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Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling: Datasets.
<p>Datasets related to the publication [1].<br> Including:</p> <ul> <li>KRAS G12X mutations derived from COSMIC v.79 [http://cancer.sanger.ac.uk/cosmic/] (KRAS_G12X_mut_COSMICv79..xlsx)</li> <li>RMSFs (300-2000ns) of GDP-systems (300_2000rmsf_GDP_systems_RAW_AVG_SE.xlsx)</li> <li>RMSFs (300-2000ns) of GTP-systems (300_2000RMSF_GTP_systems_RAW_AVG_SE.xlsx)</li> <li>PyInteraph analysis data for salt-bridges and hydrophobic clusters (.dat files for each system in the PyInteraph_data.zip-file)</li> <li>Backbone trajectories for each system (residues 4-164; frames for every 1ns). Last number (e.g. _1) refers to the replica of the simulated system.</li> <li>backbone_4-164.gro/.pdb/.tpr -files (resid 4-164) </li> </ul> <p><br> [1] Pantsar T et al. Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling. <em>PLoS Comput Biol Submitted</em> (2018)</p>
Long-term moss monitoring network for atmospheric deposition in Germany, link to research data and scientific software
<p>Research data and scientific software related to a study that aims to restructure a long-term monitoring network using moss as biomonitor for atmospheric deposition in Germany. Data from the European Moss Survey 2005 and a statistically based methodology including a decision support system were used to design the spatial network for the 2005 survey.</p>
The Global Long-term Microwave Vegetation Optical Depth Climate Archive VODCA
<p><strong>Related paper containing detailed description</strong>: <strong><a href="https://essd.copernicus.org/articles/12/177/2020/essd-12-177-2020.html">Moesinger et al. (2020)</a></strong></p> <p>Vegetation optical depth (VOD) describes the attenuation of radiation by plants. VOD a function of frequency as well as vegetation water content, and by extension biomass. VOD has many possible applications in studies of the biosphere, such as biomass monitoring, drought monitoring, phenology analyzes or fire risk management.</p> <p>We merged VOD observations from various spaceborne sensors (SSM/I, TMI, AMSR-E, AMSR2, WindSat) to create global long-term vod time series. Prior to aggregation the data has been rescaled to AMSR-E, removing systematic differences between them.</p> <p>There is a product for C-band (~6.9 GHz, 2002 - 2018), X-band (10.7 GHz, 1997 - 2018) and Ku-band (~19 GHz, 1987 - 2017). The data is global sampled on a regular 0.25 degrees grid. Each product is available as daily global netcdf4 files.</p> <p> </p> <p>Currently there is an issue with opening the file using ESA SNAP. As an alternative <a href="https://www.giss.nasa.gov/tools/panoply/">Panoply</a> can be used to quickly visualize the data. </p> <p>An update of VODCA, addressing this issue and potentially including an extension of the dataset, is foreseen to be published on Zenodo early 2020.</p> <p> </p> <p><strong>Please contact us if you have any questions, problems or suggestions for improvement!</strong></p> <p> </p> <p><strong>Files:</strong></p> <ul> <li>"VODCA_C-band_2002-2018_v01.0.0.zip" (unzipped size: ~140 GB): <ul> <li>VODCA C-band files, sorted into yearly folders</li> </ul> </li> <li>"VODCA_X-band_1997-2018_v01.0.0.zip" (unzipped size: ~180 GB): <ul> <li>VODCA X-band files, sorted into yearly folders</li> </ul> </li> <li>"VODCA_Ku-band_1987-2017_v01.0.0.zip" (unzipped size: ~270 GB) : <ul> <li>VODCA Ku-band files, sorted into yearly folders</li> </ul> </li> <li>"vodca_v01-0_K-band_2007-06-01.nc" <ul> <li>sample file of the Ku-band product</li> </ul> </li> <li>"ESA-CCI-SOILMOISTURE-LAND_AND_RAINFOREST_MASK-fv04.2.nc" <ul> <li>Contains a global land mask, VODCA only has data for land locations. Source: https://github.com/TUW-GEO/smecv-grid</li> </ul> </li> </ul> <p><strong>Variables of data in VODCA files:</strong></p> <ul> <li>"VOD": Unitless, Vegetation Optical Depth of the respective band</li> <li>"sensor_flag": Bit-flag indicating which sensors contributed to each observation. <ul> <li>Values: <ul> <li>1 = AMSR-E</li> <li>2 = AMSR2</li> <li>3 = SSM/I F8</li> <li>4 = SSM/I F11</li> <li>5 = SSM/I F13</li> <li>6 = TMI</li> <li>7 = WindSat</li> </ul> </li> </ul> </li> <li>"processing_flag": Bit-flag indicating irregularities during processing affecting the quality of the observations <ul> <li>Values: <ul> <li>0 = Everything is fine</li> <li>10 = AMSR-2 7.3 GHz band is used instead of 6.9 GHz</li> <li>11 = Sensor is scaled to matched TMI instead of AMSR-E</li> <li>12 = Sensor scaled without temporally overlapping observations</li> </ul> </li> </ul> </li> <li>"time"/"lon"/"lat": Dimensions of the data.</li> </ul> <p> </p>
Temporally enhanced RSEI and Nighttime Lights Reveal Long-Term Ecological Changes and Effective Protection in China's Inaugural National Parks
<p>China's inaugural national parks play a crucial role in preserving biodiversity and maintaining ecosystem services. These protected areas are characterized by diverse landscapes and sensitive ecological environments. Over recent decades, the interplay between intensified human activities and global climate change has posed significant challenges to the ecological quality of these regions. Accurate and scientific assessment of ecological quality is essential for informed management and policy-making.</p> <p>This dataset is based on multiple MODIS datasets, incorporating NDVI, LST, WET, and NDBSI as indicators. Using principal component analysis (PCA), we produced the Improved Remote Sensing Ecological Index (RSEI) for these parks from 2000 to 2022 at a 500m spatial resolution.</p> <p>The RSEI was calculated using four component indices: greenness, heat, dryness, and wetness. Data for dryness and wetness were derived from the 8-day composite 500m resolution surface reflectance product MOD09A1. Heat was calculated using the 8-day composite 1km resolution land surface temperature product MOD11A2, which was resampled to 500m resolution. Greenness was derived from the 16-day composite 500m resolution vegetation index product MOD13A1.</p> <p>The improved RSEI calculation method enhances the temporal stability and comparability of the data, making it more suitable for long-term ecological monitoring.</p> <p>The improved RSEI effectively integrates dynamic changes of multiple variables and offers better temporal comparability for long-term ecological monitoring. Our results indicate that the ecological environment quality within the inaugural national parks significantly improved over the study period, with more noticeable improvements following the implementation of pilot conservation programs.</p> <p>This dataset provides foundational information for understanding the long-term ecological trends in China's national parks. It serves as a crucial resource for researchers, policymakers, and conservationists dedicated to the sustainable management and development of these vital ecological regions.</p> <p>The dataset contains five RAR compressed files, each corresponding to one of the national parks. These files include the Remote Sensing Ecological Index (RSEI) data from 2000 to 2022 for each respective park:</p> <ul> <li><strong>NTLNP-RSEI.rar</strong>: Contains the RSEI data for the Northeast Tiger and Leopard National Park (NTLNP) from 2000 to 2022.</li> <li><strong>HTRNP-RSEI.rar</strong>: Contains the RSEI data for the Hainan Tropical Rainforest National Park (HTRNP) from 2000 to 2022.</li> <li><strong>WNP-RSEI.rar</strong>: Contains the RSEI data for the Wuyishan National Park (WNP) from 2000 to 2022.</li> <li><strong>SNP-RSEI.rar</strong>: Contains the RSEI data for the Sanjiangyuan National Park (SNP) from 2000 to 2022.</li> <li><strong>GPNP-RSEI.rar</strong>: Contains the RSEI data for the Giant Panda National Park (GPNP) from 2000 to 2022.</li> </ul> <p>Each of these compressed files includes the improved RSEI calculations for the respective national park, providing a comprehensive view of the ecological quality changes over the 22-year period.</p> <p>The details of the data are as follows:</p> <ul> <li><strong>Data Format</strong>: GeoTiff</li> <li><strong>Pixel Values</strong>: Represent RSEI, ranging from 0 to 1, with no units.</li> <li><strong>Compatibility</strong>: The data can be directly opened and processed using remote sensing and GIS software such as ENVI and ArcGIS.</li> <li><strong>Data Quality</strong>: Due to the application of water and snow masks to remove the influence of water bodies and snow/ice on the WET component, there are some missing data areas.</li> </ul> <p>These datasets offer valuable insights into the ecological quality changes within each national park over the specified period, making them essential for researchers, policymakers, and conservationists involved in the sustainable management and development of these protected areas.</p> <p>For using the data and code provided in this dataset, please cite the following paper:</p> <p>Wen, C., Long, T., He, G., Jiao, W., & Jiang, W. (2025). Temporally enhanced RSEI and nighttime lights reveal long-term ecological changes and effective protection in China’s inaugural national parks. <em>Ecological Indicators, 170</em>, 112981. <a href="https://doi.org/10.1016/j.ecolind.2024.112981" target="_new" rel="noopener">https://doi.org/10.1016/j.ecolind.2024.112981</a></p> <p>The calculation of the RSEI is completed using Google Earth Engine. The link to the calculation code is:</p> <p><a href="https://code.earthengine.google.com/fab5452cd224d1f06226aece4c1a1016">https://code.earthengine.google.com/089d74f423e91a0da9490f5098c55021</a></p>
Monitoring long-term peat subsidence with subsidence platens in Zegveld, The Netherlands
<p><span>Peat oxidation in peat meadow areas is causing greenhouse gas emissions as well as land subsidence. Due to yearly fluctuations in soil surface level, long-term monitoring is needed to determine long-term net subsidence rates. In the experimental peat-meadow farm at Zegveld (NL) subsidence platens were installed in 1970 in a field with low ditchwater level, and in 1973 in a field with high ditchwater level. Platens were installed at 7 different depths, allowing to investigate where in the peat profile subsidence occurs. Elevation of platens as well as soil surface has been measured with surveyor’s levelling each year at the end of winter, so that a long timeseries up to 2023 is available. Analysis showed that surface level in the field with high ditchwater level subsided by 23 cm in 50 years (4.6 mm/yr), while in the field with low ditchwater level this was 31 cm in 53 years (5.8 mm/yr). Results also showed that in the field with low ditch water level, most subsidence due to permanent shrinkage and peat oxidation occurred between 40 and 100 cm depth, while for the other field this was between 20 and 40 cm depth. Finally, in 2023 subsidence was still observed under continuously saturated conditions at 140 cm depth. Presumably, in the aerated part of the profile peat oxidation and the associated earthification process is the main cause of subsidence, while the observed subsidence in the saturated soil at 140 cm depth must be due to other processes, such as consolidation and creep.</span></p>
Open and Lite Techno-economic Dataset for Long-term Energy Systems Modelling in the Republic of South Africa
<p>An open-source lite techno-economic dataset for long term energy systems modelling in the Republic of South Africa. Includes data on electricity generation and demand, electricity imports and exports, power transmission and distribution, residual capacity, capacity factor, operational lifetime, and fixed, variable and capital costs of electricity generation technologies. It also contains estimates for renewable potential and fossil fuel reserves in South Africa.</p>
The long-term impact of church activity on social capital: lessons from post-war Czechoslovakia
<p>This is a basic set of variables used in the paper "The long-term impact of church activity on social capital: lessons from post-war Czechoslovakia", co-authored by Štěpán Mikula (Masaryk Unversity, IZA), Fabio Sabatini (Sapienza University of Rome, IZA), and Tommaso Reggiani (Cardiff University, Masaryk Unversity, IZA). The first draft of the paper is available as a MUNI ECON working paper (<a href="https://doi.org/10.5817/WP_MUNI_ECON_2023-03" target="_blank" rel="noopener">DOI 10.5817/WP_MUNI_ECON_2023-03</a>), which also includes a detailed data description.</p> <p>The current dataset is restricted to variables that are available from open sources. We are not allowed to share the complete set of variables publically.</p> <p>The table contains the following variables:</p> <ul> <li>KOD_OBEC...Municipality ID defined by <a href="https://apl2.czso.cz/iSMS/cisdet.jsp?kodcis=43">CISOB codebook</a>.</li> <li>dieceze...Diocese name (as defined in pre-1989 period)</li> <li>year</li> <li>church...Indicator variable for the presence of a church building in the municipality in 1945</li> <li>ngo_all...Density of NGOs</li> <li>ngo_other...Density of church-unrelated NGOs</li> <li>ngo_church...Density church-related NGOs</li> <li>priest_years...priests' tenure (years)</li> <li>ger_share...Share of ethnic Germans in 1930 (<a href="https://doi.org/10.1016/j.jue.2021.103385">Guzi et al. 2021</a>)</li> <li>population1950...Population in 1950 (<a href="https://csu.gov.cz/produkty/historicky-lexikon-obci-1869-az-2015">Historický atlas</a>)</li> <li>TRI_mean...Terrain Roughness Index</li> <li>CZdist...Distance to the country border</li> </ul>
Evaluating F10.7 and F30 Radio Fluxes as Long-Term Solar Proxies of Energy Deposition in the Thermosphere
<p><span>We use model simulations and observations to examine how well the F10.7 and F30 solar radio fluxes represent solar forcing in the thermosphere during the last 60 years of weakening solar activity. We found that increased saturation of F10.7 during the last two extended solar minima leads to an overestimation of solar energy deposition, which manifests as a change in the linear relation between thermospheric parameters and F10.7. On the other hand, the linear relation between thermospheric parameters and F30 remains nearly the same throughout the whole studied period because of a recently found relative increase of F30 with respect to F10.7. Therefore, F30 is a more consistent proxy than F10.7 during the last 60 years. We note that continued evaluation is needed to see how well F10.7 and F30 will serve as solar proxies in the future when solar activity may start increasing toward the next grand maximum.</span></p>
Data set for "Cell class-specific long-range axonal projections of neurons in mouse whisker-related somatosensory cortices"
<p>Data set for: Liu Y, Bech P, Tamura K, Délez LT, Crochet S, Petersen CCH (2024) Cell class-specific long-range axonal projections of neurons in mouse whisker-related somatosensory cortices. eLife 13: RP97602. https://doi.org/10.7554/eLife.97602</p> <p>There are 3 files in this upload:</p> <p>1. The file named "2024_Liu_eLife.pdf" is the Open Access pdf of the online publication in eLife.</p> <p>2. The file named "Liu_anatomy_data_code.zip" (~35 GB) is a zipped version of a folder "Liu_anatomy_data_code" (~111 GB), which contains the anatomical data analysed in the study along with the Python codes used to generate the published figures 1-7 and their associated figure supplements. </p> <p>3. The file named "Liu_function_data_code.zip" (~10 GB) is a zipped version of a folder "Liu_function_data_code" (~35 GB), which contains the functional data analysed in the study along with the Python codes used to generate the published figure 8 and its associated figure supplement. </p> <p>After unzipping, the Python codes should run as a Jupyter notebook (anatomy .ipynb code) or Python code (function .py code) in Anaconda.</p>
Coral growth data for the research article "Reconstruction of long-term sub-lethal effects of warming on a temperate coral in a climate change hotspot" in Journal of Animal Ecology
<p>This repository contains the coral growth data files used to generate the results for the following article:</p> <p> </p> <p>MJ. Vergotti, JP. D’Olivo, T. Brachert, P. Capdevila, J. Garrabou, C. Linares, P. Spreter, DK. Kersting (2024) Reconstruction of long-term sub-lethal effects of warming on a temperate coral in a climate change hot-spot. <em>Journal of Animal Ecology</em>. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2656.14225</p> <p> </p> <p><strong>Abstract: </strong>The impact of warming on zooxanthellate corals is widespread, from tropical to temperate seas, with their associated mortalities causing global concern. The temperate coral <em>Cladocora caespitosa</em> is the only zooxanthellate coral with reef-building capacity in the Mediterranean Sea, a climate change hotspot with warming rates triple the global average. Over the past two decades, <em>C. caespitosa</em> populations have suffered severe mortality events associated with marine heatwaves (MHWs). However, with monitoring efforts beginning, at best, in the 2000s, the occurrence of MHWs before to that period, as well as the sub-lethal effects of these events remain poorly understood. Here we use sclerochronology to reconstruct the histories of past stress events and long-term sub-lethal effects on <em>C. caespitosa</em> in three locations within the NW Mediterranean Sea, each with different environmental conditions. Skeletal extension, density and calcification rates were compared to the <em>in situ</em> seawater temperature of each site to assess their relationship. Additionally, we assessed the occurrence of skeletal growth anomalies to reconstruct stress events between 1991 and 2021, a period that encompasses the onset and evolution of warming-related mass mortality events in the NW Mediterranean Sea. Our results reveal a positive association between calcification and temperature, following a latitudinal temperature gradient. However, the evolution of the likelihood distribution of growth rates in the warmest site (Columbretes Islands) since the 1990s indicates a decrease in linear extension and calcification rates during the most recent years. With the increase in the frequency of MHWs and growth anomalies during the last decade, this decline suggests a recurrence in physiological stress events. These results unravel information on the long-term impacts of warming on coral growth and highlight the potential of applying sclerochronology to reconstruct sub-lethal effects of warming using <em>C. caespitosa</em>. </p> <p> </p> <p> </p> <p><strong>Funding</strong>: This research is supported by the Horizon 2020 program of research and innovation of the European Union under the MaCoBioS grant agreement, by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, project no. 401447620) and by the Spanish Ministry of Science, Innovation and Universities under the project UndResCoral (project no. PID2022-137539OA-C22). D.K.K. was supported by a Ramon y Cajal postdoctoral grant funded by the Ministry of Science and Innovation (PEICTI 2021–2023; grant no. RYC2021-033576-I). C.L. acknowledges the support by ICREA Academia. J.G. acknowledges the grant “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S) funded by AEI 10.13039/501100011033.</p>
Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes - Supplementary Tables
<p>This repository contains the Supplementary Tables for Suriyalaksh et al. Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes.</p> <p>The list of table files can be found in <a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/Supplementary%20table%20guide.pdf">Supplementary Tables guide.pdf</a></p> <p>Tables S1, S2 and S3 corresponding to physical gene-gene interaction data are in a separate repository doi:10.5281/zenodo.4382337</p> <p>Details about some of the Supplementary tables:</p> <p>TableS4_inferred_networks.csv - list of inferred GRNs for specified input combinations (set of input regulators, length of the time sequence, NI tool and prior used).</p> <p><a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS5_consensus_network_member.xlsx">TableS5_consensus_network_member.xlsx</a> - list of groups of topologically similar GRNs (from Table S4)</p> <p>Table S6: edge lists (source,target) for each one of the three consensus networks selected according to the GS validation metrics: middle PFE/AUFE, max AUFE, max PFE.<br> TableS6a_max_AUFE_GRN.txt - max AUFE; largest network - this is the one we used in the main analysis and discussion<br> TableS6b_max_PFE_GRN.xt - max PFE<br> TableS6c_middle_AUFE_PFE_GRN.txt - middle PFE/AUFE</p> <p><a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS7_qRTPCR_ddCt_network_accuracy.csv">TableS7_qRTPCR_ddCt_network_accuracy.csv</a> - gene expression count differences for RNAi knockdown GRN validation experiments. </p> <p>Table S8: Group membership for each one of the nodes in each one of the selected networks according to the SBM that best describes the observed network topology. Each column shows the group membership for each level in a SBM block hierarchy. Our analysis is in the second most coarse-grained level (level 1).</p> <p>TableS8a_max_AUFE_SBM.csv<br> TableS8b_max_PFE_SBM.csv<br> TableS8c_middle_AUFE_PFE_SBM.csv</p> <p><a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS9_glp_gs_datasets.pdf">TableS9_glp_gs_datasets.pdf</a> - list of datasets used for defining functional clusters.</p> <p>TableS14a_glp_l1_vs_fem_l1_lifespan_assay.xlsx - Day13 survival of fem-3(q20)ts vs day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L1</p> <p>TableS14b_glp_l1_vs_glp_l4_lifespan_assay.xlsx - Day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L4 vs day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L1</p> <p>TableS15a_glp1_in_vivo_fluorescence_data.xlsx - in vivo fluorescent reporter data of glp-1(e2144)ts;rrf-3(pk1426)</p> <p>TableS15b_fem3_in_vivo_fluorescence_data.xlsx - in vivo fluorescent reporter data of fem-3(q20)ts</p> <p>TableS17_input_regulators_annotated.csv - list input regulators used as input for Network Inference Tools annotated by source type (2nd column): GenAge, known transcription factors (TF) and gene with high variability in the gene expression time series (HV). The third column lists whether that regulator has an orthologue in human (y) according to WormBase (v 278).</p> <p>TableS20_epistasis_lifespan_data.xlsx - Epistasis lifespan data of glp-1(e2144)ts</p> <p>All the image (TIF) files represent representative images in the following genetic backgrounds (below) that have been treated </p> <p>with empty vector (EV) or RNAi against the gene highlighted in the title of the image. See methods section for details. </p> <p><strong>femliu1: </strong></p> <p><em>fem-3(q20)ts.; dhs-3p::dhs-3::gfp</em></p> <p><strong>femsod3:</strong></p> <p><em>fem-3(q20)ts.; sod-3p::gfp</em></p> <p><strong>glp1lgg1:</strong></p> <p><em>glp-1(e2144); lgg-1p:lgg-1:gfp</em></p>
Long-duration Superluminous Supernovae at Late Times
<p>Single-composition models in three flavours (pure O, OMg, C burn). Zone mass, power level, and clumping free parameters. Distance 10 Mpc assumed.</p>
Dataset: Environmental Impact on the Long-Term Connectivity and Link Quality of an Outdoor LoRa Network
<p>This repository contains the long-term connectivity and link quality dataset collected on <a href="https://chirpbox.github.io/">ChirpBox</a> over 4 months (May -- September 2021) in the city of Shanghai, China. </p> <p>In addition to the dataset itself, we provide evaluation scripts for data analysis and visualization, in order to facilitate data exploration and re-use. To make it clear how to use the scripts, we provide a <em>Jupyter notebook -- </em> <strong>dataset.ipynb</strong> for dataset visualization.</p> <p><strong>List of files:</strong></p> <ol> <li><em>dataset_03052021_15092021.csv</em> <ul> <li>The dataset includes LoRa connectivity and link quality, as well as environmental information, collected from May 3 to September 15, 2021.</li> </ul> </li> <li><em>data_analysis.py</em> <ul> <li>The script for dataset analysis and visualization. One can use the functions in this script to derive network-level statistics (e.g., in terms of average number of correctly-exchanged packets), link-level statistics (e.g., in terms of SNR, RSS, and PRR), and node-level statistics(e.g., in terms of number of neighbours and temperature evolution over time).</li> </ul> </li> <li><em>metadata_processing.py</em> <ul> <li>The script for pre-processing metadata into CSV files. One can use the functions in this script to convert metadata for each measurement saved in TXT and JSON formats to CSV files that include attributes such as link quality, connectivity, and environmental information, an example of which is <strong>dataset_03052021_15092021.csv</strong>.</li> </ul> </li> <li><em>dataset.ipynb </em> <ul> <li>The Jupiter notebook contains examples of visualization and metadata pre-processing of datasets with functions in <strong>data_analysis.py</strong> and <strong>metadata_processing.py</strong>.</li> </ul> </li> <li><em>topology_map.png</em> <ul> <li>The node deployment map used to create topology figures. A usage example is <strong>Figure 1</strong> shown in the notebook <strong>dataset.ipynb</strong>.</li> </ul> </li> <li><em>dataset_metadata.zip</em> <ul> <li>The dataset metadata is stored in TXT and JSON formats. Among them, link quality, connectivity and on-board sensor data are stored in TXT files and weather information are stored in JOSN files.</li> </ul> </li> <li><em>README.md</em> <ul> <li>The README.md explains all the files in this repository and gives some examples of how to use the provided scripts to analyze the dataset.</li> </ul> </li> </ol>
Stand structure and tree population dynamic attribute dataset of long abandoned strict forest reserves
<p>We provide an integrated dataset of two consecutive forest inventories, both containing plot-level, and individual tree-level data. The first provides the descriptions and measuring units (or categories) of plot-level variables (Table 1). The plot level table contains 233 records (rows), one for each selected permanent plot of six strict forest reserves located in Hungary. This dataset is georeferenced and contains information on inventories and basic stand structure attributes (Table_1_Plots ESRI shape format). </p> <p>The individual tree-level datasets were acquired by the sampling procedure, detailed in section 2.2. Species, dendrometric attributes, relative crown position, health, and decay status were documented for each tree belonging to the samples. Table 2 provides the descriptions and measuring units (or categories) of tree-level datasets in detail. Furthermore, it provides a tree history classification based on the interpretation of tree status changes. According to a simple scheme of the life and dead history of a tree, it could be classified into four main phases: establishment/regeneration phase; developmental phase; death and gradual decay of the tree trunk; terminated in decomposed/disintegrated state. The main events along these phases are ingrowth regeneration; death of the tree (mortality); disaggregation and decomposition of deadwood. We classify each sampled tree individuals into tree history categories (events and phases, Table 3) that can provide population dynamic aspects at stand level by appropriate tree aggregation functions.</p> <p>Relational link can be set between the plot-level and tree-level datasets based on the unique identification code of the site and sampling plots.</p>
Durability in materials jetting: A long-term study
<p>This file contains data for the paper "Durability in materials jetting: A long-term study"<br> For more information, please contact Ali Payami Golhin (payami.ag@gmail.com)</p>
Data from: Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep
<p>This dataset contains additional files from the manuscript: "Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep".</p> <p>The files included are:</p> <p>- All novel lncRNA transcript annotation GTF file ( lncrnas.gtf )</p> <p>- High-confidence lncRNA gene annotation GTF file ( lncrnas_evidence.gtf )</p> <p>- All novel lncRNA transcript annotation GTF file remapped to the ARS-UI_Ramb_v2.0 genome ( lncrnas_remapped_v2.gtf )</p> <p>- Raw count estimates of the extended annotation ( rawcounts.csv )</p> <p>- TPM values of the extended annotation ( tpmcounts.csv )</p> <p>- Supplementary data to the published article (.xlsx, .pdf)</p> <p> </p>
Solar cycle and long-term trends in the observed peak of the meteor altitude distributions by meteor radars
<p>The datasets here correspond to a paper by Dawkins et al., “Solar cycle and long-term trends in the observed peak of the meteor altitude distributions by meteor radars”, originally submitted in November 2022.</p> <p>The following datasets are sufficient to produce Figure 2 and 3 in the main manuscript.</p> <p>Figure 2:</p> <ul> <li>Please use the 12 individual files with filenames, “Dawkins_et_al_2022__meteor_peak_altitude__*_data.txt”. Here the asterisk should be replaced by one of the following station abbreviations: CAR, COL, CPa, DAV, KIR, KSS, ROT, SMa, SOD, SVA, TdF, and TRO.</li> <li>Each file contains 5 columns: Column 1 is year (from 1999 to 2022), Column 2 is the time series of the annual peak altitude residuals (no units), Column 3 is the corresponding standard error, Column 4 is the multilinear model fit, and Column 5 is the normalized annual solar flux (F10.7) in arbitrary units.</li> </ul> <p>Figure 3:</p> <ul> <li>Please use “Dawkins_et_al_2022__meteor_peak_altitude_trends.txt”. For ease, a description of the different columns is included within this file.</li> </ul> <p> </p>
The 30 m long-term LAke Water Secchi Depth (SD) dataset (LAWSD30) of China (1985–2020)
<p>Monitoring the water clarity of lakes is essential for the sustainable development of human society. However, existing water clarity assessments in China have mostly focused on lakes with areas > 1 km<sup>2</sup>, and the monitoring periods were mainly in the 21st century. In order to improve the understanding of spatiotemporal variations in lake clarity across China, based on the Google Earth Engine (GEE) cloud platform, a 30 m long-term LAke Water Secchi Depth (SD) dataset (LAWSD30) of China (1985–2020) was developed using Landsat series imagery and a robust water-color-parameter-based SD model. <strong><em>Noted, the LAWSD30 has been updated to 2021 using Landsat data from 2020 to 2022.</em></strong> The details are described in "<em>30 m long-term LAke Water Secchi depth (SD) dataset (LAWSD30) of China (1985–2021)_Readme_V1.1.docx</em>".</p>
TRANSIT long-distance multimodal trips model results - a Spanish case study
<p>The files downloaded present the results per scenario considered obtained with the agent-based model developed for the assessment of the Intermodal Timetable Synchronisation solution proposed in the scope of the TRANSIT project (<a href="https://www.transit-h2020.eu/">https://www.transit-h2020.eu/</a>).</p> <p>An agent-based modelling framework called <a href="https://github.com/StefanoPenazzi/jtap/tree/main">J-TAP</a> has been developed and put at work to implement a Spanish long-distance multimodal trips model. The enhanced version of J-TAP used in this work can be found on a <a href="https://github.com/NommonSolutionsAndTechnologies/jtap">github repository</a>.</p> <p>The case study is focused on modelling the long-distance travel patterns of the residents in the Valencia (Spain) area. The destinations considered include the whole of Spain. The period under study is a full year from March 2019 to February 2020 (both inclusive).The files are structured in three different scenarios:</p> <ol> <li><strong>CS01 - Baseline</strong>. The current state of the network is considered and the actual long-distance travel patterns are obtained.</li> <li><strong>CS02 - HSR connection with Madrid-Barajas airport</strong>. The long-distance travel patterns are modelled with hard measures, the high-speed rail is connected to Madrid-Barajas airport.</li> <li><strong>CS03 - HSR connection with Madrid-Barajas airport and timetable synchronisation</strong>. The effects of the timetable synchronisation are modelled.</li> </ol> <p>Each scenario includes the following files:</p> <ul> <li>ctapModelParameters. A folder containing all the information extracted from the <a href="https://neo4j.com/product/graph-data-science/?utm_program=emea-prospecting&utm_source=google&utm_medium=cpc&utm_campaign=emea-search-offers&utm_adgroup=dynamic&utm_content=dynamic&utm_placement=&utm_network=g&gclid=Cj0KCQiAwJWdBhCYARIsAJc4idAo4CEi9lU8TXwmBym8MNHpEIZHPBs3x_4phxbu76y1XKbYlFoZCjIaAiGhEALw_wcB">neo4j</a> graph database created to model the multimodal network and the agents. J-TAP contains packages that simplify network creation in the graph database. This information is stored in .json files (e.g., "Os2DsTravelCostParameter.json" contains the generalised cost for each OD pair and transport mode, "AttractivenessParameter.json" contains the attractiveness by destination, activity, time of the year and agent, etc.). The solver included in the J-TAP framework uses this information to calculate the agents plans.</li> <li>population.json. The result of the J-TAP optimisation. It includes the fitness value for each agent plan evaluated during the J-TAP execution. The best plan for each agent is selected as the plan performed by the agent. An agent plan includes: <ul> <li>activities - Sequence of activities.</li> <li>locations - Sequence of locations</li> <li>ts - Initial time of the activity</li> <li>te - Final time of the activity</li> </ul> </li> <li>LinkTimeFlow.csv. It is obtained after processing the previous file. It contains the number of agents using each link in the network (i.e., road, rail, air and cross links) in each time interval. The first column represents the link id and the rest of columns indicates the number of agents in each interval.</li> </ul> <p>The J-TAP simulation framework is explained in detail in TRANSIT's deliverable <a href="http://www.nommon-files.es/transit/TRANSIT-D5.1_Modelling_Framework_v02.00.00.pdf">D5.1. TRANSIT Modelling and Simulation Framework</a> and the complete description of the case studies and scenarios tested is included in TRANSIT's deliverable <a href="http://www.nommon-files.es/transit/TRANSIT-D6.1_Assessment_of_Intermodal_Concepts_00.02.00.pdf">D6.1. Impact Assessment of New Intermodal Concepts and Passenger Information Services: Conclusions and Recommendations</a>.</p> <p>Thank you for downloading the dataset! It would be very helpful if you share your view on the data show with us. </p>
Data for Figures in "Unexpected Long-Term Variability in Jupiter's Tropospheric Temperatures
<p>This repository provides the data submitted by the primary author that were used to create Figures 1, 2, 3, 4 and 5 in the text for the article: <strong>"Unexpected Long-Term Variability in Jupiter's Tropospheric Temperatures", by </strong> Glenn S. Orton, Arrate Antuñano, Leigh N. Fletcher, James Sinclair, Thomas Momary, Takuya Fujoyoshi, Padma Yanamandra-Fisher, Padraig T. Donnelly, Jennifer Greco, Anna Payne, Kimberly Boydstun, Laura Wakefield.</p> <p>The repository consists of five files in text (ASCII) format: (1) User Guide to Data (16 kb), (2) figure1_data.txt (1.5 MB), (3) figure2_data.txt (142 kb), figure4_data.txt (61 kb), and figure5_data.txt (59 kb). Data for Figure 3 are provided in the User Guide.</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.