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1,432 results for “data type”
Type-III Dirac fermions in HfxZr1-xTe2 topological semimetal candidate (data)
<p>This dataset contains the raw data files connected to the figures included in the paper "<em>Type-III Dirac fermions in Hf<sub>x</sub>Zr<sub>1-x</sub>Te<sub>2</sub> topological semimetal candidate</em>" by S. Fragkos et al., Journal of Applied Physics <strong>129</strong>, 075104 (2021); <a href="https://doi.org/10.1063/5.0038799">https://doi.org/10.1063/5.0038799</a></p> <p>An Open Access version of the paper can be found here: <a href="https://zenodo.org/record/4562057#.YaDC4NBBxPY">https://zenodo.org/record/4562057#.YaDC4NBBxPY</a></p>
Data files for figures in "Characteristics of the two types of Kuroshio large meanders in the Shikoku Basin"
<p>Processed data files used to create the figures in the paper "Characteristics of the two types of Kuroshio large meanders in the Shikoku Basin".</p>
Combined unsupervised and semi-automated supervised analysis of flow cytometry data reveals cellular fingerprint associated with newly diagnosed pediatric type 1 diabetes
<p>Type 1 diabetes is a chronic autoimmune disease resulting in an immune-mediated loss of pancreatic β-cells; however, an unbiased and reproducible profiling of type 1 diabetes-specific circulating immunome at disease onset has yet to be explored. In this study, fresh whole blood was collected from a pediatric cohort of 107 patients with new-onset type 1 diabetes, 85 relatives of patients with type 1 diabetes with 0-1 islet autoantibodies, 58 patients with celiac disease or autoimmune thyroiditis and 76 healthy controls. Up to 6 mL of blood was collected from each subject into a VACUETTE® TUBE 6 ml ACD-B (Greiner). Fresh whole blood underwent red blood cell lysis, was washed and stained with specific monoclonal antibodies. Fresh whole blood samples were stained with five panels of antibodies labelled as T cells, T&NK cells, B cells, Tregs and DCs/monos encompassing main subsets of T cells, NK cells, B cells, Tregs, DCs and monocytes detected using 26 surface markers and the intracellular marker forkhead box P3 (FoxP3); for the Treg panel, intracellular staining was performed after fixation and permeabilization. Cells were acquired on a BD FACSCanto-II flow cytometer equipped with FACSDiva software (Becton Dickinson, Franklin Lakes, NJ). </p>
2022 Rice Crop-type Data for Western Tanzania
<p>Rice Crop-type data from Katavi Region Tanzania was collected by the NASA Harvest Program at the University of Maryland, the Sokoine University of Agriculture, and Flamingoo Food Limited under the Optimizing Crop Yield Data Collection for Supply Chain Enhancement project (more at: https://cropanalytics.net/optimizing-yield-data/) funded by ENABLING CROP ANALYTICS AT SCALE (ECAAS) is a multi-phase initiative that aims to catalyze the development, availability, and uptake of agricultural ground and remote sensing data and applications in smallholder production systems more at (https://cropanalytics.net/)</p>
Raw data for the article entitled "Facile Solution Synthesis, Processing and Characterization of n- and p-Type Binary and Ternary Bi–Sb Tellurides"
<p>Raw data for the plots in the open access article "Facile Solution Synthesis, Processing and Characterization of n- and p-Type Binary and Ternary Bi–Sb Tellurides"</p>
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
<p>Bulk ATAC-seq data of tumour samples result in an averaged signal across different cell-types (cancer, stromal, vascular and immune cells). We propose a deconvolution framework called EPIC-ATAC (<a href="https://doi.org/10.7554/eLife.94833.1">https://doi.org/10.7554/eLife.94833.1</a>), which relies on newly identified cell-type specific ATAC-Seq marker peaks and reference profiles for all major cancer-relevant cell-types to predict the proportions of each cell-type.</p> <p>To evaluate EPIC-ATAC, we generated a bulk ATAC-Seq dataset from peripheral blood mononuclear cells (PBMCs) samples, from which the number of cells in each cell-type has been estimated using flow cytometry, as ground truth for cell proportions. The data provided in this Zenodo deposit correspond to:</p> <p>- The raw counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts.txt</p> <p>- The normalized (TPM-like) counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts_norm.txt</p> <p>- The cell fractions of each cell type in each sample: PBMC_cell_fractions.txt</p> <p>- The peaks called in each sample using MACS2 (*narrow.peaks): *_normalized.narrowPeak</p> <p>- Bed files listing ATAC-Seq fragments for each sample: *.bed</p> <p>We also evaluated EPIC-ATAC on multiple pseudobulks generated from single-cell ATAC-Seq data. We provide rds files containing the pseudobulks data used in our work for the evaluation of EPIC-ATAC. The rds files are located in the zip file "pseudobulks.zip".</p> <p>The file "additional_data.zip" contains additional files used to generate the reference profiles in EPIC-ATAC and to reproduce the main analyses performed in the manuscript: <a href="https://doi.org/10.7554/eLife.94833.1">https://doi.org/10.7554/eLife.94833.1</a>. These files are required to run the code available on the following GitHub repository: GfellerLab/EPIC-ATAC_manuscript. </p>
Supplementary data for "Heterometallic perovskite-type metal-organic framework with an ammonium cation: structure, phonons, and optical response"
<p>Optimised structures of [NH<sub>4</sub>][Na<sub>0.5</sub>M<sub>0.5</sub>(COOH)<sub>3</sub>] (M = Al, Cr)</p> <p>Phonon output for [NH<sub>4</sub>][Na<sub>0.5</sub>Cr<sub>0.5</sub>(COOH)<sub>3</sub>]</p> <p>Gif of the T’(NH<sub>4</sub><sup>+</sup>) mode (no. 23). The c-axis is the vertical direction.</p> <p>For further information please see the associated publication.</p>
Data set for "State-dependent cell-type-specific membrane potential dynamics and unitary synaptic inputs in awake mice"
<p>Data set for: Pala A, Petersen CCH (2018) State-dependent cell-type-specific membrane potential dynamics and unitary synaptic inputs in awake mice. eLife 7: e35869. DOI: https://doi.org/10.7554/eLife.35869.</p> <p>There are 12 files in this data upload:</p> <p>1. '2018_Pala_eLife.pdf' - this is a pdf version of the online publication: Pala & Petersen (2018).</p> <p>2. 'data.mat' - this is a Matlab data structure, which contains all the data for the publication.</p> <p>3. 'DataViewer.m' - this is a Matlab code for viewing the data.</p> <p>4. 'DataViewer.fig' - this is a Matlab figure file, which is the GUI layout for 'DataViewer.m'.</p> <p>5. 'PalaPetersen_Plot.m' - this is a Matlab code, which plots the figures for Pala & Petersen (2018).</p> <p>6. 'PalaPetersen_Analysis.m' - this is a Matlab code, which analyses the data for the figures of Pala & Petersen (2018).</p> <p>7. 'blankAPs.m' - this is a Matlab code, which blanks action potentials from the membrane potential trace.</p> <p>8. 'lowpassfilt.m' - this is a Matlab code, which low pass filters the LFP.</p> <p>9. 'medianFiltAPs.m' - this is a Matlab code, which median filters the membrane potential trace to remove action potentials.</p> <p>10. 'remTrialswithAPs.m' - this is a Matlab code, which removes trials with action potentials.</p> <p>11. 'retrieveSegDur.m' - this is a Matlab code, which retrieves chunks of the recording of a given length.</p> <p>12. 'suptitleAP.m' - this is a Matlab code, which puts titles above subplots.</p>
Keystroke timing and pressure data captured during touchscreen typing by early Parkinson's disease patients and healthy controls
<p><strong>DATASET</strong></p> <p>The present dataset comprises keystroke timing and pressure data that correspond to short text excerpts typed by early Parkinson’s disease (PD) patients (n=18) and healthy controls (n=15) on a common touchscreen-equipped smartphone (LG Nexus 5X with a screen of 5.2 inches in diagonal and a resolution of 1080 × 1920 pixels, running native Android 7.0). Subjects were asked to transcribe up to 11 short text excerpts, with the initial one being 200 characters-long and common for all subjects, while the rest were 40-115 characters-long, pseudorandomly drawn from the fairy tale 'The Little Prince'. Data were recorded using a custom Android Operating System input method (keyboard), developed for the purposes of the study. Additional details on exepriment design, material and methods can be found in the related research article mentioned below. </p> <p>Data consist of sequences of raw press and release timestamps (in milliseconds), as well as of values of normalized pressure (0.000-1.000) applied to initiate keystrokes, corresponding to the consecutive keys tapped during the transcription of each text excerpt. Data included in the 'Data' folder are organised in sub-folders per subject. Each sub-folder contains a number of .txt files with each one corresponding to a text excerpt typed by the particular subject. Files are named using the format S##_TEX##.txt, with S## denoting the subject's coded ID and TEX## the serial number of the transcribed text excerpt. For all subjects, file S##_TEX01.txt corresponds to the initial and common 200 characters-long text excerpt. Each file contains the sequences of raw key press/release timestamps (Tp#, Tp#) and normalized pressure (NP#), applied to initiate each keystroke, in the following format:</p> <p>{<br> Press, Tp1, Release, Tr1, NP1<br> Press, Tp2, Release, Tr2, NP2<br> .<br> .<br> . <br> Press, Tpn, Release, Trn, NPn<br> }</p> <p>where 1,2,...,n denote the serial index of the key tapped during typing.</p> <p><em>Note:</em> Out of 33 subjects, 32 managed to transcribe 8 to 11 text excerpts, while the remaining one (Subject ID: 16) typed only 5. Ten subjects (Subject IDs: 6, 14, 16, 17, 25, 27, 29, 31, 32, 33) did not manage to type the initial 200 characters-long excerpt in its entirety.</p> <p>The dataset also includes a record, in Microsoft Excel format (Demographics_Clinical_Characteristics.xlsx), of the demographic and clinical characteristics (with respect to PD) of subjects. Entries of the Excel file are linked to subjects' sub-folders and individual keystroke data text files via the coded ID of the subject.</p> <p>Demographic characteristics included:</p> <p>Age; Gender; Education level; Years of smartphone usage; Dominant hand<sup>1</sup></p> <p>Clinical characteristics included:</p> <p>Group (PD, Control); Years from diagnosis; Hoehn-Yahr disease stage; Most affected side<sup>2</sup>; Levodopa Equivalent Daily Dose; UPDRS_III<sup>3</sup> total score; UPDRS_III Item 21 Tremor-Right hand; UPDRS_III Item 21 Tremor-Left hand; UPDRS_III Item 22 Rigidity-Right hand; UPDRS_III Item 22 Rigidity-Left hand; UPDRS_III Item 23 Finger taps-Right hand; UPDRS_III Item 23 Finger taps-Left hand; UPDRS_III Item 31 Body bradykinesia/ Hypokinesia</p> <p><sup>1</sup>Dominant hand: (Relating to handedness) the operant hand generally used for performing fine motor-skills tasks.<br> <sup>2</sup>Most affected body side by Parkinson's disease<br> <sup>3</sup>UPDRS_III: Unified Parkinson's Disease Rating Scale Part III (Motor section)</p> <p> </p> <p><strong>RELATED RESEARCH</strong></p> <p>This dataset was originally used and described in the OPEN ACCESS publication: </p> <p>[1] Iakovakis, D., Hadjidimitriou, S., Charisis, V., Bostantzopoulou, S., Katsarou, Z., & Hadjileontiadis, L. J. (2018). Touchscreen typing-pattern analysis for detecting fine motor skills decline in early-stage Parkinson’s disease. Scientific reports, 8(1), 7663. <a href="http://doi.org/10.1038/s41598-018-25999-0">https://doi.org/10.1038/s41598-018-25999-0</a> </p> <p>All documents and papers that report on research that uses this dataset will acknowledge this by citing the above publication.</p> <p> </p> <p><strong>ETHICS & FUNDING</strong></p> <p>The study during which the present dataset was collected was approved by the Aristotle University of Thessaloniki Bioethics Committee of Medical School (approval no. 359/3.4.17), Thessaloniki, Greece. Informed consent, including permission for third-party access to pseudo-anonymised data, was obtained from all subjects prior to their engagement with the study. The work has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No 690494 - i-PROGNOSIS: Intelligent Parkinson early detection guiding novel supportive interventions (<a href="http://www.i-prognosis.eu">i-prognosis.eu</a>).</p> <p> </p> <p><strong>CORRESPONDANCE</strong></p> <p>Any inquiries regarding this dataset should be adressed to:</p> <p>Mr. Dimitrios Iakovakis (Electrical & Computer Engineer, PhD candidate)</p> <p>Signal Processing & Biomedical Technology Unit<br> Department of Electrical & Computer Engineering<br> Aristotle University of Thessaloniki<br> University Campus, Building D, 6th floor<br> Thessaloniki, Greece, GR54124</p> <p>Tel: +30 2310 996319<br> Fax: +30 2310 996312<br> E-mail: dimiiako12@gmail.com</p> <p> </p> <p><strong>LICENSE</strong></p> <p>This is an open access dataset, licensed under Creative Commons Attribution 4.0 International (<a href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</a>).</p> <p> </p> <p><strong>WARRANTY</strong></p> <p>This dataset comes without any warranty. Administrators of this dataset can not be held accountable for any damage (physical, financial or otherwise) caused by the use of this dataset. </p>
Data and Code for "Cell Type-specific Genome Scans of DNA Methylation Diversity Indicate an Important Role for Transposable Elements"
<p>This is a release of the gitlab repository "meta-methylome" (https://gitlab.com/okartal/meta-methylome.git) that, in addition to the code, also contains the resulting genomic data.</p> <p>Extract the directory on the command line using</p> <pre><code class="language-bash">$ tar -xhzvf meta-methylome.tar.gz</code></pre> <p>to preserve the symbolic links.</p>
Supplemental data for: Mapping lifestyle factors in blood glucose variability in adolescents with Type 1 Diabetes Mellitus- A pilot study
<div> <p>The dataset was used in the paper “Mapping lifestyle factors in blood glucose variability in adolescents with Type 1 Diabetes Mellitus- A pilot study”. The article is currently under review for publication. DOI to be inserted.</p> </div> <div> <p>A data-in-brief article is to be published to give in-depth information about the data collected to improve reproducibility "Dataset for: Lifestyle Factors and Blood Glucose Variability in Adolescents with Type 1 Diabetes Mellitus". DOI to be inserted. </p> <p> </p> <p>The aim of the study was to assess whether adolescents with T1D in Ireland meet current nutrition and physical activity (PA) guidelines and to explore the impact of nutrition and PA on glycaemic variability (GV). The dataset includes continuous glucose monitoring (CGM) data, dietary intake records, and PA metrics, providing a comprehensive view of the participants' glucose levels and associated lifestyle behaviours.</p> </div>
Soil type (World Reference Base) maps of Europe based on Ensemble Machine Learning and multiscale EO data
<h2><strong>Sub-dataset: WRB soil types probabilities (part 1)</strong></h2> <h2>Disclaimer</h2> <p>This is the first release of pan-EU predictions of soil health indicators (the Soil Health Data Cube). Use for testing purposes only. A publication describing methods used has been submitted to PeerJ and is in review. Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Commision. Neither the European Union nor the granting authority can be held responsible for them. The data is provided "as is". AI4SoilHealth project consortium and its suppliers and licensors hereby disclaim all warranties of any kind, express or implied, including, without limitation, the warranties of merchantability, fitness for a particular purpose and non-infringement. Neither AI4SoilHealth project Consortium nor its suppliers and licensors, makes any warranty that the Website will be error free or that access thereto will be continuous or uninterrupted. You understand that you download from, or otherwise obtain content or services through, the Website at your own discretion and risk.</p> <h2>Description</h2> <p>This dataset covers pan-European areas, including Ukraine, the UK, and Turkey. This data cube could be used for applications such as soil property mapping and comprehensive soil health assessment across Europe. The dataset spans four depth ranges and multiple time periods, providing information for studies on soil organic carbon stock and dynamics.</p> <p>This dataset is part of the "Soil type (World Reference Base) map of Europe based on Ensemble Machine Learning and multiscale EO data" dataset. Check the related identifiers section below to access other parts of the dataset.</p> <p>This data set includes:</p> <ul> <li><strong>Soil types classification and relative entropy:</strong><br> This data includes hard classes maps (185 soil type classes) produced by ensemble model and relative entropy (Kullback-Leibler divergence) maps in added information (bit) over a dummy distribution (scaled 1000x). </li> <li><strong>Soil types probabilities (part 1):</strong><br> This data includes 92 averaged probabilities (0-1) maps for classes from <strong>abruptic.acrisols</strong> to <strong>gleyic.arenosols</strong>. The probabilites were scaled 100x (0-100). </li> <li><strong>Soil types probabilities (part 2):</strong><br> This data includes 93 averaged probabilities maps for classes from <strong>gleyic.cambisols</strong> to <strong>vitric.andosols</strong>. The probabilites were scaled 100x (0-100). </li> </ul> <h3>Related identifiers</h3> <ul> <li><a href="https://zenodo.org/records/13838407">WRB soil types classification and relative entropy</a></li> <li><a href="https://zenodo.org/records/13837830">WRB soil types probabilities (part 1)</a></li> <li><a href="https://zenodo.org/records/13837832">WRB soil types probabilities (part 2)</a></li> </ul> <h3>Data Details</h3> <ul> <li><strong>Time period:</strong> long term.</li> <li><strong>Type of data:</strong> Soil types classification and model probabilities.</li> <li><strong>How the data was collected or derived:</strong> The data was derived using ensemble ML models.</li> <li><strong>Statistical methods used:</strong> Relative entropy (Kullback-Leibler divergence)</li> <li><strong>Limitations or exclusions in the data:</strong> The dataset does not include data for Svalbard. </li> <li><strong>Coordinate reference system:</strong> EPSG:3035</li> <li><strong>Bounding box (Xmin, Ymin, Xmax, Ymax):</strong> (900,000, 899,000, 7,401,000, 5,501,000)</li> <li><strong>Spatial resolution:</strong> 30m</li> <li><strong>Image size:</strong> 216,700P x 153,400L</li> <li><strong>File format:</strong> Cloud Optimized Geotiff (COG) format.</li> </ul> <h3>Support</h3> <p>If you discover a bug, artifact, or inconsistency, or if you have a question please raise a GitHub issue: GitLab Issues (tbc)</p> <h3>Name convention</h3> <p>To ensure consistency and ease of use across and within the projects, we follow the standard Ai4SoilHealth and Open-Earth-Monitor file-naming convention. The convention works with 10 fields that describe important properties of the data. In this way users can search files, prepare data analysis etc, without needing to open files. For example, in <strong>soil.types_ai4sh.ensemble_c_30m_s_20220101_20221231_epsg.3035_v20240917.tif</strong>, the fields are:</p> <ol> <li><strong>generic variable name:</strong> soil.types = soil types</li> <li><strong>variable procedure combination:</strong> ai4sh.ensemble.abruptic.acrisols = AI4SH project, ensemble model, abrupitc acrisols soil type.</li> <li><strong>Position in the probability distribution/variable type:</strong> m = mean | c = class | p = probability</li> <li><strong>Spatial support:</strong> 30m</li> <li><strong>Depth reference:</strong> s = surface</li> <li><strong>Time reference begin time:</strong> 20220101 = 2022-01-01</li> <li><strong>Time reference end time:</strong> 20221231 = 2022-12-31</li> <li><strong>Bounding box:</strong> eu = pan-Europe</li> <li><strong>EPSG code:</strong> epsg.3035</li> <li><strong>Version code:</strong> v20240917 = version from 2024-09-17</li> </ol>
Soil type (World Reference Base) maps of Europe based on Ensemble Machine Learning and multiscale EO data
<h2><strong>Sub-dataset: WRB soil types probabilities (part 2)</strong></h2> <h2>Disclaimer</h2> <p>This is the first release of pan-EU predictions of soil health indicators (the Soil Health Data Cube). Use for testing purposes only. A publication describing methods used has been submitted to PeerJ and is in review. Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Commision. Neither the European Union nor the granting authority can be held responsible for them. The data is provided "as is". AI4SoilHealth project consortium and its suppliers and licensors hereby disclaim all warranties of any kind, express or implied, including, without limitation, the warranties of merchantability, fitness for a particular purpose and non-infringement. Neither AI4SoilHealth project Consortium nor its suppliers and licensors, makes any warranty that the Website will be error free or that access thereto will be continuous or uninterrupted. You understand that you download from, or otherwise obtain content or services through, the Website at your own discretion and risk.</p> <h2>Description</h2> <p>This dataset covers pan-European areas, including Ukraine, the UK, and Turkey. This data cube could be used for applications such as soil property mapping and comprehensive soil health assessment across Europe. The dataset spans four depth ranges and multiple time periods, providing information for studies on soil organic carbon stock and dynamics.</p> <p>This dataset is part of the "Soil type (World Reference Base) map of Europe based on Ensemble Machine Learning and multiscale EO data" dataset. Check the related identifiers section below to access other parts of the dataset.</p> <p>This data set includes:</p> <ul> <li><strong>Soil types classification and relative entropy:</strong><br> This data includes hard classes maps (185 soil type classes) produced by ensemble model and relative entropy (Kullback-Leibler divergence) maps in added information (bit) over a dummy distribution (scaled 1000x). </li> <li><strong>Soil types probabilities (part 1):</strong><br> This data includes 92 averaged probabilities (0-1) maps for classes from <strong>abruptic.acrisols</strong> to <strong>gleyic.arenosols</strong>. The probabilites were scaled 100x (0-100). </li> <li><strong>Soil types probabilities (part 2):</strong><br> This data includes 93 averaged probabilities maps for classes from <strong>gleyic.cambisols</strong> to <strong>vitric.andosols</strong>. The probabilites were scaled 100x (0-100). </li> </ul> <h3>Related identifiers</h3> <ul> <li><a href="https://zenodo.org/records/13838407">WRB soil types classification and relative entropy</a></li> <li><a href="https://zenodo.org/records/13837830">WRB soil types probabilities (part 1)</a></li> <li><a href="https://zenodo.org/records/13837832">WRB soil types probabilities (part 2)</a></li> </ul> <h3>Data Details</h3> <ul> <li><strong>Time period:</strong> long term.</li> <li><strong>Type of data:</strong> Soil types classification and model probabilities.</li> <li><strong>How the data was collected or derived:</strong> The data was derived using ensemble ML models.</li> <li><strong>Statistical methods used:</strong> Relative entropy (Kullback-Leibler divergence)</li> <li><strong>Limitations or exclusions in the data:</strong> The dataset does not include data for Svalbard. </li> <li><strong>Coordinate reference system:</strong> EPSG:3035</li> <li><strong>Bounding box (Xmin, Ymin, Xmax, Ymax):</strong> (900,000, 899,000, 7,401,000, 5,501,000)</li> <li><strong>Spatial resolution:</strong> 30m</li> <li><strong>Image size:</strong> 216,700P x 153,400L</li> <li><strong>File format:</strong> Cloud Optimized Geotiff (COG) format.</li> </ul> <h3>Support</h3> <p>If you discover a bug, artifact, or inconsistency, or if you have a question please raise a GitHub issue: GitLab Issues (tbc)</p> <h3>Name convention</h3> <p>To ensure consistency and ease of use across and within the projects, we follow the standard Ai4SoilHealth and Open-Earth-Monitor file-naming convention. The convention works with 10 fields that describe important properties of the data. In this way users can search files, prepare data analysis etc, without needing to open files. For example, in <strong>soil.types_ai4sh.ensemble_c_30m_s_20220101_20221231_epsg.3035_v20240917.tif</strong>, the fields are:</p> <ol> <li><strong>generic variable name:</strong> soil.types = soil types</li> <li><strong>variable procedure combination:</strong> ai4sh.ensemble.abruptic.acrisols = AI4SH project, ensemble model, abrupitc acrisols soil type.</li> <li><strong>Position in the probability distribution/variable type:</strong> m = mean | c = class | p = probability</li> <li><strong>Spatial support:</strong> 30m</li> <li><strong>Depth reference:</strong> s = surface</li> <li><strong>Time reference begin time:</strong> 20220101 = 2022-01-01</li> <li><strong>Time reference end time:</strong> 20221231 = 2022-12-31</li> <li><strong>Bounding box:</strong> eu = pan-Europe</li> <li><strong>EPSG code:</strong> epsg.3035</li> <li><strong>Version code:</strong> v20240917 = version from 2024-09-17</li> </ol>
Soil type (World Reference Base) maps of Europe based on Ensemble Machine Learning and multiscale EO data
<h2><strong>Sub-dataset: WRB soil types classification and relative entropy</strong></h2> <h2>Disclaimer</h2> <p>This is the first release of pan-EU predictions of soil health indicators (the Soil Health Data Cube). Use for testing purposes only. A publication describing methods used has been submitted to PeerJ and is in review. Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Commision. Neither the European Union nor the granting authority can be held responsible for them. The data is provided "as is". AI4SoilHealth project consortium and its suppliers and licensors hereby disclaim all warranties of any kind, express or implied, including, without limitation, the warranties of merchantability, fitness for a particular purpose and non-infringement. Neither AI4SoilHealth project Consortium nor its suppliers and licensors, makes any warranty that the Website will be error free or that access thereto will be continuous or uninterrupted. You understand that you download from, or otherwise obtain content or services through, the Website at your own discretion and risk.</p> <h2>Description</h2> <p>This dataset covers pan-European areas, including Ukraine, the UK, and Turkey. This data cube could be used for applications such as soil property mapping and comprehensive soil health assessment across Europe. The dataset spans four depth ranges and multiple time periods, providing information for studies on soil organic carbon stock and dynamics.</p> <p>This dataset is part of the "Soil type (World Reference Base) map of Europe based on Ensemble Machine Learning and multiscale EO data" dataset. Check the related identifiers section below to access other parts of the dataset.</p> <p>This data set includes:</p> <ul> <li><strong>Soil types classification and relative entropy:</strong><br> This data includes hard classes maps (185 soil type classes) produced by ensemble model and relative entropy (Kullback-Leibler divergence) maps in added information (bit) over a dummy distribution (scaled 1000x). </li> <li><strong>Soil types probabilities (part 1):</strong><br> This data includes 92 averaged probabilities (0-1) maps for classes from <strong>abruptic.acrisols</strong> to <strong>gleyic.arenosols</strong>. The probabilites were scaled 100x (0-100). </li> <li><strong>Soil types probabilities (part 2):</strong><br> This data includes 93 averaged probabilities maps for classes from <strong>gleyic.cambisols</strong> to <strong>vitric.andosols</strong>. The probabilites were scaled 100x (0-100). </li> </ul> <h3>Related identifiers</h3> <ul> <li><a href="https://zenodo.org/records/13838407">WRB soil types classification and relative entropy</a></li> <li><a href="https://zenodo.org/records/13837830">WRB soil types probabilities (part 1)</a></li> <li><a href="https://zenodo.org/records/13837832">WRB soil types probabilities (part 2)</a></li> </ul> <h3>Data Details</h3> <ul> <li><strong>Time period:</strong> long term.</li> <li><strong>Type of data:</strong> Soil types classification and model probabilities.</li> <li><strong>How the data was collected or derived:</strong> The data was derived using ensemble ML models.</li> <li><strong>Statistical methods used:</strong> Relative entropy (Kullback-Leibler divergence)</li> <li><strong>Limitations or exclusions in the data:</strong> The dataset does not include data for Svalbard. </li> <li><strong>Coordinate reference system:</strong> EPSG:3035</li> <li><strong>Bounding box (Xmin, Ymin, Xmax, Ymax):</strong> (900,000, 899,000, 7,401,000, 5,501,000)</li> <li><strong>Spatial resolution:</strong> 30m</li> <li><strong>Image size:</strong> 216,700P x 153,400L</li> <li><strong>File format:</strong> Cloud Optimized Geotiff (COG) format.</li> </ul> <h3>Support</h3> <p>If you discover a bug, artifact, or inconsistency, or if you have a question please raise a GitHub issue: GitLab Issues (tbc)</p> <h3>Name convention</h3> <p>To ensure consistency and ease of use across and within the projects, we follow the standard Ai4SoilHealth and Open-Earth-Monitor file-naming convention. The convention works with 10 fields that describe important properties of the data. In this way users can search files, prepare data analysis etc, without needing to open files. For example, in <strong>soil.types_ai4sh.ensemble_c_30m_s_20220101_20221231_epsg.3035_v20240917.tif</strong>, the fields are:</p> <ol> <li><strong>generic variable name:</strong> soil.types = soil types</li> <li><strong>variable procedure combination:</strong> ai4sh.ensemble.abruptic.acrisols = AI4SH project, ensemble model, abrupitc acrisols soil type.</li> <li><strong>Position in the probability distribution/variable type:</strong> m = mean | c = class | p = probability</li> <li><strong>Spatial support:</strong> 30m</li> <li><strong>Depth reference:</strong> s = surface</li> <li><strong>Time reference begin time:</strong> 20220101 = 2022-01-01</li> <li><strong>Time reference end time:</strong> 20221231 = 2022-12-31</li> <li><strong>Bounding box:</strong> eu = pan-Europe</li> <li><strong>EPSG code:</strong> epsg.3035</li> <li><strong>Version code:</strong> v20240917 = version from 2024-09-17</li> </ol>
Characterizing cell-type spatial relationships across length scales in spatially resolved omics data: data repository
<h1>CRAWDAD</h1> <p>Spatially resolved omics (SRO) technologies enable the identification of cell types while preserving their organization within tissues. Application of such technologies offers the opportunity to delineate cell-type spatial relationships, particularly across different length scales, and enhance our understanding of tissue organization and function. To quantify such multi-scale cell-type spatial relationships, we develop CRAWDAD, Cell-type Relationship Analysis Workflow Done Across Distances, as an open-source R package with source code and additional documentation at https://jef.works/CRAWDAD/.</p> <p>During CRAWDAD's development, we generated simulated datasets and new cell-type annotations for human spleen data, provided here. The external datasets such as the mouse cerebellum, mouse embryo, mouse brain, and human breast cancer data used in the paper can be found in their original publication. See more information in CRAWDAD's data availability statement.</p> <h2>Simulated Datasets</h2> <ul> <li>sim.csv: the simulated data. Used in Figure 1 b-g, Supplementary Figure 1 a-c, and Supplementary Figure 9 a-b.</li> <li>ext_sim.csv: the extended simulated data. Used in Supplementary Figure 1 d-f.</li> <li>null_sim_visualization.csv: the null simulated data. Used to generate the plots Supplementary Figure 2 a-d.</li> <li>null_sim_1.csv - null_sim_10.csv: the 10 null simulated datasets. Used to quantitatively compare CRAWDAD, Squidpy’s co-occurrence implementation, and Ripley’s K Cross.</li> </ul> <h2>HuBMAP Datasets</h2> <ul> <li>pkhl.csv: annotated cell types and positions of sample HBM389.PKHL.936 from donor HBM966.VNKN.965. Used in Figure 5 a-h, Supplementary Figure 5 a, Supplementary Figure 7 a-c, and Supplementary Figure 8 c. doi:10.35079/HBM389.PKHL.936</li> <li>xxcd.csv: annotated cell types and positions of sample HBM772.XXCD.697 from donor HBM966.VNKN.965. Used in Figure 5 d-h, Supplementary Figure 5 a-c, and Supplementary Figure 7 a-c. doi:10.35079/HBM772.XXCD.697</li> <li>fsld.csv: annotated cell types and positions of sample HBM342.FSLD.938 from donor HBM245.ZWNT.288. Used in Figure 5 e-f, h, Supplementary Figure 5 a-c, Supplementary Figure 6 a-b, and Supplementary Figure 7 a-c. doi:10.35079/HBM342.FSLD.938</li> <li>pbvn.csv: annotated cell types and positions of sample HBM825.PBVN.284 from donor HBM245.ZWNT.288. Used in Figure 5 e-f, h, Supplementary Figure 5 a-c, Supplementary Figure 6 a-b, and Supplementary Figure 7 a-c. doi:10.35079/HBM825.PBVN.284</li> <li>ksfb.csv: annotated cell types and positions of sample HBM556.KSFB.592 from donor HBM298.KGNJ.374. Used in Figure 5 e-f, h, Supplementary Figure 5 a-c, Supplementary Figure 6 a-b, and Supplementary Figure 7 a-c. doi:10.35079/HBM556.KSFB.592</li> <li>ngpl.csv: annotated cell types and positions of sample HBM568.NGPL.345 from donor HBM298.KGNJ.374. Used in Figure 5 e-f, h, Supplementary Figure 5 a-c, Supplementary Figure 6 a-b, and Supplementary Figure 7 a-c. doi:10.35079/HBM568.NGPL.345</li> </ul> <h2>External Datasets</h2> <ul> <li>Mouse cerebellum: Used in Figure 2 a-e, Supplementary Figure 3 a-b, Supplementary Figure 4 a-d, and Supplementary Figure 8 a.</li> <li>Mouse embryo: Used in Figure 2 f-j, Supplementary Figure 3 c-d, Supplementary Figure 4 e-h, and Supplementary Figure 8 b.</li> <li>Human breast cancer: Used in Figure 3 a-c.</li> <li>Mouse brains: Used in Figure 4 a-e.</li> </ul>
Data set for "Cell type-specific membrane potential changes in dorsolateral striatum accompanying reward-based sensorimotor learning"
<p>Data set for: Sippy T, Chaimowitz C, Crochet S, Petersen CCH (2021) Cell type-specific membrane potential changes in dorsolateral striatum accompanying reward-based sensorimotor learning. FUNCTION 2: zqab049. https://doi.org/10.1093/function/zqab049</p> <p>There are 2 files in this upload:</p> <p>1. The file named "<strong>2021_Sippy_FUNCTION.pdf</strong>" is the Open Access pdf of the online publication in FUNCTION.</p> <p>2. The file named "<strong>Sippy_data_code.zip</strong>" (~5 GB) is a zipped version of a folder ‘<em>Sippy_data_code</em>’, which contains the data analyzed in the study along with the Matlab codes used to generate the published figures. To access the data and the codes, first unzip the file, add the folder with subfolders to the Matlab path and run the different codes. The current folder must be the main folder (‘<em>Sippy_data_code</em>’). You first need to run ‘AnalyzeDataStructure.m’ and afterwards you can run the other codes. Each code computes and plots the results used in the corresponding figure. Figures are saved in the subfolder ‘Figures’.</p> <p>The subfolder ‘<em>Data</em>’ contains the data structure ‘<em>Data.mat</em>’ to be analyzed, as well as a Matlab file called ‘<em>p_value_colormap.mat</em>’ used to plot the p value color bars in some figures.</p> <p>The subfolder ‘<em>Functions</em>’ contains functions called by the main codes.</p> <p>The subfolder ‘<em>Codes</em>’ contains the following codes:</p> <p><em>‘AnalyzeDataStructure.m’: </em>computes the results and saves them as a new data structure called ‘<em>Analyzed_Data</em>’, in the subfolder ‘<em>Results</em>’.</p> <p><em>‘Figure_1.m’: </em>computes and plots the results for the panels D, E and F of Figure 1.</p> <p><em>‘Figure_2.m’: </em>computes and plots the results for the panels D-G and I-K of Figure 2.</p> <p><em>‘Figure_3.m’: </em>computes and plots the results for the panels A-F of Figure 3.</p> <p><em>‘SuppFigure_2.m’: </em>computes and plots the results for the panels B, D and F of Supplementary Figure 2.</p> <p><em>‘SuppFigure_3.m’: </em>computes and plots the results for the panels A-D of Supplementary Figure 3.</p> <p><em>‘SuppFigure_4.m': </em>computes and plots the results for the panels A-C of Supplementary Figure 4.</p> <p> </p> <p>The data structures contain the following fields:</p> <p><em>‘Mouse_Name’</em>: name of the mouse.</p> <p><em>‘Mouse_RecordingDate’</em>: date of recording (YMD).</p> <p><em>‘Mouse_DateOfBirth’</em>: date of birth of the mouse (YMD).</p> <p><em>‘Mouse_Sex’</em>: sex of the mouse (F or M).</p> <p><em>‘Mouse_Genotype’</em>: genotype of the mouse (strain of the two parents): A2A-Cre = Adora2a-Cre mice; D1-Cre = Drd1a-Cre mice; TdTomato = Lox-Stop-Lox-tdTomato mice; D1TdTomato = Drd1a-tdTomato mice; D2GFP = Drd2-GFP mice.</p> <p><em>‘Mouse_Level’</em>: Training level (NAÏVE or EXPERT).</p> <p><em>‘Cell_Counter’</em>: cell recorded in a given mouse.</p> <p><em>‘Cell_Type’</em>: type of the recorded cell (dSPN, iSPN or TAN).</p> <p><em>‘Cell_TargetedBrainArea’</em>: Brain area targeted (DLS).</p> <p><em>‘Cell_Recovered’</em>: Indicate cells that have been labelled and anatomically recovered (TRUE).</p> <p><em>‘Cell_Coordinates’</em>: Cell coordinates (in mm) relative to bregma (Lateral, AP, Ventro-dorsal)</p> <p><em>‘Cell_Fluorescence’</em>: expression of the genetically encoded fluorophore (FALSE or TRUE) and fluorophore (TdTomato or GFP). A neuron recorded in a Drd1a-tdTomato x Drd2-GFP (cf <em>Mouse_Genotype</em>) with <em>Cell_Fluorescence= {TRUE, TdTomato} is considered as a dSPN </em>(cf <em>Cell_Type</em>).</p> <p><em>‘Sweep_Counter’</em>: number of the sweep recorded for a given neuron (data were acquired across successive continuous sweeps of 30-300 s).</p> <p><em>‘Sweep_Type’</em>: experimental condition during that sweep (characterization = electrophysiological identification of the neurons; behavior = behavioral task).</p> <p><em>‘Sweep_MembranePotential’</em>: membrane potential recording (mV) after cutting of the APs.</p> <p><em>‘Sweep_CurrentInjected’</em>: current injected into the cell (pA).</p> <p><em>‘Sweep_PiezoLick’</em>: voltage signal from the piezo sensor attached to the water spout used to detect licking in behavior sweeps.</p> <p><em>‘Sweep_Trial’</em>: voltage command triggering the onset of each trial (both Catch and Stimulus trials) in behavior sweeps.</p> <p><em>‘Sweep_WhiskerStim’</em>: voltage command triggering the onset of each whisker stimulus in behavior sweeps.</p> <p><em>‘Sweep_Valve’</em>: voltage command triggering the opening of the valve delivering the reward in Hit trials.</p> <p><em>‘Sweep_SamplingRate’</em>: sampling rate (sample.s<sup>-1</sup>) of the recorded signals for each sweep.</p> <p><em>‘Sweep_TimeStamp’</em>: time at the beginning of the recorded sweep (H/min/s).</p> <p><em>‘Sweep_Reward’</em>: voltage command indicating reward availability during the response window following whisker stimulus in behavior sweeps.</p> <p><em>‘Sweep_APThresh’</em>: Threshold (V) used to detect action potentials (AP) during current injection.</p> <p> </p>
New Data Types in Data Management and Archiving [Webinar recording]
<p>New Data Types in Data Management and Archiving workshop focused on the management, archiving and access to new types of data (NDTs), i.e. administrative, transactional and social media data. The program consisted of four presentations tackling various issues related to handling the NDTs in data repositories and sharing these data in the community of social researchers. Martin Vávra (CSDA) was speaking about current capacities among CESSDA SPs for handling NDTs, Brian Kleiner (FORS) was talking about the coordinated approach to handling NDTs CESSDA SPs. Yevhen Voronin (GESIS) gave a presentation about social media data sharing in social research and Pascal Jurgens (Johannes Gutenberg University Mainz) was speaking about Social Science in the Embattled Digital Age: Adversarial Creation, Use and Sharing of New Data Types. The speakers’ presentations were followed by the panel discussion, where audience members were encouraged to participate and brought in their own experiences of archivists, data managers and researchers. The event was a part of the CESSDA training activities.</p> <p>The video is available on the <a href="https://www.youtube.com/watch?v=j13GsqwDO2Q">CESSDA Training YouTube channel.</a></p>
Global Crop Type Validation Data Set for ESA WorldCereal System
<p>This dataset was created by using a new IIASA tool, called “Street Imagery validation” (<a href="https://svweb.cloud.geo-wiki.org/">https://svweb.cloud.geo-wiki.org/</a>) where users could check street level images (e.g., Google Street Level images, Mapillary etc.) and identify the crop type where it is possible. The advantage of this tool is that there are plenty of georeferenced images with dates, going back in time. The disadvantage is that users need to check plenty of images where only few will clearly show cropland fields that are mature enough to be identified. To make the data collection more efficient, we provided our experts with preliminary maps of points in agricultural areas where street level images are available for the year 2021. Then, the experts checked those locations in an opportunistic way. The dataset is completely independent from all the existing maps and the reference datasets.</p> <p>There are 3 main data records uploaded:</p> <ol> <li>sv_croptype_poly.zip – an archive with a shapefile containing all the collected polygons with crop type information. Not all the polygons correspond to actual field boundaries.</li> <li>sv_croptype_validations.csv – a table with crop type observations with centroid coordinates in WGS84</li> <li>sv_worldcereal_validation.csv – a table with a subset of crop type observations used in validation of WorldCereal crop type maps for 2021.</li> </ol> <p>Fields:</p> <ul> <li>"id" – unique observation identifier;</li> <li>"imgSource" – source of imagery used for visual inspection;</li> <li>"imgLoc" – image location;</li> <li>"svImgDate" – image date;</li> <li>"imageIdKey" – image unique identifier;</li> <li>"submitedAt" – date of submission of crop type observation;</li> <li>"cropType" - crop type observation;</li> <li>"irrType" – irrigation type;</li> <li>"x", "y" – centroids of submitted polygons in WGS84.</li> </ul>
Maximum temperature data from thermal safety assessment of type 21700 lithium-ion batteries with NMC, NCA and LFP cathodes by means of Accelerating Rate Calorimetry (ARC)
<p>Data of safety investigation and thermal abuse behavior of commercial type 21700 LIB cells is provided.</p> <p>It has been acquired with Accelerating Rate Calorimetry (ARC), using a Thermal Hazard Technology type ES ARC.</p> <p>Moreover, thermal abuse was done by means of the so-called Heat-Wait-Seek (HWS) test, at different states of charge (SOC) from 0 to 100.</p> <p>Different cathode chemistries are compared (NMC, NCA and LFP), as well as for NCA chemistry, the high energy (HE) and high power (HP) cell design.</p> <p>For each cell, data includes the maximum temperature measured during thermal abuse at the surface on the center of the cell. Additionally, the mean value and standard deviation for each cell type and state of charge is provided.</p> <p>This data is supporting this article in the journal Batteries:</p> <p><a href="https://doi.org/10.3390/batteries9050237">https://doi.org/10.3390/batteries9050237</a></p> <p>Additional supporting material to this article are the exothermal data for thermal abuse, that are published here:</p> <p><a href="https://doi.org/10.5281/zenodo.7707929">https://doi.org/10.5281/zenodo.7707929</a></p> <p> </p>
Bulk RNA-Seq PBMC data of SLE patients and healthy volunteers/ profiling of 29 individual immune cell types as well as PBMCs of healthy donors
<p>This Zenodo project contains processed gene expression data from two publicly available data sets. It includes the gene expression data of peripheral blood mononuclear cells (PBMCs) of systemic lupus erythematosus (SLE) patients as well as healthy volunteers (GSE122459). The project also comprises the bulk RNA-Seq profiling of 29 immune cell types as well as PBMCs of healthy individuals (GSE107011). In both cases, the raw RNA-Seq data was downloaded, aligned and processed. The gene expression data is available in form of a count matrix (GSE107011) or count matrix and transcript-per-million (TPM) values (GSE122459). For the latter, an annotation file is attached. Further details are provided in the information file. </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.