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Data associated with the FLooded Upland Dynamics EXperiment (FLUDEX), conducted at the IISD Experimental Lakes Area 1997 to 2003, investigating reservoir flooding impacts on ecosystems, particularly the release of mercury and greenhouse gases.
The data included in this repository were collected over the course of the FLooded Upland Dynamics Experiment (FLUDEX) conducted at the IISD Experimental Lakes Area (IISD-ELA) from 1997 to 2003. A plethora of data was collected over five years of flooding three upland reservoir sites, in order to examine the relationship between the amount of flooded, and thus decomposed, terrestrial organic matter and the production of methylmercury (MeHg), total mercury (THg), and greenhouse gases (GHGs) in the reservoirs. Findings from this experiment suggest that the amount of organic carbon stored in a flooded site does not directly influence the amount of THg, MeHg, and GHGs produced, but it does affect the persistence of mercury in the reservoir and food web. This version of the repository contains data collected on water chemistry, benthic invertebrate (chironomid) emergence, mercury and methylmercury concentrations in the water and food web, stable isotopes of carbon and nitrogen in emerging insects and zooplankton, and abundance and biomass of zooplankton, phytoplankton, and bacteria. This data package contains only some of the data from the FLUDEX project. IISD-ELA hopes to add more data in subsequent versions.
Langenheim Plant Species Data (1953) and Associated Resurvey Datasets (2014), Gunnison Basin, Colorado, USA
Quantitative plant abundance data were collected from the same 121 sites at two time periods separated by 65 years (1948-1952 and 2012-2014) in the Colorado Rocky Mountains to examine changes in plant community composition. The sites range in elevation from 2600m to 4100m. Approximately 30 sites were sampled from each of four habitat types: sagebrush (2528-3119m, n=27 sites), spruce-fir forest understory (3001-3520m, n=31 sites) , upland herb = montane meadow (3124-3850m, n=30 sites), and alpine (3549-4013m, n=33 sites). The earlier data set was collected by Jean H. Langenheim (1953, 1962) and consisted of counts of species occurrences along approximately 100m paced transects, noting species touching her boot tip every pace (n=100 sampled points per site). The later data set was collected by Stephanie D. Zorio (2015, 2016) consisting of counts of species occurrences every 1m along 300m transects (n=300 sampled points per site). The sites resurveyed by Zorio (2015, Zorio et al. 2016) were placed as close as possible to the original sites based on the written descriptions of Langenheim, but are only approximate. The GPS coordinates given for the resurveyed sites are the centerpoint of 2 perpendicular 150m transects, one across the slope and the other perpendicular to the slope. GPS coordinates for alpine sites along narrow ridges are the start and end points of three 100m transects along the ridge. Georeferenced localities and environmental site data are presented in Table 2: Lang Zorio Env Site Data. Langenheim’s original data were extracted from tables in her thesis (Langenheim 1953). These data omitted species that occurred in fewer than 14% of sites of a given habitat type (constancy). Species that occurred at very low frequencies (<1% per site) were only denoted as an x in the tables. Zorio converted these to frequencies of 0.5 for quantitative comparative purposes. This data set contains 157 species from 27 families across all sites and habitats. Species in seve
Phytoplankton, benthic algae, and associated environmental data from Lake Okeechobee, Florida, USA, August 2023 - November 2023
This data package contains phytoplankton, periphytometer, and environmental data collected from the South Florida Water Management District’s (SFWMD) Aquifer Storage and Recovery (ASR) monitoring sites and the Indian Prairie marsh during the 2023 rainy season. We collected phytoplankton from a surface water grab and benthic algae from artificial substrates (periphytometers) that were placed outside for three weeks. We also collected associated nutrient measurements and environmental data. Collections occurred twice from August to November 2023. Data were collected to better understand how phytoplankton and benthic algae differed in their responses to TN:TP ratios in a hypereutrophic lake known to have spatial differences in limiting nutrients. Data collection for this data package is complete.
Sap-flux and associated environmental data from ash tree monitoring at four urban parks in St. Paul, Minnesota, USA, from May to November of 2023.
We measured the sap flux density of eighteen ash trees (Fraxinus spp.) of varying health and canopy conditions across four urban parks in the City of St. Paul, MN, USA in summer 2023 with a low-cost, compact data logger system we designed in-house. Although many ash trees in the city have either been killed or removed to control the spread of Emerald Ash Borer, chemical insecticide treatments are available for trees that are in early stages infestation. The trees selected for the research have all been receiving insecticide treatment for a few years, but their health and canopy conditions vary. We also have collocated temperature, soil moisture, and precipitation measurements at the same site for summer 2023.
Data associated with the following publication: Developing the Playground Play Value and Usability Audit Tool (PVUA): An Evaluation of Content Validity via an Expert Panel
<p>This data set contains the supporting data associated with the following publication:</p> <p>Morgenthaler, T., Loebach, J., Lynch, H., Pentland, D., Kottorp, A., & Schulze, C. (in press). Developing the Playground Play Value and Usability Audit Tool (PVUA): An Evaluation of Content Validity via an Expert Panel. Children, Youth and Environments. [DOI was not yet available when the data set was published]</p> <p>The data set includes the following files:</p> <ul> <li>read me file [contains all relevant information to understand and reuse this data set] </li> <li>13 additional files [for description, see read me file]</li> </ul> <p>For more information, please contact the lead researcher, Thomas Morgenthaler (tom.morgenthaler@gmail.com or 121101888@umail.ucc.ie)</p> <p> </p>
CryoEM Maps and Associated Data Submitted to the 2015/2016 EMDataBank Map Challenge
<p>Files and metadata associated with the EMDataBank/Unified Data Resource for 3DEM 2015/2016 Map Challenge hosted at challenges.emdatabank.org are deposited.</p> <p>All members of the Scientific Community--at all levels of experience--were invited to participate as Challengers, and/or as Assessors.</p> <p>Seven benchmark raw image datasets were selected for the challenge. Six are selected from recently described single particle structure determinations with image data collected as multi-frame movies; one is based on simulated (in silico) images. All of the raw image datasets are archived at pdbe.org/empiar.</p> <p>27 Challengers created 66 single particle reconstructions from the targets, and then uploaded their results with associated details. 15 of the reconstructions were calculated using the SDSC Gordon supercomputer.</p> <p>This map challenge was one of two community-wide challenges sponsored by EMDataBank in 2015/2016 to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model.</p> <p> </p>
Data of European University Association (EUA) Open Access Survey 2017-2018
<p>This database refers to the data collected by the European University Association (EUA) for its Open Access Survey 2017-2018, which gathered responses from universities and higher education institutions across Europe. The full report published by the association is available at <a href="https://eua.eu/resources/publications/826:2017-2018-eua-open-access-survey-results.html">https://eua.eu/resources/publications/826:2017-2018-eua-open-access-survey-results.html</a>.</p> <p>The data included in this database refers only to those universities and higher education institutions that accepted their data to be available in open access (n=266). All information that could lead to the identification of individual universities and higher education institutions was removed from the database. The following files are available:</p> <ul> <li>Questionnaire</li> <li>Database in the following formats: .sav (IBM SPSS Statistics), .xlsx (Microsoft Excel) and .csv</li> <li>Codebook: includes information on all the variables and their coding.</li> </ul>
Image data of co-localization of IgG and HEV ORF2 protein in a case of hepatitis E-associated kidney disease
<p><span>Image data for a co-localization study of IgG with HEV ORF2 protein in a </span><span>de novo immune complex-mediated glomerulonephritis (GN) case in</span><span> a kidney transplant recipient </span><span>with chronic hepatitis E (Leblond and Helmchen, et al. 2024).<span> </span>Immunofluorescence images are provided for 25 glomeruli at low magnification (20x, 0.227 micron/pixel) and for 16 glomeruli at high magnification (100x, 0.0454 micron/pixel). For each example glomeruli the green channel represents IgG antibody staining with FITC, and the magenta channel represent anti-HEV ORF2 staining using Alexa Fluor 546.</span></p> <p><span>Methods: </span></p> <p><span>Mouse monoclonal antibody clone 1E6 against the HEV ORF2 protein was incubated for 1h at a dilution of 1:125 followed by a mix of Alexa Fluor 546-conjugated goat anti-mouse antibody (Invitrogen BV, A11018) and FITC-conjugated Rabbit anti-Human IgG (Gamma chain, Diagnostic Biosystem, F008) for 1hat a dilution of 1:50. Following automated staining, the slides were hand -washed in distilled H<sub>2</sub>O. Tissue was covered with Vectashield® Antifade Mounting Medium with DAPI (VectorLaboratories, H-1200), covered with a coverslip and stored at 4°C until evaluation.</span></p> <p><span>Immunofluorescence images were acquired with an upright fluorescence microscope (AxioImager.Z2 controlled by ZEN Blue software; 89 North Photofluor LM-75 light source, and Axiocam 503 mono camera; Zeiss, Jena, Germany), equipped with the following objectives: 20x (NA 0.5, Plan-NEOFLUAR), 40x (NA 1.4 oil, Plan-APOCHROMAT), and 100x (NA 1.45 oil, Plan-APOCHROMAT) objectives. This setup provides an excellent spatial resolution (nominally about 200 nm lateral resolution in our study; pixel size was 45.4 nm for 100x objective). High resolution images were taken with the 100x objective using the ApoTome.2 module with deconvolution (grid 5 lp/mm; section thickness 0.7 µm). We used Vysis Abbott Chroma filter sets (Blue: excitation (ex) 335-383 nm, emission (em) 420-470; green: ex 481-507 nm; em 521-551 nm; red: ex 534-556 nm, em 574- 606 nm). Co-localization of IgG and HEV ORF2 staining was quantified using Fiji software (Schindelin et al., 2012) and the JACoP ImageJ plug-in. </span></p>
Environmental and biological data associated with captive-reared Delta Smelt Study, Sacramento-San Joaquin Delta, CA, January-March 2019
The endangered Delta Smelt Hypomesus transpacificus is an osmerid fish endemic to the upper San Francisco Estuary. A captive breeding program for the species led by the Fish Culture and Conservation Laboratory (FCCL), University of California, Davis, began in 1996 to create a refuge population. In order to better understand how captive Delta Smelt would fare in conditions outside of the hatchery, we placed captive-reared fish in enclosures in the Sacramento San-Joaquin Delta, and evaluated their ability to survive, feed, and maintain condition. Fish were acclimated in the hatchery at FCCL, tagged, swabbed, weighed, measured, and transferred to enclosures in the field. There were three types of enclosures (n=2 for each type), varying in mesh size and wrap condition. In January 2019, 384 adult Delta Smelt (243 days post hatch) were transferred to enclosures in Rio Vista. In February 2019, 360 adult Delta Smelt (278 days post hatch) were transferred to enclosures in the Deepwater Shipping Channel. For each deployment, fish remained in enclosures for approximately one month, then were retrieved from enclosures, euthanized, identified, weighed and measured. A subset were also analyzed for diet contents. During the one-month long deployments, cages were checked for biofouling, damage, and dead fish, and water quality measurements and zooplankton samples were collected.
Ecosystem metabolism and associated environmental data for a forested, meadow and reforested reach of White Clay Creek, Chester Co., Pennsylvania; 1971-1975 and 1997-2010
Ecosystem metabolism data for a 3rd-order Piedmont stream were collected during two periods: P1- April 1971 – Dec 1975, and P2- May 1997 – January 2010. Measures were made in a meadow and a forested reach during each period and in a reforested (formerly meadow) reach during the latter years of P2. During P1, measures were made by transferring streambed substrata to chambers in water jackets located on the streambank and measuring dissolved oxygen changes over diel periods. During P2, open system measures of dissolved O2 change were made for several days in warm and cold seasons, with reaeration determined from a propane injection experiment. Metabolism estimates were determined from diel curves of dissolved O2 change. Photosynthetically active radiation (PAR) and chlorophyll were measured concurrent with many measurements in P1 and all measures during P2, and temperature with all measures. Water chemistry parameters (NH4-N, NO3-N, PO4-P, SiO2, Cl, SO4, total alkalinity, pH) associated with each run are included in the data set, as are days since storm of various thresholds. Field procedures, analytical methods and data analyses are detailed in Bott, T.L. & J. D. Newbold, 2023. A multi-year analysis of factors affecting ecosystem metabolism in forested and meadow reaches of a Piedmont Stream. Hydrobiologia
Data associated with the 2019 Freshwater Oil Spill Remediation Study (FOReSt) assessing the use of enhanced Monitored Natural Recovery (eMNR) and shoreline washing agent (SWA) of diluted bitumen spills conducted in shoreline enclosures at the IISD Experimental Lakes Area, ON, Canada from 2019 to 2020
The following package includes data from the 2019 Freshwater Oil spill Remediation Study (FOReSt) at the IISD Experimental Lakes Area studying the use of enhanced monitored natural recovery (eMNR) and shoreline washing agent (SWA) as a secondary remediation method for diluted bitumen spills in freshwater shoreline enclosures. This package includes data tables on polycyclic aromatic compound chemistry in water and sediments, basic water quality, nutrient chemistry, and tritium chemistry monitored in the experimental and reference enclosures, and lake reference sites over the duration of the study. Data included in this package was first collected and used in the paper by Palace et al., titled Polycyclic aromatic compounds in freshwater ecosystems following non-invasive remediation of controlled diluted bitumen spills: The Freshwater Oil Spill Remediation Study (FOReSt) at the Experimental Lakes Area, Canada.
Stable carbon and nitrogen isotope data from Arctic coastscapes associated with coastal invertebrate and fish food webs, 1999-2022
Stable carbon and nitrogen isotope data are commonly used to elucidate food web structure and partition food source importance to consumers. Here, stable isotope data were gathered from across the coastal Arctic to assess how differences in coastal type (i.e., coastscape) and longitudinal region differ across the Arctic. Data were collected between 1999-2022.
Microclimate data associated with green infrastructure in Lancaster Pennsylvania, 2022
Green stormwater infrastructure (GSI) is being increasingly implemented as a stormwater management practice. A key reason for its popularity is the potential for co-benefits, such as heat mitigation, in addition to stormwater management functions. This data is the result of field investigation of heat patterns around GSI in Lancaster, Pennsylvania, providing some of the first ever direct measurements of microclimate and thermal comfort near GSI. During summer 2022, we collected data along transects at 10 rain gardens. Microclimate variables were quantified using a Kestrel 5400 Heat Stress Tracker and were used to calculate metrics that represent heat stress experienced by a human such as wet bulb globe temperature (WBGT) and mean radiant temperature (MRT). Measurements were also made at nearby impervious surface and lawn reference sites.
Summary of tundra pond zooplankton and associated environmental data from the Barrow, AK IBP tundra ponds (1970s & 2010s)
A comparison of historic (1970s) and more recent (2010s) zooplankton and environmental data from Arctic tundra ponds near Utqiaġvik, AK has given us valuable insight into changes in zooplankton communities that have occurred in recent times.
Periphyton and Associated Environmental Data Relative from Samples Collected from the Greater Everglades, Florida, USA from September 2005 to November 2014
This data package contains peripihyton and environmental data collected annually during the wet season between 2005 and 2014 from sites distributed throughout the greater Everglades ecosystem. This project is part of the Comprehensive Everglades Restoration Program's Monitoring and Assessment Plan intended to document baseline variability in periphyton attributes for assessing the effectiveness of restoration projects. A total of 200 primary sampling units (PSU) of 800 m x 800 m are nested in 32 landscape units and each year, random coordinates are 'drawn' within each PSU and one sampleable draw is visited in each. Sampled periphyton is processed for diatoms, slides are prepared, and 500 frustules are enumerated and identified to the lowest possible taxonomic resolution per slide. Taxon abundances are then relativized to the total count. These data accompany environmental, periphyton biomass, and soft algal abundance datasets.
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.
Data Associated with Chemical Cartography with APOGEE: Two-process Parameters and Residual Abundances for 288,789 Stars from Data Release 17
<p>Stellar abundance measurements are subject to systematic errors that induce extra scatter and artificial correlations in elemental abundance patterns. We derive empirical calibration offsets to remove systematic trends with surface gravity log(g) in 17 elemental abundances of 288,789 evolved stars from the SDSS APOGEE survey. We fit these corrected abundances as the sum of a prompt process tracing core-collapse supernovae and a delayed process tracing Type Ia supernovae, thus recasting each star's measurements into the amplitudes A_cc and A_Ia and the element-by-element residuals from this two-parameter fit. Here we present the log(g)-calibrated abundances, fit parameters, process amplitudes, and element-by-element abundance residuals of 288,789 stars (310,427 spectra) in APOGEE DR17 that accompany <a href="https://arxiv.org/abs/2403.08067" target="_blank" rel="noopener">the paper</a>.</p> <p>calibration_values_final.dat contains all derived calibration offsets, including the grids of log(g) calibration offsets and zero-point offsets for two-process model analysis. The first five rows of this catalog are reproduced in Table 2 of the paper.</p> <p>logg_calib_example.ipynb is a Jupyter notebook containing Python code to load calibration_values_final.dat, extract the log(g) calibration offsets for specific element, and apply calibration offsets to 10 sample stars.</p> <p>2process_residual_abund_catalog_final.fits is the catalog of 310,427 APOGEE DR17 spectra (288,789 unique stars) containing calibrated abundances, two-process fit parameters, and abundance residuals. A full listing of columns in this catalog is given in Table 5 of the paper.</p> <p>catalog_examples.ipynb is a Jupyter notebook containing Python code to load 2process_residual_abund_catalog_final.fits, cross match with other catalogs (using AstroNN and the APOGEE DR17 Globular Cluster Value-Added Catalog as examples), and make some example plots utilizing the cross-matched data.</p>
Associated data from: An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae
<p>This dataset includes two custom BED files described in "An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in <em>Saccharomyces cerevisiae</em>" (Ridenour and Donczew, submitted), which were used to define counting windows for processing SLAM-seq data in SLAM-DUNK (version 0.4.3) [1]. The BED files contain all annotated open reading frames (ORFs) in the<em> Saccharomyces cerevisiae</em> genome or the <em>Schizosaccharomyces</em><em> pombe</em> genome and were created using BEDOPS (version 2.4.3) [2]. All ORFs were then extended 250 bp beyond their stop position to capture 3′ untranslated regions (UTRs) using SAMtools (version 1.14) [3] and BEDTools (version 2.30.0) [4]. The reference genome annotations for <em>S. cerevisiae</em> strain S288C (version R64-3-1, RefSeq Assembly GCF_000146045.2) and <em>S. pombe</em> strain 972h- (version ASM294v2, RefSeq Assembly GCF_000002945.1) were retrieved from the NCBI Datasets repository. The <em>S. cerevisiae </em>chromosome names were modified to reflect standard nomenclature (https://www.yeastgenome.org/).</p>
Data associated with the following publication: "Giant thermoelectric response of confined electrolytes with thermally activated charge carrier generation"
<p>Data associated with the following publication: "Giant thermoelectric response of confined electrolytes with thermally activated charge carrier generation" (DOI: <a title="" href="https://doi.org/10.48328/tudatalib-1376">https://doi.org/10.48328/tudatalib-1376</a>)</p>
Data from 'Local Regions Associated With Interdecadal Global Temperature Variability in the Last Millennium Reanalysis and CMIP5 Models'
<p><strong>Abstract from '<em>Local Regions Associated With Interdecadal Global Temperature Variability in the Last Millennium Reanalysis and CMIP5 Models</em>':</strong></p> <p>Despite the importance of interdecadal climate variability, we have a limited understanding of which geographic regions are associated with global temperature variability at these timescales. The instrumental record tends to be too short to develop sample statistics to study interdecadal climate variability, and Coupled Model Intercomparison Project, Phase 5 (CMIP5) climate models tend to disagree about which locations most strongly influence global mean interdecadal temperature variability. Here we use a new paleoclimate data assimilation product, the Last Millennium Reanalysis (LMR), to examine where local variability is associated with global mean temperature variability at interdecadal timescales. The LMR framework uses an ensemble Kalman filter data assimilation approach to combine the latest paleoclimate data and state-of-the-art model data to generate annually resolved field reconstructions of surface temperature, which allow us to explore the timing and dynamics of preinstrumental climate variability in new ways. The LMR consistently shows that the middle- to high-latitude north Pacific and the high-latitude North Atlantic tend to lead global temperature variability on interdecadal timescales. These findings have important implications for understanding the dynamics of low-frequency climate variability in the preindustrial era.</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.