM), and variable fluorescence (Fv/Fm) from CCE-CalCOFI Augmented cruises in the California Current System, 2012 - October 2020.
Active and passive fluorescence measurements are made using the ALFA5 system (Chekalyuk and Hafez, 2013) on water from the ship’s underway system (these are not samples from bottles!) during CalCOFI cruises while on station. The instrument uses excitation at 405 and 510 nm to measures passively the fluorescence of chlorophyll-a (Chl), three different phycoerythrins (PE1, PE2 and PE3) and chromophoric dissolved organic matter (CDOM). Variable fluorescence (Fv/Fm) is measured actively using pump-during-probe (PDP) measurements of Chl a fluorescence induction. Fluorescence measurements are normalized to the water’s Raman fluorescence. ALF data are merged with CTD and bottle data that were collected by the CalCOFI group.
Coweeta Synoptic Data from 49 sampling sites in the Upper Little Tennessee River Basin from 2009 to 2010 (active channel width, bankfull width, and channel depth data)
This data was generated as part of synoptic sampling conducted at the Coweeta LTER between June 2009 and May 2010. 49 wadeable streams with low levels of development were sampled throughout the Upper Little Tennessee River Basin in the Southern Appalachians. Active channel width, bankfull width, and channel depth were measured every 5 meters for 150 meters at synoptic stream sites. Effects of riparian vegetative conditions on a suite of channel morphological variables were investigated: active channel width, variability of width within a reach, large wood frequency, mesoscale habitat distributions, median particle size, and percent fines. At each site, a uniform 150 meter section of stream was surveyed. Within each reach active channel width, bankfull channel width, and channel depth were measured every 5 meters. Active channel width was defined as the vegetationless channel bed from left vegetation break to right vegetation break. A whitepaper on the Synoptic field sampling activites can be found at: http://coweeta.uga.edu/publications/white%20paper%20summary%20of%20synoptic%20sampling.pdf
Muskox body temperature and activity data
<p>Data on muskox (<em>Ovibos moschatus</em>) daily body temperature (mean, range, max, mean) and activity (mean count) collected from free-ranging muskoxen at Zackenberg, NE Greenland.</p> <p>New version has less significant figures to reflect the resolution of temperature and activity data.</p>
Data for paper titled : Comparing Clothing-Mounted Sensors with Wearable Sensors for Movement Analysis and Activity Classification (published in Sensors (MDPI))
<p>Data for paper titled : Comparing Clothing-Mounted Sensors with Wearable Sensors for Movement Analysis and Activity Classification (published in Sensors (MDPI))</p>
Raw data for Kierdorf et al, "Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila"
<p>This upload contains the raw data corresponding to the publication "Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila" by Katrin Kierdorf et al., eLife 2020.</p>
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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.