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18,621 results for “development;”
Data for "Gut microbial genes are associated with neurocognition and brain development in healthy children"
<p><strong>Datasets accompanying<em> Gut microbial genes are associated with neurocognition and brain development in healthy children</em>, submitted to Nature Microbiology.</strong></p> <p><strong>Contents:</strong></p> <ul> <li> fecal_samples_master.csv <ul> <li>Metadata for all fecal samples processed by the Klepac-Ceraj Lab at Wellesley College</li> </ul> </li> <li>filemakerdb.csv <ul> <li>Initial export and parsing (long form) of deidentified patient metadata from internal filemnaker pro database</li> </ul> </li> <li>gbm.txt <ul> <li>Info about potentially neuroactive gene sets</li> <li>This was acquired as Supplementary Dataset 1 from <a href="https://doi.org/10.1038/s41564-018-0337-x">https://doi.org/10.1038/s41564-018-0337-x</a></li> </ul> </li> <li>batchXXX_analysis_noknead.tar.gz <ul> <li>Sequencing batches 001-012 (see fecal_samples_master.csv for metadata about samples contained in each batch)</li> <li>Each tarball contains: <ul> <li><strong>cluster.yaml</strong>: configuration file for snakemake pipeline (<a href="https://github.com/Klepac-Ceraj-Lab/snakemake_workflows">repo link</a>)</li> <li><strong>config.yaml</strong>: run configuration for snakemake pipeline</li> <li><strong>.snakemake/</strong>: metadata about snakemake pipeline runs on engaging cluster at MIT</li> <li><strong>output/</strong>: outputs from metaphlan2 and humann2 analysis runs. Note: kneaddata sequence files were not included, but will be uploaded to SRA (link to come)</li> </ul> </li> </ul> </li> <li>All <a href="https://www.uniprot.org/">uniprot</a> searches were performed 2019-09-19 <ul> <li>uniprot-abxr.tsv <ul> <li>search term: "keyword:\"Antibiotic resistance [KW-0046]\" AND reviewed:yes"</li> </ul> </li> <li>uniprot-carbohydrate.tsv <ul> <li>search term: "keyword:\"Carbohydrate metabolism [KW-0119]\" AND reviewed:yes"</li> </ul> </li> <li>uniprot-fa.tsv <ul> <li>search term: (keyword:\"Fatty acid biosynthesis [KW-0275]\" OR keyword:\"Fatty acid metabolism [KW-0276]\") AND reviewed:yes"</li> </ul> </li> </ul> </li> </ul>
Physiological parameters for three farm animal species (cattle, sheep, and swine) as the basis for the development of generic physiologically based kinetic models
<p><strong>IMPORTANT : PLEASE DISREGARD VERSION 1 OF THIS UPLOAD SINCE IT INCLUDES ERRONEOUS INFORMATION.</strong></p> <p>This excel file (DOI: 10.5281/zenodo.3433224) provides physiological parameters and their inter-individual variability (mean, coefficient of variation, sample size) for three farm animal species: cattle (<em>Bos taurus</em>), sheep (<em>Ovis aries</em>), and swine (<em>Sus scrofa domesticus</em>). These physiological parameters were estimated based on the results of extensive literature searches and specific experimental data described in Lautz et al., (2020). This file is associated with R codes (DOI: 10.5281/zenodo.3432796) for generic PBK models, partition coefficient Quantitative Structure Activity Relationship (QSAR) models for each farm animal species and parameterisation of the model.</p> <p>The full data collection and implementation of the models using case studies are described in Lautz et al., 2020 (10.1016/j.toxlet.2019.10.008).</p>
MESINESP: Medical Semantic Indexing in Spanish - Development dataset
<p><em><strong>Please use the <a href="https://doi.org/10.5281/zenodo.4612274">MESINESP2 corpus (the second edition of the shared-task)</a> since it has a higher level of curation, quality and is organized by document type (scientific articles, patents and clinical trials).</strong></em></p> <p> </p> <p> </p> <p><strong>Introduction</strong></p> <p>The Mesinesp (Spanish BioASQ track, see https://temu.bsc.es/mesinesp) development set has a total of 750 records indexed manually by seven experienced medical literature indexers. Indexing is done using <em>DeCS codes, a sort of Spanish equivalent to MeSH terms</em>. Records were distributed in a way that each article was annotated, at least, by two different human indexers.</p> <p>The data annotation process consisted in two steps:</p> <ol> <li>Manual indexing step. DeCS codes were manually assigned to each record following the DeCS manual indexing guidelines.</li> <li>Manual validation and consensus. The joined set of manually indexed DeCS codes generated by both indexers were manually revised and corrections were done.</li> </ol> <p>These annotations were analyzed, resulting in an agreement using the Jaccard index.</p> <p>Records consisted basically in medical literature abstracts and titles from the IBECS and LILACS databases.</p> <p><strong>Zip structure</strong><br> The zip file contains two different development sets:</p> <ul> <li><em>Official development set</em>, which has the union of the annotations, with an agreement of macro = 0.6568 and micro = 0.6819. This set is composed by all the different (unique) DeCS codes that have been added by any annotator for each document; and</li> <li><em>Core-descriptors development set</em>, which has the intersection of the annotations, with an agreement of macro = 1.0 and micro = 1.0. This set is composed of the common DeCS codes that have been added by two or more annotators for each document.</li> </ul> <p><strong>Corpus format</strong></p> <p>Each dataset is a JSON object with one single key named "articles", which contains a list of documents. So, the raw format of the file is one line per document plus two additional lines (the first and the last) to enclose that list of documents and the expected type of data is as follows:</p> <pre><code class="language-json">{"articles":[ {"abstractText":str,"db":str,"decsCodes":list,"id":str,"journal":str,"title":str,"year":int}, ... ]}</code></pre> <p>To clarify, the order of appearance of the fields in each document is as follows (note that this example it is pretty printed for readability purposes):</p> <pre><code class="language-json">{ "articles": [ { "abstractText": "Content of the abstract", "db": "Name of the source database", "decsCodes": [ "code1", "code2", "code3" ], "id": "Id of the document", "journal": "Name of the journal", "title": "Title of the document", "year": 2019 } ] }</code></pre> <p>Note: The fields "db", "journal" and "year" might be null.</p> <p>Copyright (c) 2020 Secretaría de Estado de Digitalización e Inteligencia Artificial</p>
What Skills do IT Companies Look for in New Developers?
<p>This dataset contains the package for replicating the study "What Skills do IT Companies Look for in New Developers?".</p> <p>* high-level-hard-skills.csv: the list of hard skills with their categories;</p> <p>* jobs_complete.csv: This is the main file of this study. It basically contains the information about the jobs analyzed in this study;</p> <p>* script.html: Report which presents the results obtained in this study;</p> <p>* soft-skills-tagged.zip: Zip file with the soft skills annotated in this study;</p>
Tree measurements and summaries of the field plots used to develop Rojo and Montero (1996) yield tables for Pinus sylvestris L. in central Spain
<p>Tree measurements for principal trees and trees marked for thinning and summaries of the Pinus silvestris L. plots measured for the construction of Rojo and Montero (1996) Pinus sylvestris L. yield tables for central Spain. PRM_Functions.R contains R functions implementing parameter recovery methods to transform Rojo and Montero (1996) Pinus sylvestris L. yield tables into a diameter distribution model.</p> <p><strong>Trees.csv: </strong>Comma separated file with headers in the first row. Each record represents a measured tree. Fields:</p> <ul> <li>"PlotID": Identifier of the plot where the tree was measured</li> <li>"Type": Code indicating if the tree was marked for thinning.</li> <li>"ID_tree" Tree_Identifier</li> <li>"DBH1": First Diameter at breast height measurement for the tree.(mm)</li> <li> "DBH2" Second diameter at breast height measurement for the tree. The second measurement was taken in the direction perpendicular to the first measurement. (mm)</li> <li>"DBHmean": Mean of DBH 1 and DBH 2 <strong>and converted to cm</strong> (cm)</li> </ul> <p><strong>Plot_summaries.csv: </strong>Comma separated file with headers in the first row. Data digitized from Annex II of Rojo and Montero (1996). Each record contains different forest attributes of the plot. Fields:</p> <ul> <li>"PlotID": Identifier of the plot where the tree was measured</li> <li>"Age": Age of the plot determined from tree cores (Years)</li> <li>"Ho" Assman Dominant height for the plot (meters)</li> <li>"SiteIndex": Site index for the plot in meters. Site index is defined as the dominant height in meters measured or expected for the plot for an Age of 100 years.</li> <li>"MeanH" Mean tree height (m)</li> <li>"Dg" Quadratic mean diameter (cm)</li> <li>"Do" Dominant diameter. Mean diameter of the 100 largest trees of a hectare (cm)</li> <li>"N" Stand density (trees per hectare)</li> <li>"G" Plot basal area (m<sup>2</sup>/ha)</li> <li>"V" Total plot volume per unit area (m<sup>3</sup>/ha)</li> <li>"DeltaV" Periodic increment of merchantable volume (m<sup>3</sup>/ha)</li> <li>"Bark" Average percentage of total volume that is Bark. (%)</li> </ul> <p><strong>PRM_Functions.R: </strong>R functions to solve parameter recovery systems of equations based on mean and quadratic mean diameter and dominant diameter, quadratic mean diameter and stand density. Details provided as comments.</p> <p><strong>References</strong></p> <p>Rojo Alberto, Montero G (1996) El pino silvestre en la Sierra de Guadarrama: historia y selvicultura de los Pinares de Cercedilla, Navacerrada y Valsain. Ministerio de Agricultura, Pesca y Alimentación, Secretaria General Tecnica, Centro de Publicaciones, Madrid</p>
Developing a deep Learning network to retrieve ocean hydrographic profiles in the North Atlantic from combined satellite and in situ measurements: test datasets.
<p>We provide here the datasets used for the test and assessment of a deep learning algorithm which is presently candidate for the development of a daily 3D ocean product covering the North Atlantic at 1/10° resolution, over the 2010-2018 period, as part of the European Space Agency World Ocean Circulation project (ESA-WOC). The method is based on a stacked Long Short-Term Memory neural network, coupled to a Monte-Carlo dropout approach, and allows to project satellite-derived sea surface temperature, sea surface salinity and absolute dynamic topography data at depth after training with sparse co-located in situ vertical hydrographic profiles (Buongiorno Nardelli, 2020, doi:<a href="https://www.researchgate.net/deref/http%3A%2F%2Fdx.doi.org%2F10.3390%2Frs12193151?_sg%5B0%5D=0xE-347r7Hvb80klJcEo811AhUiXq-twG_E6l4yB-BfIKkVtW-lVLGcO02mTFkUczvozYYI0WCPyUBFR3kzWNGGZKg.ftvLheFrzHIJriO4qW2bdxalvR_TWt3MpwUfvto3EemhRgvDRGwJ9Mdy4Xr0IcGCfICivf4j-VqTgKxVvXRogA">10.3390/rs12193151</a>). </p> <p>The test dataset presented here includes different sets of co-located temperature and salinity vertical profiles: </p> <ul> <li>in situ observations extracted from the quality controlled Argo and CTD profiles produced by Copernicus Marine Environment Monitoring Service CORA 5.2 (<a href="http://marine.copernicus.eu/services-portfolio/access-to-products/">http://marine.copernicus.eu/services-portfolio/access-to-products/</a>, product_id: INSITU_GLO_TS_REP_OBSERVATIONS_013_001_b, doi: 10.17882/46219TS1, Szekely et al., 2019) and interpolated through a spline on a regularly spaced vertical grid (with 10 m intervals);</li> <li>climatological profiles extracted from World Ocean Atlas 2013 optimally interpolated monthly fields (Locarnini et al., 2013; Zweng et al., 2013), interpolated through a spline on a regularly spaced vertical grid (with 10 m intervals), upsized to a 1/10° horizontal grid through a cubic spline and linearly interpolated in time between the central day of each month;</li> <li>synthetic profiles obtained through three different techniques: multivariate EOF reconstruction, a 2 layer feed-forward network (with 1000 units in each hidden layer) and a stacked LSTM network (with 2 LSTM layers and 35 hidden units)</li> </ul> <p><em>References:</em></p> <p>Buongiorno Nardelli, B.: A Deep Learning network to retrieve ocean hydrographic profiles from combined satellite and in situ measurements, 2020, <em>submitted</em>.</p> <p>Locarnini, R. A., Mishonov, A. V., Antonov, J. I., Boyer, T. P., Garcia, H. E., Baranova, O. K., Zweng, M. M., Paver, C. R., Reagan, J. R., Johnson, D. R., Hamilton, M. and Seidov, D.: World Ocean Atlas 2013. Vol. 1: Temperature., S. Levitus, Ed.; A. Mishonov, Tech. Ed.; NOAA Atlas NESDIS, 73(September), 40, doi:10.1182/blood-2011-06-357442, 2013.</p> <p>Szekely, T., Gourrion, J., Pouliquen, S. and Reverdin, G.: The CORA 5.2 dataset for global in situ temperature and salinity measurements: Data description and validation, Ocean Sci., 15(6), 1601–1614, doi:10.5194/os-15-1601-2019, 2019.</p> <p>Zweng, M. M., Reagan, J. R., Antonov, J. I., Mishonov, A. V., Boyer, T. P., Garcia, H. E., Baranova, O. K., Johnson, D. R., Seidov, D. and Bidlle, M. M.: World Ocean Atlas 2013, Volume 2: Salinity, NOAA Atlas NESDIS, 119(1), 227–237, doi:10.1182/blood-2011-06-357442, 2013.</p> <p> </p>
ARMOR and NALMA data corresponding to 2008 storms analyzed in "Examining conditions supporting the development of anomalous charge structures in supercell thunderstorms in the Southeastern United States"
<p>Total lightning and dual-polarization Doppler velocity data are available from the National Aeronautics and Space Administration (NASA) Marshall Space Flight Center (MSFC) North Alabama Lightning Mapping Array (NALMA) and the C-band University of Alabama in Huntsville (UAH) Advanced Radar for Meteorological and Operational Research (ARMOR), respectively, over selected periods on 6 February 2008 and 11 April 2008. NALMA data are provided in American Standard Code for Information Interchange (ASCII) format and ARMOR data are provided in Raw and quality-controlled Universal Format (UF), where quality control methods are described below. </p> <p> </p> <p>The NALMA data are provided in hourly files which include undecimated point location (source-level) data corresponding to the detection of very high frequency (VHF) radiation emitted during the breakdown of lightning (Rison et al., 1999; Thomas et al., 2001). Source locations were reported from active sensors configured in an 11-sensor array distributed throughout North Alabama and South Central Tennessee, the center of which is located at 34.72641, -86.64533 (Koshak et al. 2004). Data files include information on the time that each source was detected (UTC seconds of the day), the latitude, longitude, and altitude of each source’s location (decimal degrees and m, respectively), the reduced chi<sup>2</sup> value associated with data processing (unitless), a station mask indicating which sensors contributed to the resolved location of each source (unitless). These data are provided in a line-by-line format of (f15.9 f10.6 f11.6f 7.1 f5.2 f5.1 4x). The 2008 data files additionally include a header section that provides further information about each sensor in the network and its relative contribution to the dataset. </p> <p> </p> <p>The hourly fine naming conventions are as follows for the February 2008 data:</p> <p>LMA_NA_6.2_125_2008-02-06_10-00-00.dat.gz</p> <p>LMA_NA: LMA file designator corresponding to the NALMA</p> <p>2008-02-06: year (YYYY)-month (MM)-day (DD)</p> <p>10-00-00: UTC time, (HH)-minute (MM)-second (SS)</p> <p> </p> <p>And for the April 2008 data:</p> <p>LYLOUT_080411_180000_3600.dat.gz</p> <p>LYLOUT: LMA file designator</p> <p>080411: date in order of last two digits of year (YY), month (MM), and day (DD)</p> <p>180000: UTC time in order of hour (HH), minute (MM), and second (SS)</p> <p>3600: length of period covered in file in seconds (3600 s = 1 hour)</p> <p> </p> <p>ARMOR data are provided as sets of 14 (14) sampling volumes corresponding to the 6 February 2008 (11 April 2008) periods between 1002 UTC and 1119 UTC (1844 UTC and 1952 UTC). Each RAW and processed UF file contains horizontal reflectivity (dBZ), differential reflectivity (dB), Doppler velocity (m s<sup>-1</sup>), spectrum width (m s<sup>-1</sup>), differential phase (º), and total power (dBZ) data. Horizontal reflectivity and differential reflectivity data were corrected for attenuation and differential attenuation, differential propagation phase (º) was estimated, and specific differential phase (º km<sup>-1</sup>) was calculated during post-processing (Hubbert and Bringi 1995, Bringi et al. 2001).</p> <p> </p> <p>Acknowledgments: </p> <p>NALMA data were collected with support from NASA MSFC Award NNM05AA22A.</p> <p> </p> <p>References:</p> <p>Bringi, V. N., Keenan, T. D., & Chandrasekar, V. (2001). Correcting C-band radar reflectivity and differential reflectivity data for rain attenuation: A self-consistent method with constraints. <em>IEEE Transactions on Geoscience and Remote Sensing</em>, <em>39</em>(9), 1906–1915. https://doi.org/10.1109/36.951081</p> <p>Hubbert, J., and V. N. Bringi, 1995: An iterative filtering technique for the analysis of copolar differential phase and dual-frequency radar measurements. <em>Journal of Atmospheric and Oceanic Technology</em>, <strong>12</strong>, 643–648. </p> <p>Koshak, W. J., Solakiewicz, R. J., Blakeslee, R. J., Goodman, S. J., Christian, H. J., Hall, J. M., … Cecil, D. J. (2004). North Alabama Lightning Mapping Array (LMA): VHF source retrieval algorithm and error analyses. <em>Journal of Atmospheric and Oceanic Technology</em>, <em>21</em>(4), 543–558. https://doi.org/10.1175/1520-0426(2004)021<0543:NALMAL>2.0.CO;2</p> <p>Rison, W., Thomas, R. J., Krehbiel, P. R., Hamlin, T., & Harlin, J. (1999). A GPS-based three-dimensional lightning mapping system: Initial observations in Central New Mexico. <em>Geophysical Research Letters</em>, <em>26</em>(23), 3573–3576.</p> <p>Thomas, R. J., Krehbiel, P. R., Hamlin, T., Harlin, J., & Shown, D. (2001). Observations of VHF source powers radiated by lightning. <em>Geophysical Research Letters</em>, <em>28</em>(1), 143–146. https://doi.org/10.1029/2000GL011464</p> <p> </p>
A video tutorial on CHADA preliminary development and use
<p>This video is intended to give practical guidelines on how to prepare a CHADA case study, based on the guidelines and templates that are already available in this Zenodo community.</p>
Organisation for Economic Co-operation and Development (OECD) data for Antalya (Turkey), Antwerp (Belgium), Cork (Ireland), Thessaloniki (Greece) (source: OECD)
<p>The data have been collected via the official OECD Application Programming Interface (API)<strong> </strong>and<strong> </strong>includes the following indicators:</p> <ul> <li>EmpPlaRes - Employment at place of residence</li> <li>LfPartRa - Labour Force and Participation rate</li> <li>UnemReg - Unemployment in regions </li> <li>RegGdpTL2 - Regional Gross Domestic Product (Large regions TL2)</li> <li>GDPLT3 - Gross Domestic Product (Small regions TL3)</li> <li>RegEmIndu - Regional Employment by industry (ISIC rev 4)</li> <li>RegGVAWorker - Regional GVA per worker</li> <li>RegIncPC - Regional income per capita</li> </ul> <p>Source: https://data.oecd.org/api/</p>
Modeling the metabolic profile of Mytilus edulis reveals molecular signatures linked to gonadal development, sex and environmental site
<p>Metabolomics dataset used in the publication "Modeling the metabolic profile of Mytilus edulis reveals molecular signatures linked to gonadal development, sex and environmental site"</p> <p>Jaanika Kronberg, Jonathan J. Byrne, Jeroen Jansen, Philipp Antczak, Adam Hines, John Bignell, Ioanna Katsiadaki, Mark R. Viant and Francesco Falciani </p> <p>Metabolomics dataset for metabolic bins 1 to 1045 for 376 mussels as used in the publication.</p> <p>Mussel metadata are described in a separate file (spectrum number, sample label, sex, site, species, month, temperature of water, salinity of water, ADG rate, gonadal stage, parasite load)</p> <p>Species 1: Mytilus edulis, species 2: hybrid, species 3: Mytilus galloprovincialis</p>
Developing Digital Image Processing methods to quantify internal and interfacial convection in the Hele-Shaw cell, with applications to the laboratory ice-ocean boundary layer
<p>This dataset provides the video and image files obtained from Schlieren optical experiment 3 performed in the <span>Laboratoire de Glaciologie (GLACIOL)</span> at the Universite de libre Bruxelles. A document detailing the visual data and supporting figures is presented (DataOverview.pdf). </p>
Dataset for "Development of allocentric representations using self-motion information"
<p>The present .csv file contains the raw data from a 2017 data collection. Specifically, children from six to 11 years old were tested with a non-visual spatial orientation task, in which they were required to i) observe animal-shaped landmarks located in each of the 4 angles of the experimental room; ii) be guided by the experimenter along a two-legged segment; iii) indicate the location of the four landmarks.</p>
Anthropogenic emissions of CH4, N2O, F-gases and BC from GAINS, for EU-countries plus CH, NO, UK developed under the EYE-CLIMA project - March 2025 update
<p><span>As part of the EYE-CLIMA project, GAINS emission data for CH<sub>4</sub>, N<sub>2</sub>O, BC and selected F-gases (HFC-125, HFC-134a, HFC-143a, HFC-23, HFC-32 and SF<sub>6</sub></span>) were released for all EU-27 countries plus UK, Switzerland, and Norway for the period 1990 to 2020 (with exception of F-gases, from 2005 only, and BC/CH<sub>4</sub> emissions from agricultural waste burning, from 2000). Results have been documented in EYE-CLIMA deliverable D2.8 (<a href="http://folk.nilu.no/~rthompson/eyeclima_reports/EYECLIMA_D2.8.pdf">http://folk.nilu.no/~rthompson/eyeclima_reports/EYECLIMA_D2.8.pdf</a>), and they are publicly available at the Zenodo repository under <a href="https://doi.org/10.5281/zenodo.11032177">https://doi.org/10.5281/zenodo.11032177</a>. All data is available on a 0.1°x0.1° grid and in monthly resolution. Emissions are attributed to the respective source categories according to GNFR.</p> <p>The motivation of an update resulted from the need to extending the emission data time series to 2023. With underlying statistics and national emission data currently available till 2022 only (the latter submitted to UNFCCC only by December 2024), the historical data series also could only be established for 2022. Here we use the GAINS scenario feature to extrapolate between 2022 historical data and the first scenario point, 2025 which is based on IEA’s Word Energy Outlook 2023 (https://www.iea.org/reports/world-energy-outlook-2023). Obviously, this also means that emission results for 2023 are not any more based on robust statistics but represent an extrapolation.</p> <p>Extrapolation of spatially explicit data is only possible when the spatial resolution conveys a realistic signal. For the sector “agricultural waste burning” (files with “AWB” as sector, see notation below) spatial allocation is based on actual observation from satellites. As such data products on agricultural fires have been made available until 2022 only, no spatial or temporal signal exists for 2023. The time series provided thus has to end in 2022. No recommendation can be given to modellers, other than to either use 2022 also for 2023 (understanding that the pattern will be strikingly different) or to use a five-year average (which will remove a lot of spatial specificity).</p> <p>The updated dataset covers files as follows (internally, all files now carry version number V05):</p> <p>ALL_FLUX_ALL_EUR_MOD_MONTH_19900101_20231231_GAINS_IIASA_V05.csv</p> <p>BC_FLUX_ALL_EUR_MOD_MONTH_19900101_20231231_GAINS_IIASA_V05.nc</p> <p>BC_FLUX_AWB_EUR_MOD_MONTH_20000101_20221231_GAINS_IIASA_V05.nc</p> <p>CH4_FLUX_ALL_EUR_MOD_MONTH_19900101_20231231_GAINS_IIASA_V05.nc</p> <p>CH4_FLUX_AWB_EUR_MOD_MONTH_20000101_20221231_GAINS_IIASA_V05.nc</p> <p>HFC_FLUX_ALL_EUR_MOD_YEAR_20050101_20231231_GAINS_IIASA_V05.nc</p> <p>N2O_FLUX_ALL_EUR_MOD_MONTH_19900101_20231231_GAINS_IIASA_V05.nc</p> <p>SF6_FLUX_ALL_EUR_MOD_YEAR_20050101_20231231_GAINS_IIASA_V05.nc</p> <p>This is version 2.0 of the dataset. It extends from version 1.0 by covering into the year 2023, but also benefits from a number of additional GAINS improvements. Emissions of emitted compounds are provided as kg/m²/s. File names follow the notation developed for the H-Europe project EYE-CLIMA, i.e. species _ variable-type _ sector _ region _ method (MOD=model) _ timestep _ fromTime _ toTime _ model _ institute _ version . filetype.</p> <p>This version is available at <a href="https://doi.org/10.5281/zenodo.15536170">https://doi.org/10.5281/zenodo.15536170</a>. The generic address of the dataset is <a href="https://doi.org/10.5281/zenodo.10886780">https://doi.org/10.5281/zenodo.10886780</a>, resolving to the latest update available at Zenodo. No further updates are planned in EYE-CLIMA, so this version is expected to also reflect the final update within the project.</p> <p>Compared to version 1.0, GAINS benefitted from a number of new developments such as the following:</p> <p>*) Previously, GAINS has been available in five-year timesteps only (with the aim of allowing for scenarios at that resolution). For data version 1.0, a makeshift solution was found to convert into annual data. A recent update now allows, for historic data, to store and retrieve information on an annual basis (from 1990).</p> <p>*) The energy data were obtained from IEA’s world energy balances 2024 (July version, https://www.iea.org/data-and-statistics/data-product/world-energy-balances#documentation), extending into 2022 and extrapolated towards 2025, downscaled from IEA to GAINS sectors and sub-sectors. Additionally, the annual activity of industrial production is estimated using a linear approach, based on five-year timestep data.</p> <p>*) Agricultural statistics were retrieved from Eurostat (and from FAO globally) and extended to 2022, extrapolated towards 2025.</p> <p>*) Interpretation of GAINS data was reconfirmed and updated in consultations with national experts of multiple EU countries. While the process resulted in revised emission projections to be used in the Clean Air Outlook 4 (see <a title="Protected by Check Point: https://environment.ec.europa.eu/topics/air/clean-air-outlook_en" href="https://protect.checkpoint.com/v2/r02/___https:/environment.ec.europa.eu/topics/air/clean-air-outlook_en___.YzJlOmlpYXNhOmM6bzoyYzdiNDRhNDI4Njc3ZjI5MGFjMTU1N2I2OWVmNzM2ZTo3OjE5OTM6ZTFiY2IzMDMxZGViNGE0MjI0ODRmNWQ4NzA3ZDY3Njc4M2U2NzUxNmEwNzQ0ODViNDBhODc1NmNhZmMzY2FlMjpoOkY6Tg"><span lang="EN-GB">https://environment.ec.europa.eu/topics/air/clean-air-outlook_en</span></a><span lang="EN-GB">). While the details of improvements on the individual aspects cannot be disclosed, they are useful to describe historic data most adequately, and have been integrated also in this assessment. That not only leads to changes in absolute emissions for a given year, but also affects trends that now are more plausible and confirmed through the exchange with the national experts.</span></p> <p><span lang="EN-GB">*) Technical adjustments have improved the precision of temporal allocation of emissions and the conversion of grid sizes to actual area.</span></p>
C2D2: An Open-Source, Pan-European, Harmonised Crop Development Database for Use in Regulatory Pesticide Exposure Modelling and Risk Assessment.
<p>There is a regulatory need for crop development dates to assess current default values used within chemical exposure assessments as well as to justify refinements within risk assessments. However, a readily available pan-European crop phenology database covering key FOCUS (FOrum for the Co-ordination of pesticide fate models and their USe) crops and scenarios to meet this need is not currently available. Therefore, we describe the development of a harmonised, pan-European, CropLife Europe Crop Development Database, C2D2, that is fully aligned with this regulatory requirement utilising efficacy trials data generated for regulatory submissions when registering plant protection products under Regulation (EU) 1107/2009. Evaluation of C2D2 against an independent dataset showed good agreement for equivalent time periods, crop growth stages and geographical regions. We illustrate how this database can be used to evaluate existing default crop development dates mandated by regulatory agencies for use within exposure assessments. Despite the large dataset compiled and the geographical coverage of C2D2, not all FOCUSsw/gw scenarios have sufficient data to facilitate comparison, with less significant scenarios, like FOCUSgw Porto, being under-represented. For those scenarios with sufficient data, clear differences between C2D2 and crop development dates assumed in the FOCUS modelling framework (using the AppDate tool) are often indicated over some/many growth stages suggesting that amendment of the existing representation of crop development within the risk assessment process may be required. C2D2 is freely available under a Creative Commons licence to facilitate innovation in exposure science to allow for more accurate and realistic risk assessment leading to enhanced crop and environmental protection.</p>
1,237 Annotated Developer Apologies from GitHub
<p><em><strong>Software Developer Apologies</strong></em></p> <p>This dataset contains 1,237 GitHub comments with apology annotations (apology vs not apology), released as part of the following publication:</p> <ul> <li>Benjamin S. Meyers. <a href="https://scholarworks.rit.edu/theses/11609/">Human Error Assessment in Software Engineering.</a> Rochester Institute of Technology. 2023. </li> </ul> <p><em><strong>Included Files</strong></em></p> <p>The "github_apologies.csv" file contains the full dataset of 1,237 GitHub comments with apology annotations. In total, there are 365 comments containing an apology (872 non apologies). The comments themselves are a subset of those included in <a href="../records/5603093">88.6 Million Developer Comments from GitHub</a>.</p> <p><em><strong>Annotation Details</strong></em></p> <p>Full details are provided in the above publication. We implemented a naive classifier (Precision: 41.7%, Recall: 99.7%, F1: 86.9%, Accuracy: 91.1%) using counts of apology lemmas. 91% of developer comments containing at least one apology lemma matched our manual annotations. Agreement between raters was almost perfect (Cohen's Kappa = 0.94).</p> <p><em><strong>CSV Fields</strong></em></p> <ul> <li><strong>ID</strong>: Unique identifier for the comment.</li> <li><strong>SOURCE</strong>: Whether this comment originates from a commit, issue, or pull request.</li> <li><strong>COMMENT_URL</strong>: The URL linking to the comment.</li> <li><strong>COMMENT_TEXT</strong>: The raw comment text.</li> <li><strong>NUM_APOLOGY_LEMMAS</strong>: The count of apology lemmas present in the comment.</li> <li><strong>CLASSIFIER_LABEL</strong>: The automatically assigned label ("Apology" or "Not Apology").</li> <li><strong>RATER_1_LABEL</strong>: The manually assigned label ("Apology" or "Not Apology") from Rater 1.</li> <li><strong>RATER_2_LABEL</strong>: The manually assigned label ("Apology" or "Not Apology") from Rater 2.</li> <li><strong>AGREED_LABEL</strong>: The agreed upon label ("Apology" or "Not Apology") after Rater 1 and Rater 12 resolved disagreements.</li> </ul> <p><em><strong>Contact</strong></em></p> <p>Please contact Benjamin S. Meyers (<a href="mailto:bsm9339@rit.edu">email</a>) with questions about this data and its collection.</p> <p><em><strong>Acknowledgments</strong></em></p> <p>Collection of this data has been sponsored in part by the National Science Foundation (grant 1922169), by the NSA Science of Security Lablet program (grant H98230-17-D-0080/2018-0438-02), and by a Department of Defense DARPA SBIR program (grant 140D63-19-C-0018).</p>
200 Annotated Developer Human Errors from GitHub
<p><em><strong>Software Engineers' Human Errors</strong></em></p> <p>This dataset contains 200 GitHub comments with manual human error annotations, released as part of the following publication:</p> <ul> <li>Benjamin S. Meyers. <a href="https://scholarworks.rit.edu/theses/11609/">Human Error Assessment in Software Engineering.</a> Rochester Institute of Technology. 2023.</li> </ul> <p><em><strong>Included Files</strong></em></p> <p>The "developer_human_errors.csv" file contains the full dataset of 200 software defect descriptions annotated with human error types (slips, lapses, mistakes) and T.H.E.S.E. categories.</p> <p><em><strong>CSV Fields</strong></em></p> <ul> <li><strong>ID</strong>: Unique identifier for the comment.</li> <li><strong>SOURCE</strong>: Whether this comment originates from a commit, issue, or pull request.</li> <li><strong>COMMENT_URL</strong>: The URL linking to the comment.</li> <li><strong>COMMENT_TEXT</strong>: The raw comment text.</li> <li><strong>HUMAN_ERROR_TYPE</strong>: Whether the software defect described is a slip, lapse, or mistake.</li> <li><strong>THESE_V4_ID</strong>: Manually assigned T.H.E.S.E. category with labels corresponding to Version 4 of T.H.E.S.E.</li> <li><strong>THESE_NAME</strong>: Name corresponding to manually assigned T.H.E.S.E. category.</li> </ul> <p><em><strong>Annotation Details</strong></em></p> <p>Human error types span slips, lapses, and mistakes from James Reason's Generic Error Modelling System (GEMS):</p> <ul> <li><strong>Slips</strong>: Failures of attention.</li> <li><strong>Lapses</strong>: Failures of memory.</li> <li><strong>Mistakes</strong>: Failures of planning.</li> </ul> <p>T.H.E.S.E. categories are summarized below:</p> <ul> <li>S01: Typos & Misspellings</li> <li>S02: Syntax Errors</li> <li>S03: Overlooking documented Information</li> <li>S04: Multitasking Errors</li> <li>S05: Hardware Interaction Errors</li> <li>S06: Overlooking Proposed Code Changes</li> <li>S07: Overlooking Existing Functionality</li> <li>S08: General Attentional Failure</li> <li>L01: Forgetting to Finish a Development Task</li> <li>L02: Forgetting to Fix a Defect</li> <li>L03: Forgetting to Remove Development Artifacts</li> <li>L04: Working with Outdated Source Code</li> <li>L05: Forgetting an Import Statement</li> <li>L06: Forgetting to Save Work</li> <li>L07: Forgetting Previous Development Discussion</li> <li>L08: General Memory Failure</li> <li>M01: Code Logic Errors</li> <li>M02: Incomplete Domain Knowledge</li> <li>M03: Wrong Assumption Errors</li> <li>M04: Internal Communication Errors</li> <li>M05: External Communication Errors</li> <li>M06: Solution Choice Errors</li> <li>M07: Time Management Errors</li> <li>M08: Inadequate Testing</li> <li>M09: Incorrect/Insufficient Configuration</li> <li>M10: Code Complexity Errors</li> <li>M11: Internationalization/String Encoding Errors</li> <li>M12: Inadequate Experience Errors</li> <li>M13: Insufficient Tooling Access Errors</li> <li>M14: Workflow Order Errors</li> <li>M15: General Planning Failure</li> </ul> <p><em><strong>Contact</strong></em></p> <p>Please contact Benjamin S. Meyers (<a href="mailto:bsm9339@rit.edu">email</a>) with questions about this data and its collection.</p> <p><em><strong>Acknowledgments</strong></em></p> <p>Collection of this data has been sponsored in part by the National Science Foundation (grant 1922169), by the NSA Science of Security Lablet program (grant H98230-17-D-0080/2018-0438-02), and by a Department of Defense DARPA SBIR program (grant 140D63-19-C-0018).</p>
Developing Learning Paths - The Learning Paths Protocol
<p>Learning Paths (LPs) are pathways that guide learners through a set of learning courses or materials to be undertaken progressively to acquire the desired knowledge and skills on a subject of interest. In this video, we explain how to develop learning paths step-by-step using the Learning Paths protocol. </p>
Data: "Using butterfly survey data to model habitat associations in urban developments", JEJ Cooper et al., (2023)
<p>This data package has been used to examine the responses of UK butterfly species </p> <p>to different features of the urban environment. 'JC_WCBSmodel.Rdata' presents the</p> <p>butterfly abundance data, and supporting information about </p> <p>species and sites. This data can be fed through the script '04_model_builder.R', to </p> <p>produce the models reported in the research article. '00_functions.R' is a script </p> <p>containing functions which support the modelling process, which is loaded as part of </p> <p>the 04_model_builder script. </p> <p> </p> <p>Summaries of the resulting models are an output of that script - </p> <p>'Butterfly_GAM_Outputs.xlsx'. These are represented graphically in the manuscript, </p> <p>using scripts '06_01_Map'.R:'06_03_Cross_Validation'. '06_04_Model_Metric.R' </p> <p>is a further summary of the .xlsx file, found in the Supplementary Materials. </p> <p>'06_05_graphic_4_twitter.R' produces a condensed version of the figure resulting </p> <p>from the script '06_02_Metric_Summary.R'</p> <p> </p> <p>Dataset descriptions are found in the attached readme.txt</p> <p>........................................................................................</p> <p>We would also greatly appreciate if you could fill out <a href="https://forms.gle/DCc58VXpdmqnTmTk8" target="_blank" rel="noopener">this very short form</a> to tell us how you intend to use these data. Thanks in advance!</p>
Analyzing marine biofilms developed on carbon nanotube-modified surfaces by 3D OCT approach
<p>Glass, epoxy resin, and carbon nanotubes (CNT) composite were analyzed regarding wettability by water contact angle measurement, and roughness by atomic force microscopy. Cyanobacterial biofilms formed by Nodosilinea cf. nodulosa LEGE 10377 were developed on these surfaces for seven weeks and under controlled hydrodynamic conditions. Biofilm wet weight and structural parameters such as biofilm thickness, contour coefficient, biovolume, porosity, and average size of non-connected pores obtained from Optical Coherence Tomography (OCT) were assessed.</p>
Development of an Amine Transaminase-Lipase Cascade for Chiral Amide Synthesis under Flow Conditions
<p>The use of multienzymatic systems has gained increasing attention as a method of choice for complex (asymmetric) syntheses. Incompatibilities between substrates, reagents and/or enzymes in one-pot batch conditions can hamper the applicability of a pursued cascade, so the use of flow systems provide useful synthetic solutions. The implementation of immobilised enzymes in continuous flow reactors allows the compartmentalisation and segregation of the enzymes in separate reactors, leading to otherwise disfavoured reaction cascades. Here, an amine transaminase and a lipase have been immobilised on polymer-coated controlled porosity glass carrier materials and studied for the first time together in the transamination of a prochiral ketone followed by acylation of the corresponding chiral amine in flow mode, two incompatible transformations under batch. Thus, the preparation of (<em>R</em>)-<em>N</em>-(1-phenoxypropan-2-yl)acetamide was accomplished after optimisation of the reaction conditions.</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.