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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>
ADDRESSING TAX COMPLIANCE ISSUES FOR LOAN-BASED PAYMENT TYPES: DEVELOPMENT OF THE TAX BUFFER MECHANISM AND ITS USE IN THE FINTECH INDUSTRY
<p>In the modern world of the fintech industry, tax changes are one of the key problems, especially with fixed loans. This study examines the Tax Buffer mechanism, designed to effectively manage tax obligations that vary depending on the jurisdiction and stages of delivery of goods. The main task of the mechanism is to automatically recalculate taxes to minimize the risk of errors and reduce the burden on the accounting and legal departments of the company. The implementation of this solution allows you to reduce the number of manual operations, reduce transaction costs and improve the customer experience by eliminating the need to notify users of every change in the amount of taxes. The results of the implementation of the mechanism have shown its high efficiency: a significant reduction in the number of errors and financial disputes, as well as an increase in operational efficiency. The Tax Buffer mechanism is an important innovation that helps to increase the resilience of fintech companies to changes in tax legislation.</p>
Usability Evaluation of the Agriculture Product Types Ontology (APTO)
<p><strong>Recommended citation</strong>:<br><br>Soares, F. M., Saraiva, A. M., Pires, L. F., Drucker, D. P., Braghetto, K. R., Santos, L. O. B. D. S., Moreira, D. D. A., Corrêa, F. E., & Delbem, A. C. B. (2025). A novel ux-based approach for ontology evaluation: Applying tree testing to the agricultural product types ontology. <em>IEEE Access</em>, 13, <a href="https://doi.org/10.1109/ACCESS.2025.3595447">https://doi.org/10.1109/ACCESS.2025.3595447</a><br><br>In evaluating the APTO ontology, we selected tree testing as the primary UX measuring protocol. We believe tree testing is particularly suitable for ontology evaluation as it combines various metrics, such as time on task and task success, to assess how users navigate and understand a hierarchy of concepts. This method allows us to trace user paths through the ontology's structure, identifying which aspects of the modeling may be confusing or inaccurate from the user's perspective. By analyzing these user interactions, we can gain valuable insights into how the ontology's design impacts usability, ultimately guiding improvements to better align with user needs.<br><br>Update in this version: images of pietrees.<br><br><br></p>
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>
Assembly of enterohemorrhagic Escherichia coli type IV pilin PpdD and its variants
<p>Assembly of the EHEC major type IV pilin PpdD was analyzed in a reconstituted TP assembly system described in LunaRico et al. Mol Microbiol. 2019 Mar;111(3):732-749. doi: 10.1111/mmi.14188. Bacteria of strain BW25113 F'tet harboring plasmids pMS41 and pCHAP8565 (or its variants) were grown for 2 days at 30°C on M9 plates containing 0.5% glycerol, amplicillin (100 ug/ml) chloramphenicol (25 ug/ml) and 1 mM IPTG.</p> <p>Bacteria were collected and fractionated as described in Luna Rico et al Methods Mol Biol. 2018;1764:291-305. doi: 10.1007/978-1-4939-7759-8_18. Cell and sheared fractions were analysed by electrophoresis on 10 % Tris-Tricin gels, transferred on nitrocellulose and probed with anti-MalE-PpdD polyclonal antibodies. The fluorescence signal was developed with ECL2 (Thermo) and recorded with Typhoon FLA9000 imager (GE).</p> <p>The signal was quantified using ImageJ. The fractions of PpdD assembled into pili were quantified and analysed using Prism9.</p> <p>The images uploaded here are the raw data used to produce the Fig. 4B of the article Karami et al., Structure, 2021.</p>
A database solutions for the type two assembly line balancing problems
<p> Assembly Line Balancing Problems have a significant impact on performance of manufacturing systems, specially for the cases of mass production. These problems are widely cited and treated in the literature. </p> <p>One from the most important variants of those problems is the “Task Restrictions Assembly Line Balancing Problem” of type 2. For this problem, a set of tasks need to be affected to a predefined number of stations m from the way that minimises the cycle time and respects a set of constraints related to precedence and compatibility between tasks (Triki et al., 2016).</p> <p>For this variant we suggest an innovative speed and effective approach based on the hybridisation of two powerful tools: the ant colony optimisation and the genetic algorithm. The effectiveness of this approach is evaluated through a set of instances collected from the literature (Thomas, 1990; Triki et al., 2016) .</p> <p>This document presents the best generated solutions for those problems. </p> <p> </p> <p> </p>
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>
TF-Marker: A comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human.
<p>Here, we developed the TF-Marker database (TF-Marker, http://bio.liclab.net/TF-Marker/) which is committed to a comprehensive manual curation of TFs and related markers with experimental evidence in specific cell and tissue types in human. Currently, through reviewing <strong>2,091</strong> published literature, we have manually classified TFs and related markers into five types according to their functions: 1) <strong>TF</strong>: TFs, which regulate the expression of markers; 2) <strong>T Marker</strong>: markers, which are regulated by TFs (TF and T Marker pairs can identify cell types more specifically); 3) <strong>I Marker</strong>: markers, which influence the activity of TFs (I Markers can also influence the development of specific cells and tissues); 4) <strong>TFMarker</strong>: TFs, which play roles as markers (TFMarkers are cell/tissue-specific TFs used as cell markers in biology experiments); and 5) <strong>TF Pmarker</strong>: TFs, which play roles as potential markers. By curating thousands of published literature, <strong>5,905</strong> entries including <strong>1,316</strong> TFs, <strong>1,092</strong> T Markers, <strong>473</strong> I Markers, <strong>1,600</strong> TFMarkers and <strong>1,424</strong> TF Pmarkers, were annotated in <strong>383</strong> cell types and <strong>95</strong> tissue types in human. Moreover, TF-Marker divided markers into disease markers and tissue/cell-specific markers. TF-Marker is an elaborate database, which provides TFs and related markers supported by experimental evidence. We believe TF-Marker will provide strong support for research into cell/tissue-specific TFs and related markers.</p>
Neurometabolic changes in a rat pup model of type C HE - 1H MRS dataset (hippocampus)
<p>1H MRS in hippocampus was used to study longitudinally the effect of chronic liver disease (bile duct ligated rat model) in the brain (type C hepatic encephalopathy) of animals having developed disease a post natal day 15 (p15) corresponding to ~4 months old human brain. The dataset contains MR spectra and LCModel Quanifications from 7 bile duct ligated and 8 control animals at week 2, 4 and 6 after surgery.</p> <p>Please cite the following manuscript if you are using these data</p> <p><a href="https://pubmed.ncbi.nlm.nih.gov/37148431/">Neurometabolic changes in a rat pup model of type C hepatic encephalopathy depend on age at liver disease onset - PubMed (nih.gov)</a></p>
The Vibrio Type III Secretion System 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins
<p>Supplementary Dataset for the work entitled "The Vibrio Type III Secretion System 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins".</p> <p>This dataset includes files for the T3SS2 reconstructed phylogenetic tree (Newick tree and fasta file), hierarchical clustering data analysis file from MORPHEUS, Table S1 with genome accession numbers, and all the data of the absence/presence of T3SS2-related components, Table S2 with the prediction of novel effector proteins.</p>
Biomechanical Study of the Eye with Keratoconus-Type Corneal Ectasia Using a 3D Geometric Model
<p>The aim is to analyze the effect of an increment of intraocular pressure applied to eyes with different severities of keratoconus disease. Finite element models of normal, keratoconus, and keratoglobus eyes were built. The load condition was equal, but the material was different. Besides, data about corneal curvature and thickness was contrasted too.</p>
Spatiotemporal dynamics in freshwater amphipod assemblages are associated with surrounding terrestrial land use type - Dataset
<p>Biological assemblages are the result of dynamic processes that have explicit temporal and spatial dimensions. While biodiversity patterns can be directly inferred from the structure of these assemblages, an assessment of changes through time and space is needed to understand how organisms initially assembled and how they are responding to local environmental and biotic factors. Small freshwater streams are particularly affected by contemporary anthropogenic activities and biological invasions, yet are commonly less studied, as studies often focus on lakes and large streams. Here, we conducted a spatially explicit analysis of keystone shredder assemblages across eight years in twelve replicated small tributary streams. In each stream, we monitored multiple sites per km stream length. By assessing temporal beta diversity dynamics, defined by the gain or loss of species or abundance-per-species at individual sites, we show that changes in amphipod assemblages occur within the context of the surrounding terrestrial matrix and reflect recent amphipod colonization history. While amphipod composition was mostly constant in streams located in forested catchments, streams embedded in catchments with more extensive agricultural land use displayed more pronounced temporal changes, either driven by colonization of unoccupied upstream locations, or by more pronounced but undirected fluctuations in gains and losses of species or abundance-per-species. Our study thus suggests that agricultural landscapes might destabilize aquatic amphipod assemblages, causing higher temporal changes in community structures, and highlighting the vulnerability of aquatic ecosystems to terrestrial land use drivers.</p>
Mapping ecosystem types and land cover types in the Seychelles granitic islands, using Earth Engine and Sentinel-2
<p>We share here maps produced using Earth Engine: https://code.earthengine.google.com/?accept_repo=users/bsenterre/gis</p> <p>The maps include a land cover classification based on Sentinel-2, at 10m resolution, using an Object-Based Image Analysis approach, for the Seychelles granitic islands. Based on the land cover, landform (modeled using TauDEM), altitude and expert knowledge, we then derived a model of ecosystem types, with 3 maps: current distribution, potential distribution and prehuman distribution.</p> <p>A report exists (18th May 2022) that describes in detail the methodology, and it is being used for the preparation of a publication. The maps uploaded here are in raster format (geotif), crs=4326, and are accompanied by QGIS legend files (.qml), so they should load in QGIS with their legend automatically.</p>
Cessation of anti-diabetic medications by 'Daily 2-Only Meals-and- Exercise' lifestyle modification and remission of Type-2 Diabetes Mellitus
<p>This is the dataset describing details of the patient's age, gender, weight, waist circumference, HBA1C levels and Fasting Insulin levels from the date of enrolment in the study and subsequent changes at monthly intervals. </p>
Graph 4: Publication Types for Heiner Müller's Writings 1978-1988
<p>Graph 4 shows the publication types that Heiner Müller used to publish his writing in the years from 1978-1988.</p>
Graph 2: Publication Type and Venue of Heiner Müller's Writings
<p>This graph shows the different publication types and publication venues that Heiner Müller used to publish his writings (essays, articles, speeches, etc.) from 1968 until 1998.</p>
Graph 3: Publication Types for Heiner Müller's Writings 1967–1977
<p>Graph 3 shows the publication types that Heiner Müller used to publish his writing in the years from 1967–1977.</p>
Graph 5: Publication Types for Heiner Müller's Writings 1989-1998.
<p>Graph 5 shows the publication types that Heiner Müller used to publish his writing in the years from 1989-1998.</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.