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7,739 results for “individualization”
Root Systems of Individual Plants Worldwide 2022
The above- and below-ground sizes and shapes of plants strongly influence plant competition, community structure, and plant-environment interactions, but the plant size and shape across climate regimes remain incompletely understood. In this study I seek to understand how plant geometries respond to varying climates via trade-offs in shoot height and width, and root depth and spread. I more than doubled the Root Systems of Individual Plants (RSIP) database to contain 5,647 observations, to our knowledge the largest database describing the maximum rooting depth, lateral spread, and shoot size of terrestrial plants in the world. Shoot size and root system size strongly covary. Across climatic gradients woody plants show deeper-narrower root systems in arid climates and taller shoots in humid climates. Phylogeny greatly influences shoot size. Rooting depth is primarily influenced by climate seasonality and lateral root spread is strongly influenced by shoot size. Using our newly expanded global database I found that shoot size covaries strongly with rooting system size; however, these relationships are not static across the climate space, as the geometries of plants shift considerably.
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Fish Individual 2001 - 2004
Fish Data collected for Biocomplexity Project; Landscape Context - Coordinated Field Studies. The eight sportfishes of concern in this dataset; Bluegill, Pumpkinseed, Bluegill-Pumpkinseed hybrid, Largemouthbass, Smallmouthbass, Rockbass, Walleye, and Yellowperch, are the only species for which standard metrics (length (mm) and weight (g)) were taken. All other fish were identified to species and counted. Sampling Frequency: annually Number of sites: 58
Individual plant growth and reproduction in the black sand extended growing season experiment for East Knoll, Audubon, Lefty, and Trough sites, 2018 - 2020.
As a result of climate change, the Rocky Mountain Front Range is experiencing warmer summers and earlier snowmelt. Due to the importance of snow for regulating soil temperature, growing season length, and available moisture in alpine ecosystems, even small shifts in the snow-free period could have large impacts. The focus of the Black Sand Extended Growing Season Length Experiment is to examine how terrain-related differences in climate exposure influence the way alpine habitats respond to climate change via earlier snowmelt. To simulate how climate exposure may affect plant communities, NWT LTER researchers established 5 experimental sites, each containing a pair 10 x 40m rectangular plots. These sites include north and south facing aspects, subalpine and alpine tundra meadows and a range of hydrological conditions (e.g. dry meadows, moist meadows, wet meadows). We accelerated snowmelt in one plot at each site by adding chemically inert black sand, while keeping the second plot as an unmanipulated control; black sand was added to control plots after snow had naturally melted. We used open top warming chambers (OTCs) to increase summer temperature in three subplots within each of the 10 x 40 m plots. This dataset includes measurements of growth and reproduction for Geum plants as well as counts of buds and flowers were counted and recorded for each tagged study plant, within all snow and warming treatments at all sites except Soddie.
Individual Brain Charting
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Cortical myelin measured by the T1w/T2w ratio in individuals with depressive disorders and healthy controls
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HOSENG trial – HOme-based oral SElf-testiNG for absent and refusing individuals during a door-to-door HIV testing campaign: a cluster randomised clinical trial in rural Lesotho
<p>These are pseudo-anonymised data from the HOSENG randomized trial: " HOSENG trial – HOme-based oral SElf-testiNG for absent and refusing individuals during a door-to-door HIV testing campaign: a cluster randomised clinical trial in rural Lesotho". The data dictionary explains the data available in the dataset. Between July 2018 and December 2018, 10516 eligible individuals from 106 consenting villages were enrolled from two districts of Lesotho, and followed up for a maximum of 120 days. Main manuscript reference, DOI: <a href="https://doi.org/10.1016/s2352-3018(20)30233-2">10.1016/S2352-3018(20)30233-2. </a>The protocol was published, DOI:10.1186/s13063-019-3469-2.</p>
Update of: The Global Fire Atlas of individual fire size, duration, speed and direction
<p>This is an updated and extended record of the Global Fire Atlas introduced by Andela et al. (2019). Input data (burned area and land cover products) are updated to the MODIS Collection 6.1 (the original version featured in Andela et al. (2019) was based on collection 6.0 burned area and collection 5.1 land cover products, respectively). The timeseries is extended to cover the period 2002 to August 2024.</p> <h2><strong>Methodological Notes:</strong></h2> <p>The method employed to create the dataset precisely follows the approach described by Andela et al. (2019).</p> <p>The input burned area product is MCD64A1 Collection 6.1. It is described by Giglio et al. (2018) and available at: https://lpdaac.usgs.gov/products/mcd64a1v061/. </p> <p>The input land cover product is MCD12Q1 Collection 6.1. It is described by Sulla-Menashe et al. (2019) and available at: https://lpdaac.usgs.gov/products/mcd12q1v061/. </p> <p>Note that while the methods have remained the same compared to Andela et al. (2019), we do observe small differences between the Global Fire Atlas products originating from differences between the MCD64A1 collection 6.1 burned area data used here and the collection 6 data used in the original product. In addition, we observe more substantial differences in the dominant land cover class associated with each fire due to the differences between the MCD12Q1 collection 6.1 data used here and collection 5.1 data used in the original product. </p> <p>Please note that the year string in filenames refers to the locally-defined fire season in which the fire ignited, not the calendar year. For each MODIS tile, the fire season is defined as the twelve months centred on the month with peak burned area (see Andela et al., 2019). For example, for a MODIS tile with peak burned area in December, the 2023 fire season would be defined as the period from July 2023 to June 2024, with the current record ending in August 2024. This is particularly relevant in the Southern extratropics and the northern hemisphere subtropics, where the fire seasons often span the new year. The local definition of the fire season is based on climatological peak in burned area as described by Andela et al. (2019).</p> <p>Here we extended the time-series to include the fire season of 2002, and extended the time-series until February 2025.</p> <h2> </h2> <h2><strong>Usage Notes:</strong></h2> <h3><strong>Incomplete Observations for the Latest Fire Seasons:</strong></h3> <p>Please note that the year string in filenames refers to the locally-defined fire season in which the fire ignited, not the calendar year. As such, the time-series can be incomplete for the latest fire season (e.g. the "2024 fire season") and also for the penultimate fire season (e.g. the "2023 fire season") due to the way that fire seasons are defined (see above). For example, if the month with peak burned area for a tile is December, then full data covering the 2023 fire season in that tile are not available until midway through the 2024 calendar year. This contrasts with the original dataset from Andela et al. (2019), which only included the data for entire fire seasons between 2003 and 2016. </p> <h3><strong>Observational Outages:</strong></h3> <p>For the purpose of time-series analysis, we note that the 2002 product may have been affected by outages of Terra-MODIS (most notably, June 15 2001 - July 3 2001 and March 19 2002 - March 28 2002), which affects the burn date estimates and Global Fire Atlas product. Following the launch of Aqua-MODIS in May 2002 burn date estimates are more reliable as estimated from both MODIS sensors onboard Terra and Aqua. </p> <h3><strong>File Naming Convention:</strong></h3> <p>GFA_v<em>{time-stamp}</em>_<em>{data-type}</em>_<em>{fire_season}</em>.<em>{file_type}</em></p> <p><em>{time-stamp}</em><strong> </strong>= Date that code was run.</p> <p><em>{data-type}</em><strong> </strong>= “ignitions” or “perimeters” for vector files; “day_of_burn”, “direction”, “fire_line”, or “speed” for raster files.</p> <p><em>{fire_season} </em>= the locally-defined fire season in which the fire was ignited (see more below).</p> <p><em>{file_type} </em>= ".shp" for vector files; ".tif" for raster files. </p> <p>Please note that the year string in filenames refers to the locally-defined fire season in which the fire ignited, not the calendar year. Hence the file GFA_v20240409_perimeters_2003.shp can include fires from the 2003 fire season that ignited in the calendar years 2002 or 2004. </p> <h3>Coordinate systems (Map Projections):</h3> <p>Vector data are provided on the WGS84 projection.</p> <p>Raster data are provided on the MODIS sinusoidal projection used in NASA tiled products. The WKT string defining this projection is:</p> <pre><code>'PROJCS["unnamed",GEOGCS["Unknown datum based upon the custom spheroid",DATUM["Not_specified_based_on_custom_spheroid",SPHEROID["Custom spheroid",6371007.181,0]],PRIMEM["Greenwich",0],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]]],PROJECTION["Sinusoidal"],PARAMETER["longitude_of_center",0],PARAMETER["false_easting",0],PARAMETER["false_northing",0],UNIT["metre",1,AUTHORITY["EPSG","9001"]],AXIS["Easting",EAST],AXIS["Northing",NORTH]]'</code></pre> <p> </p> <h2><strong>Data Layers:</strong></h2> <p><em><strong>Table 1: Overview of the Global Fire Atlas data layers. </strong></em>The shapefiles of ignition locations (point) and fire perimeters (polygon) contain attribute tables with summary information for each individual fire, while the underlying 500 m gridded layers reflect the day-to-day behavior of the individual fires. In addition, we provide aggregated monthly summary layers at a 0.25° resolution for regional and global analyses.</p> <table> <tbody> <tr> <td>File name</td> <td>Content</td> </tr> <tr> <td>SHP_ignitions.zip</td> <td>Shapefiles of ignition locations with attribute tables (see Table 2)</td> </tr> <tr> <td>SHP_perimeters.zip</td> <td>Shapefiles of final fire perimeters with attribute tables (see Table 2)</td> </tr> <tr> <td>GeoTIFF_direction.zip</td> <td>500 m resolution daily gridded data on direction of spread (8 classes)</td> </tr> <tr> <td>GeoTIFF_day_of_burn.zip</td> <td>500 m resolution daily gridded data on day of burn (day of year; 1-366)</td> </tr> <tr> <td>GeoTIFF_speed.zip</td> <td>500 m resolution daily gridded data on speed (km/day)</td> </tr> <tr> <td>GeoTIFF_fire_line.zip</td> <td>500 m resolution daily gridded data on the fire line (day of year; 1-366)</td> </tr> <tr> <td>GeoTIFF_monthly_summaries.zip</td> <td>Aggregated 0.25° resolution monthly summary layers. These files include the sum of ignitions, average size (km2), average duration (days), average daily fire line (km), average daily fire expansion (km2/day), average speed (km/day), and dominant direction of spread (8 classes). </td> </tr> </tbody> </table> <p> </p> <p><em><strong>Table 2: Overview of the Global Fire Atlas shapefile attribute tables. </strong></em>The shapefiles of ignition locations (point) and fire perimeters (polygon) contain attribute tables with summary information for each individual fire.</p> <table> <tbody> <tr> <td>Attribute</td> <td>Explanation / units</td> </tr> <tr> <td>lat, lon</td> <td>Coordinates of ignition location (°)</td> </tr> <tr> <td>size</td> <td>Fire size (km2)</td> </tr> <tr> <td>perimeter</td> <td>Fire perimeter (km)</td> </tr> <tr> <td>start_date, start_DOY</td> <td>Start date (yyyy-mm-dd), start day of year (1-366)</td> </tr> <tr> <td>end_date, end_DOY</td> <td>End date (yyyy-mm-dd), end day of year (1-366)</td> </tr> <tr> <td>duration</td> <td>Duration (days)</td> </tr> <tr> <td>fire_line</td> <td>Average length of daily fire line (km)</td> </tr> <tr> <td>spread</td> <td>Average daily fire growth (km2/day)</td> </tr> <tr> <td>speed</td> <td>Average speed (km/day)</td> </tr> <tr> <td>direction, direc_frac</td> <td>Dominant direction of spread (N, NE, E, SE, S, SW, W, NW) and associated fraction</td> </tr> <tr> <td>MODIS_tile</td> <td>MODIS tile id</td> </tr> <tr> <td>landcover, landc_frac</td> <td>MCD12Q1 dominant land cover class and fraction (UMD classification), provided for 2002-2023</td> </tr> <tr> <td>GFED_regio</td> <td>GFED region (van der Werf et al., 2017; available at https://www.globalfiredata.org/)</td> </tr> </tbody> </table> <p> </p> <p> </p>
Example Microscopy Metadata JSON files produced using Micro-Meta App to document example microscopy experiments performed at individual core facilities
<p>Example <strong>Microscopy Metadata </strong>(Microscope.JSON and Settings.JSON)<strong> files </strong>produced using<strong> <a href="https://wu-bimac.github.io/MicroMetaApp.github.io/">Micro-Meta App</a> </strong>to document the <strong>Hardware Specifications</strong> of example Microscopes and the <strong>Image Acquisition Settings</strong> utilized to acquire example images as listed in the table below.</p> <blockquote> <p>For each facility, the dataset contains two JSON files:</p> <ol> <li><strong>Microscope.JSON file</strong> (e.g., 01_marcello_uliverpool_cci_zeiss_axioobserz1_lsm710.json)</li> <li><strong>Settings.JSON file</strong> (indicated with the name of the image and with the _AS suffix)</li> </ol> </blockquote> <p><strong>Micro-Meta App was</strong> developed as part of a <strong>global community initiative</strong> including the <a href="http://www.4dnucleome.org/"><strong>4D Nucleome (4DN)</strong> </a>Imaging Working Group, <strong>BioImaging North America (BINA)</strong> <a href="https://www.bioimagingna.org/qc-dm-wg">Quality Control and Data Management Working Group</a>, and <strong>QUAlity and REProducibility for Instrument and Images in Light Microscopy</strong> (<a href="https://quarep.org/"><strong>QUAREP-LiMi</strong></a>), to extend the <strong>Open Microscopy Environment (OME)</strong> <a href="https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome.html">data model</a>.</p> <blockquote> <p>The works of this <strong>global community effort</strong> resulted in multiple publications featured on a recent <strong>Nature Methods FOCUS ISSUE </strong>dedicated to <a href="https://www.nature.com/collections/djiciihhjh">Reporting and reproducibility in microscopy</a>.</p> </blockquote> <blockquote> <p><strong>Learn More!</strong> For a thorough description of <strong>Micro-Meta App</strong> consult our recent <a href="https://doi.org/10.1038/s41592-021-01315-z">Nature Methods</a> and <a href="https://doi.org/10.1101/2021.05.31.446382">BioRxiv.org</a> publications!</p> </blockquote> <p> </p> <table> <tbody> <tr> <td><strong>Nr.</strong></td> <td><strong>Manufacturer</strong></td> <td><strong>Model</strong></td> <td><strong>Tier</strong></td> <td><strong>Εxperiment Type</strong></td> <td><strong>Facility Name</strong></td> <td><strong>Department and Institution</strong></td> <td><strong>URL</strong></td> <td><strong>References</strong></td> </tr> <tr> <td>1</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer Z1 (with LSM 710 scan head)</strong></td> <td>1</td> <td>3D visualization of superhydrophobic polymer-nanoparticles</td> <td>Centre for Cell Imaging (CCI)</td> <td>University of Liverpool</td> <td>https://cci.liv.ac.uk/equipment_710.html</td> <td>Upton et al., 2020</td> </tr> <tr> <td>2</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer (Axiovert 200M)</strong></td> <td>2</td> <td>Μeasurement of illumination stability on Chinese Hamster Ovary cells expressing Paxillin-EGFP</td> <td>Advanced BioImaging Facility (ABIF).</td> <td>McGill University</td> <td>https://www.mcgill.ca/abif/equipment/axiovert-1</td> <td>Kiepas et al., 2020</td> </tr> <tr> <td>3</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer Z1 (with Spinning Disk)</strong></td> <td>2</td> <td>Immunofluorescence imaging of cryosection of Mouse kidney</td> <td>Imagerie Cellulaire; Quality Control managed by Miacellavie (https://miacellavie.com/)</td> <td>Centre de recherche du Centre Hospitalier Université de Montréal (CR CHUM), University of Montreal</td> <td>https://www.chumontreal.qc.ca/crchum/plateformes-et-services (the web site is for all core facilities, not specifically for the core facility hosting this microscope)</td> <td>Pilliod et al., 2020</td> </tr> <tr> <td>4</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Imager Z2 (with Apotome)</strong></td> <td>2</td> <td>Immunofluorescence imaging of mitotic division in Hela cells using </td> <td>Bioimaging Unit</td> <td>Newcastle University</td> <td>https://www.ncl.ac.uk/bioimaging/</td> <td>Watson et al., 2020</td> </tr> <tr> <td>5</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer Z1</strong></td> <td>2</td> <td>Fluorescence microscopy of human skin fibroblasts from Glycogen Storage Disease patients.</td> <td>Life Imaging Center (LIC)</td> <td>Centre for Integrative Signalling Analysis (CISA), University of Freiburg</td> <td>https://miap.eu/equipments/sd-i-abl/</td> <td>Hannibal et al., 2020</td> </tr> <tr> <td>6</td> <td><strong>Leica Microsystems</strong></td> <td><strong>DMI6000B</strong></td> <td>2</td> <td>3D immunofluorescence imaging rhinovirus infected macrophages </td> <td>IMAG'IC Confocal Microscopy Facility</td> <td>Institut Cochin, CNRS, INSERM, Université de Paris</td> <td>https://www.institutcochin.fr/core_facilities/confocal-microscopy/cochin-imaging-photonic-microscopy/organigram_team/10054/view</td> <td>Jubrail et al., 2020</td> </tr> <tr> <td>7</td> <td><strong>Leica Microsystems</strong></td> <td><strong>DM5500B</strong></td> <td>2</td> <td>Immunofluorescence analysis of the colocalization of PML bodies with DNA double-strand breaks</td> <td>Bioimaging Unit</td> <td>Edwardson Building on the Campus for Ageing and Vitality, Newcastle University</td> <td>https://www.ncl.ac.uk/bioimaging/equipment/leica-dm5500/#overview</td> <td>da Silva et al., 2019; Nelson et al., 2012<br> </td> </tr> <tr> <td>8</td> <td><strong>Leica Microsystems</strong></td> <td><strong>DMI8-CS (with TCS SP8 STED 3X)</strong></td> <td>2</td> <td>Live-cell imaging of N. benthamiana leaves cells-derived protoplasts</td> <td>Center for Advanced Imaging (CAi)</td> <td>School of Mathematics/Natural Sciences, Heinrich-Heine-Universität Düsseldorf</td> <td>https://www.cai.hhu.de/en/equipment/super-resolution-microscopy/leica-tcs-sp8-sted-3x</td> <td>Singer et al., 2017; Hänsch et al., 2020</td> </tr> <tr> <td>9</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti</strong></td> <td>2</td> <td>Immunofluorescence analysis of the cytoskeleton structure in COS cells</td> <td>Advanced Imaging Center (AIC)</td> <td>Janelia Research Campus, Howard Hughes Medical Institute</td> <td>https://www.janelia.org/support-team/light-microscopy/equipment</td> <td>Abdelfattah et al., 2019; Qian et al., 2019; Grimm et al., 2020</td> </tr> <tr> <td>10</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti-E (HCA)</strong></td> <td>2</td> <td>Τime-lapse analysis of the bursting behavior of amine-functionalized vesicular assemblies</td> <td>Light Microscopy Facility (IALS-LIF)</td> <td>Institute for Applied Life Sciences, University of Massachusetts at Amherst</td> <td>https://www.umass.edu/ials/light-microscopy</td> <td>Fernandez et al., 2020</td> </tr> <tr> <td>11</td> <td><strong>Nikon Instruments/Coleman laboratory (customized)</strong></td> <td><strong>TIRF HILO Epifluorescence light Microscope (THEM)/ Eclipse Ti</strong></td> <td>2</td> <td>Single-particle tracking of Halo-tagged PCNA in Lox cells</td> <td>Coleman laboratory</td> <td>Anatomy and Structural Biology Department, The Albert Einstein College of Medicine</td> <td>https://einsteinmed.org/faculty/12252/robert-coleman/</td> <td>Drosopoulos et al., 2020</td> </tr> <tr> <td>12</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti (with Andor Dragon Fly Spinning Disk)</strong></td> <td>2</td> <td>Investigation of the 3D structure of cerebral organoids</td> <td>Montpellier Resources Imagerie</td> <td>Centre de Recherche de Biologie cellulaire de Montpellier (MRI-CRBM), CNRS, Univerity of Montpellier</td> <td>https://www.mri.cnrs.fr/en/optical-imaging/our-facilities/mri-crbm.html</td> <td>Ayala-Nunez et al., 2019</td> </tr> <tr> <td>13</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti2</strong></td> <td>2</td> <td>Ιmmunofluorescence imaging of cryosections of mouse hearth myocardium </td> <td>Neuroscience Center Microscopy Core</td> <td>Neuroscience Center, University of North Carolina</td> <td>https://www.med.unc.edu/neuroscience/core-facilities/neuro-microscopy/</td> <td>Aghajanian et al., 2021</td> </tr> <tr> <td>14</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti2</strong></td> <td>2</td> <td>Live-cell imaging of bacterial cells expressing GFP-PopZ</td> <td>Microscopy Resources on the North Quad (MicRoN)</td> <td>Harvard Medical School </td> <td>https://micron.hms.harvard.edu/</td> <td>Lim and Bernhardt 2019; Lim et al., 2019</td> </tr> <tr> <td>15</td> <td><strong>Olympus/Biomedical Imaging Group (customized)</strong></td> <td><strong>TIRF Epifluorescence Structured light Microscope (TESM)/IX71</strong></td> <td>3</td> <td>3D distribution of HIV-1 in the nucleus of human cells</td> <td>Biomedical Imaging Group</td> <td>Program in Molecular Medicine, University of Massachusetts Medical School</td> <td>https://trello.com/b/BQ8zCcQC/tirf-epi-fluorescence-structured-light-microscope</td> <td>Navaroli et al., 2012</td> </tr> <tr> <td>16</td> <td><strong>Olympus/Computer Vision Laboratory (customized)</strong></td> <td><strong>3D BrightField Scanner/IX71</strong></td> <td>3</td> <td>Transmitted light brightfield visualization of swimming spermatocytes</td> <td>Laboratorio Nacional de Microscopia Avanzada (LNMA) and Computer Vision Laboratory of the Institute of Biotechnology</td> <td>Universidad Nacional Autonoma de Mexico (UNAM)</td> <td>https://lnma.unam.mx/wp/</td> <td>Pimentel et al., 2012; Silva-Villalobos et al., 2014</td> </tr> </tbody> </table> <p><strong>Getting started</strong></p> <p>Use these videos to get started with using Micro-Meta App after installation into OMERO and downloading the example data files:</p> <ol> <li><a href="https://vimeo.com/562022222">Video 1</a></li> <li><a href="https://vimeo.com/562022281">Video 2</a></li> </ol> <p><strong>More information</strong></p> <blockquote> <p>For full information on how to use Micro-Meta App please utilize the following resources:</p> <ol> <li>Micro-Meta App <a href="https://wu-bimac.github.io/MicroMetaApp.github.io/">website</a></li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/index.html">Full documentation</a></li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/docs/intro/installation.html">Installation</a> instructions</li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/docs/tutorials/index.html#step-by-step-instructions">Step-by-Step Instructions</a></li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/docs/tutorials/VideoTutorials.html#micro-meta-app-video-tutorials">Tutorial Videos</a></li> </ol> </blockquote> <p><strong>Background</strong></p> <p>If you want to learn more about the importance of <strong>metadata and quality contro</strong>l to ensure full <strong>reproducibility, quality and scientific value</strong> in light microscopy, please take a look at our recent publications describing the development of community-driven light <strong>4DN-BINA-OME Microscopy Metadata</strong> specifications <a href="https://doi.org/10.1038/s41592-021-01327-9">Nature Methods</a> and <a href="https://doi.org/10.1101/2021.04.25.441198">BioRxiv.org</a> and our <a href="https://arxiv.org/abs/1910.11370">overview manuscript</a> entitled <strong>A perspective on Microscopy Metadata: data provenance and quality control</strong>.</p> <p> </p> <p> </p>
Graphs of data for elderly individuals (aged 60 to 120 years) with syphilis in Brazil
<p>A set of data graphs containing informations on elderly people with syphilis in Brazil, aged between 60-120 years with syphilis in Brazil, aged between 60-120 years and contains spreadsheet results of trend analysis of acquired syphilis, by regions of Brazil, in the period 2010-2020, referring to the article entitled "<strong>ACQUIRED SYPHILIS IN OLDER PEOPLE IN BRAZIL FROM 2010-2020".<br><br><br></strong>The dataset used to plot the graphs can be found at: <a href="https://doi.org/10.5281/zenodo.10086131">https://doi.org/10.5281/zenodo.10086131</a></p>
From the collective to the individual: transformation processes at the transition from the 4th to the 3rd millennium BC in the German low mountain zone
<p>Data collected by Clara Drummer, Kiel 2022.</p> <p>Clara Drummer, Vom Kollektiv zum Individuum: Transformationsprozesse am Übergang vom 4. zum 3. Jahrtausend v. Chr. in der Deutschen Mittelgebirgszone. Scales of transformation Bd. 13 (Leiden 2022).https://d-nb.info/1241580332</p> <p>CRC 1266: "Scales of Transformation - Human-Environmental Interaction in Prehistoric and Archaic Societies."<br> "Regional and Local Patterns of 3rd Millennium Transformations of Social and Economic Practic-es in the Central German Mountain Range (D2)" Deutsche Forschungsgemeinschaft (DFG) - Projektnummer 128675135 https://gepris.dfg.de/gepris/projekt/316739879</p> <p>Data for the analyses of the decisive transformation in the Hessian-Westphalian area from the Wartberg society to the Corded Ware groups. The work discusses above all the social aspects of the change. This includes, on the one hand, a more detailed analysis of burial rituals and, on the other hand, the integration of, for example, available aDNA results into the overall analysis.</p>
Ovenbird song recordings from Alberta (Canada) with individual labels and spatial locations, 2015-2016
This dataset includes spatially localized and individually identified Ovenbird songs. We used automated species detection and acoustic localization to localize Ovenbird singing events from microphone arrays in Alberta, Canada (2015-2016). We then hand-annotated songs to individuals based on acoustic characteristics. This dataset includes the manual annotations and annotations from automated individual identification approaches. This data publication pertains to the manuscript [in prep] by Lapp et al on Ovenbird individual identification and provides further details on the study and the individual identification approach.
warmXtrophic: plant community responses to the individual and interactive effects of climate warming and herbivory across multiple years at Kellogg Biological Station Long-Term Ecological Research Sites (KBS LTER), Michigan, USA, and University of Michigan Biological Station (UMBS), Michigan, USA.
Climate change has both direct and indirect effects on ecological communities. Whereas most climate change ecology experiments manipulate abiotic drivers to measure direct effects of climate on species or communities, fewer quantify the indirect effects through biotic interactions, especially over multiple sites and years. In this factorial experiment we manipulate temperature through open-top chambers, and the level of insect herbivory through insecticide. At two early successional field sites separated by 3 degrees of latitude and 3°C of mean annual temperature (University of Michigan Biological Station, Pellston, MI and Kellogg Biological Station, Hickory Corners, MI), 6 replicate 1-m2 plots per treatment were installed in May 2015. 12 plots per site are at ambient temperature, 12 are warmed with year-round non-UV filtering polycarbonate and wood frame construction OTCs for tall-stature plants (Welshofer et al. 2018 MEE). Insecticide reduces insect herbivory in half the plots (Welshofer et al. 2018 Oecologia). Over the course of the experiment, OTCs warmed the plant communities by 1.9°C-3.0°C on average over the growing season. Each year, through 2021, plant traits and community responses were measured at the species level: plant phenology (green-up, flowering, flowering duration, seed set); plant percent cover (aerial % cover of the 1m2 plot); plant traits (specific leaf area, C and N content), herbivory damage to leaves, and plant species biomass (only in 2021). Further methodological details are found within each response variable metadata. This experiment is ongoing and further data package updates are planned. L0 data is available upon request. R scripts can be found here: https://github.com/SpaCE-Lab-MSU/warmXtrophic. The biotic and abiotic community context and relative strengths of direct vs. indirect effects may yield ecological surprises under climate change unless addressed together. Large-scale experiments like this one can improve our ability to unde
Nekton individual data from flume net collections along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
The flume nets were deployed with the purpose of capturing salt marsh nekton. Nekton species were identified to the lowest taxonomic level using species keys. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70μM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2016 and at Clubhead Creek in 2005 and from 2009 till 2016. Years 2017-2020 are enrichment recovery years.
Estimates of nitrogen and phosphorus excretion rates in individual marine and estuarine animals
This dataset contains nitrogen and phosphorus excretion rate, as well as dry biomass, estimates for individual vertebrate and invertebrate animals in marine and estuarine environments. This dataset is a product of an LTER Synthesis Working Group aimed at evaluating the spatiotemporal variability in consumer nutrient dynamics in the wake of global change across eight long-term ecological research projects. These projects include seven long-term ecological research programs (LTER) funded by the National Science Foundation: (1) California Current Ecosystem, (2) Florida Coastal Everglades, (3) Moorea Coral Reef, (4) Northern Gulf of Alaska, (5) Plum Island Ecosystems, (6) Santa Barbara Coastal, and (7) Virginia Coast Reserve LTER projects. Additionally, the dataset includes data from (8) The Partnership for Interdisciplinary Science of Coastal Oceans (PISCO) research program. The temporal coverage of each time series data varies among projects, with the earliest record in 1997 and the most recent in 2023. This data package also includes two folders of R scripts used for data harmonization, identical to those in the LTER Synthesis Working Group: Consumer-Mediated Nutrient Dynamics Project, v2.0.0. You can find the release in GitHub here: https://github.com/lter/lterwg-marine-cnd/releases/tag/v2.0.0
individual_dMRI_fMRI
Open the record for dataset details and reuse information.
Individual Differences in Fluid Reasoning and RAPM-like Problem Solving
Open the record for dataset details and reuse information.
Three-channel surface electrogastrogram (EGG) dataset recorded during fasting and post-prandial states in 20 healthy individuals
<p>This repository contains Electrogastrography signals termed Electrogastrograms (<a href="https://en.wikipedia.org/wiki/Electrogastrogram">EGG</a>) recorded with surface Ag/AgCl electrodes placed over stomach and pre-processed in 20 healthy individuals (8 Females and 12 Males). The method for EGG recording and pre-processing together with subjects' data can be found in <a href="http://doi.org/10.1515/bmt-2017-0218">Popović et al. 2019</a>.</p> <p>For each subject, EGG was recorded from three locations before (fasting state) and after (postprandial state) a commercial oat meal (274 kcal). Two 20 minutes recordings (files) are obtained for each subject - fasting and postprandial.</p> <p>Naming convention for files: <strong>subjects ID _ type of recording (fasting / postprandial)</strong>.</p> <p>Sample rate was set at 2 Hz and <a href="https://en.wikipedia.org/wiki/Analog-to-digital_converter">A/D card</a> had 16 bits resolution. Gain of the amplifier was set at 1000. Overall, file size is 7200 samples (2400 samples for each channel). All signals were filtered with 3<sup>rd</sup> order band-pass <a href="https://en.wikipedia.org/wiki/Butterworth_filter">Butterworth filter</a> with cut-off frequencies of 0.03 Hz and 0.25 Hz. In order to avoid phase distortion, zero-phase digital filtering was performed in <a href="https://www.mathworks.com/products/matlab.html">Matlab</a> R2013a by <a href="https://www.mathworks.com/help/signal/ref/filtfilt.html">filtfilt()</a> function. <a href="https://www.gnu.org/software/octave/">GNU Octave</a> code for analysis of EGG signals with statistical calculations presented in <a href="http://doi.org/10.1515/bmt-2017-0218">Popović et al. 2019</a> is also provided (<a href="https://zenodo.org/record/3878435/files/eggAnalysis.m?download=1">eggAnalysis.m</a>).</p> <p>For convenient test download and appropriate preview, we provided all signals in <a href="https://en.wikipedia.org/wiki/Zip_(file_format)">.zip</a> and sample signal for ID1 in <a href="https://en.wikipedia.org/wiki/Text_file">.txt</a> form.</p> <p><strong>Dataset contents</strong></p> <ol> <li><a href="https://zenodo.org/api/files/7ef74d7b-694f-4047-b9e5-ef530e8b245d/EGG-database.zip?versionId=84315b6b-58da-4655-83f4-8f1d43c3b02c">EGG-database.zip</a>, data files, text format</li> <li><a href="https://zenodo.org/record/3878435/files/eggAnalysis.m?download=1">eggAnalysis.m</a>, GNU Octave code</li> <li><a href="https://zenodo.org/api/files/7ef74d7b-694f-4047-b9e5-ef530e8b245d/README.txt">README.txt</a>, metadata for data files, text format</li> <li><a href="https://zenodo.org/api/files/7ef74d7b-694f-4047-b9e5-ef530e8b245d/ID1_fasting.txt?versionId=47d0bd09-1a87-42f2-a3e5-ef0c4b4a18e2">ID1_fasting.txt</a> and <a href="https://zenodo.org/api/files/7ef74d7b-694f-4047-b9e5-ef530e8b245d/ID1_postprandial.txt?versionId=c8936a32-2896-44d6-bf3d-2ee37887766c">ID1_postprandial.txt</a>, sample data files for subject ID1, text format</li> </ol> <p><strong>Data files contain numerical values with decimal point according to the following structure</strong></p> <ol> <li>column - CH1* (recorded samples from channel 1)</li> <li>column - CH2* (recorded samples from channel 2)</li> <li>column - CH3* (recorded samples from channel 3)</li> </ol> <p>* For exact anatomical locations for EGG channels CH1, CH2, and CH3, please refer to <a href="http://doi.org/10.1515/bmt-2017-0218">Popović et al. 2019</a>.</p> <p>If you find these signals useful for your own research or teaching class, please cite both relevant paper and dataset as:</p> <ol> <li> <p>Popović, N.B., Miljković, N. and Popović, M.B., 2019. Simple gastric motility assessment method with a single-channel electrogastrogram. <em>Biomedical Engineering/Biomedizinische Technik</em>, <em>64</em>(2), pp.177-185, doi: <a href="https://doi.org/10.1515/bmt-2017-0218">10.1515/bmt-2017-0218</a>.</p> </li> <li> <p>Popović, N.B., Miljković, N. and Popović, M.B., 2020. Three-channel surface electrogastrogram (EGG) dataset recorded during fasting and post-prandial states in 20 healthy individuals [Data set]. <em>Zenodo</em>, doi: <a href="https://doi.org/10.5281/zenodo.3730617">10.5281/zenodo.3730617</a>.</p> </li> </ol> <p>DISCLAIMER: The GNU Octave code is provided without any guarantee and it is not intended for medical purposes.</p>
Measuring individual and group flow in collaborative improvisational dance.
<p>Flow is a state of being fully absorbed and experiencing feelings of energised focus, deep involvement, and success in the process of doing things. Flow plays a vital role in innovation and creativity, as all such processes require high intrinsic motivation to break through to a new level of complexity of thoughts and ideas, while the social environment rarely provides sufficient extrinsic rewards to motivate people to extensive creative work. Meanwhile, the vast majority of creative activities have a primarily social character: e.g. theatre making, music, and dancing. Thus, group flow became central in group creativity research.</p> <p>Group flow shares many aspects with individual flow, but inevitably has differences, due to its collaborative nature. In this study, we compare individual and group flow in dance improvisation, to explore the cognitive processes and strategies underlying group improvisation and their relation to flow experience; in particular, those that might support the aspects of group flow that are dependent upon understanding the other group members’ states and intentions.</p> <p>To assess flow experience, we used a video-stimulated recall method, <em>Flow </em>(Łucznik, Loesche, 2017), which allowed participants to mark on the video-recording of the activity those moments when they remembered experiencing flow. We identified group flow as the moments when then the majority of a group declared themselves as being in flow.</p> <p>This dataset consists of the data and analysis used in the 'Measuring individual and group flow in collaborative improvisational dance.' article (in press).</p>
State of Wildfires 2024-25: Regional Summaries of Burned Area, Fire Emissions, and Individual Fire Characteristics for National, Administrative and Biogeographical Regions
<p>This dataset supports the State of Wildfires 2024-25 report under review at <em>Earth System Science Data</em> (Kelley et al., <em>under review)</em>. It is an update of the State of Wildfires 2023-24 report (Jones et al. 2024). The dataset provides annual data and final-year anomalies in burned area (BA), fire carbon (C) emissions, and fire properties (e.g. distributional statistics for fire count, size, rate of growth). Annual data relate to the global fire season defined as March-February (e.g., March 2024-February 2025), aligning with an annuall lull in the global fire calendar (see Jones et al., 2024). The complete methodology is described by Kelley et al. (<em>under review</em>).</p> <h3>Citation</h3> <p>Work utilising our regional summaries should <strong>cite both Kelley et al. (under review) AND the primary reference for the variable(s) of interest</strong> as follows:</p> <ul> <li>Giglio et al. (2018) for MODIS MCD64A1 BA.</li> <li>van der Werf et al. (2017) for GFED4.1s fire C emissions.</li> <li>Kaiser er al. (2012) for GFAS fire C emissions.</li> <li>van der Werf et al. (2017) AND Kaiser er al. (2012) for the average of GFED4.1s and GFAS fire C emissions.</li> <li>Andela et al. (2019) for the Global Fire Atlas.</li> <li>Giglio et al. (2016) for the Fire Radiative Power (FRP) observations.</li> <li>Chuvieco et al. (2024) for FireCCIS311 BA.</li> <li>Giglio et al. (2024) for VIIRS VNP64A1 BA.</li> </ul> <h3>Input Data</h3> <p><strong>Burned Area (BA)</strong></p> <ul> <li>BA data from NASA’s MODIS BA product (MCD64A1) are extended from Giglio et al. (2018) and are available from <a href="https://lpdaac.usgs.gov/products/mcd64a1v061/">Giglio et al. (2021)</a>. <ul> <li>Period: 2002-February 2025</li> <li>Resolution: 500m, daily</li> </ul> </li> <li>BA data from ESA's Climate Change Initiative BA product (FireCCIS311) are extended from Lizundia-Loiola et al. (2022) and are available from <a href="Chuvieco,%20E.;%20Pettinari,%20M.L.;%20Lizundia-Loiola,%20J.;%20Khairoun,%20A.;%20Danne,%20O.;%20Boettcher,%20M.;%20Storm,%20T.%20(2024):%20ESA%20Fire%20Climate%20Change%20Initiative%20(Fire_cci):%20Sentinel-3%20SYN%20Burned%20Area%20Grid%20product,%20version%201.1.%20NERC%20EDS%20Centre%20for%20Environmental%20Data%20Analysis,%2029%20February%202024.%20https://catalogue.ceda.ac.uk/uuid/da8e669a74334c82a56e0b470bc4ef04">Chuvieco et al. (2024)</a>. <ul> <li>Period: 2019-February 2025</li> <li>Resolution: 300m, daily</li> </ul> </li> <li>BA data from NASA’s VIIRS BA product (VNP64A1) are available from <a href="https://lpdaac.usgs.gov/products/vnp64a1v002/">Giglio et al. (2024)</a>. <ul> <li>Period: 2012-February 2025 (only the data after 2019 are used for consistency in the comparisons between MCD64A1, FireCCIS311, and VNP64A1).</li> <li>Resolution: 500m, daily</li> </ul> </li> </ul> <p><strong>Fire Carbon (C) Emissions</strong></p> <ul> <li>GFED4.1s fire C emissions data are extended from van der Werf and are available at <a href="https://globalfiredata.org/">https://globalfiredata.org/</a>. <ul> <li>Period: 2003-February 2025</li> <li>Resolution: 0.25 degree, daily</li> </ul> </li> </ul> <ul> <li>GFAS fire C emissions data are extended from Kaiser et al. (2012) and are available from the <a href="https://confluence.ecmwf.int/display/CKB/CAMS+global+biomass+burning+emissions+based+on+fire+radiative+power+%28GFAS%29%3A+data+documentation">ECMWF Confluence Server</a>. <ul> <li>Period: 2003-February 2025</li> <li>Resolution: 0.1 degree, daily</li> </ul> </li> </ul> <p><strong>Global Fire Atlas (Individual Fire Properties)</strong></p> <ul> <li>Global Fire Atlas data are extended from Andela et al. (2019) and are available from the repository maintained by <a href="https://doi.org/10.5281/zenodo.11400062">Andela and Jones (2025)</a>. <br> <ul> <li>Period: 2002-February 2025</li> <li>Driven by 500m MODIS BA data (collection 6.1)</li> </ul> </li> </ul> <p><strong>Fire Intensities</strong></p> <ul> <li>FRP data are extended from MOD14A1 and MYD14A1 (Giglio et al., 2016) and are available at <a href="https://lpdaac.usgs.gov/products/mod14a1v061/">Giglio and Justice (2021)</a>.<br> <ul> <li>Period: 2002-February 2025</li> <li>Resolution: 1km, daily</li> </ul> </li> </ul> <h3>Regional Analysis</h3> <p>We performed "cookie-cutting" (spatial and temporal masking) of the above input data sets to features in each of the following regional layers (e.g. per country in the "Countries" layer). </p> <p>The statistics derived from cookie-cutting are listed below. Full details in Kelley et al. (2025).</p> <div> <table> <tbody> <tr> <td> <p>Layer</p> </td> <td> <p>Short Form </p> </td> <td> <p>Source</p> </td> </tr> <tr> <td> <p>Biomes</p> </td> <td> <p>NA</p> </td> <td> <p>Olson et al. (2001)</p> </td> </tr> <tr> <td> <p>Ecoregions</p> </td> <td> <p>NA</p> </td> <td> <p>Olson et al. (2001)</p> </td> </tr> <tr> <td> <p>Continents</p> </td> <td> <p>NA</p> </td> <td> <p>ArcGIS Hub (2024)</p> </td> </tr> <tr> <td> <p>Continental Biomes</p> </td> <td> <p>NA</p> </td> <td> <p>See above</p> </td> </tr> <tr> <td> <p>Countries</p> </td> <td> <p>NA</p> </td> <td> <p>EU Eurostat (2020)</p> </td> </tr> <tr> <td> <p>UC Davis Global Administrative Areas (GADM) Level 1</p> </td> <td> <p>GADM-L1</p> </td> <td> <p>UC Davis (2022)</p> <br><br></td> </tr> <tr> <td> <p>Intergovernmental Panel on Climate Change Sixth Assessment Report (AR6) Working Group I (WGI) Reference Regions </p> </td> <td> <p>IPCC AR6 WGI Regions</p> </td> <td> <p>Iturbide et al. (2020)</p> </td> </tr> <tr> <td> <p>Global C Project Regional C Cycle Assessment and Processes (RECCAP2) Reference Regions</p> </td> <td> <p>RECCAP2 Regions</p> </td> <td> <p>Ciais et al. (2022)</p> </td> </tr> <tr> <td> <p>Global Fire Emissions Database (GFED) Basis Regions</p> </td> <td> <p>GFED4.1s Regions</p> </td> <td> <p>van der Werf et al. (2006)</p> </td> </tr> </tbody> </table> </div> <h3> </h3> <h3>Regional Statistics and Anomalies</h3> <ul> <li><strong>Burned Area (BA)</strong> <ul> <li>Calculated regional totals for each fire season.</li> <li>Relative and standardized anomalies from historical data (since 2002).</li> <li>Ranking amongst all recorded fire seasons.</li> <li>Onset, peak, and cessation based on monthly deviations from climatological means.</li> </ul> </li> </ul> <ul> <li><strong>Carbon Emissions</strong> <ul> <li>Calculated regional totals for each fire season.</li> <li>Relative and standardized anomalies from historical data (since 2003).</li> <li>Ranking amongst all recorded fire seasons.</li> <li>Onset, peak, and cessation based on monthly deviations from climatological means.</li> <li>Statistics available for GFAS, GFED, and their mean.</li> </ul> </li> </ul> <ul> <li><strong>Individual Fire Properties</strong> <ul> <li>Based on values of individual fire size and rate of growth ignition from the ignition point vectors of the Global Fire Atlas.</li> <li>Calculated regional count.</li> <li>Calculated regional maxima and 95th percentiles of fire size and rate of growth for each fire season.</li> <li>Relative and standardized anomalies from historical data (since 2002).</li> <li>Ranked anomalies among all recorded fire seasons.</li> </ul> </li> </ul> <ul> <li><strong>Fire Intensity</strong> <ul> <li>Based on active fire observations of FRP, which are pooled within each fire of the Global Fire Atlas.</li> <li>For each fire, the 95th percentile value of all FRP observations is the assigned intensity value (i.e. a "peak fire intensity" omitting any spurious high-end values).</li> <li>Regionally, the peak fire intensity values are averaged across individual fires.</li> <li>Relative and standardized anomalies from historical data (since 2002).</li> <li>Ranked anomalies among all recorded fire seasons.</li> </ul> </li> </ul>
LAUTx - Individual Tree Point Clouds From Austrian Forest Inventory Plots
<p>This dataset contains manually segmented tree point clouds from Personal Laser Scanning (PLS) data, and additionally automatic segmented trees from the same point clouds. The raw point cloud data has been published in LAUT - Terrestrial and Personal laser scanner data from Austrian forest Inventory plots (<a href="https://doi.org/10.5281/zenodo.3698956">https://doi.org/10.5281/zenodo.3698956</a>) and six of those plots were processed for this data. Purpose of this data is to serve as benchmarking for automatic tree segmentation algorithms.</p>
ScienceDex guides
Understand access before you commit
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.