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882 results for “3D models”
Correlated-k table for H2 dominated atmospheres for 3D Climate Modelling
<p>Correlated-k table for H2 dominated atmospheres with a variable amount of water vapour built by incorporating absorption data files from the HITRAN database and using the exo\_k code by J.Leconte. This correlated-k tables are created to use with Generic-PCM model to simulate the atmospheres of H2 dominated planets.</p> <p>The calculation of radiative transfer can be performed using the correlated-k method, which efficiently determines net radiative fluxes by categorizing spectral lines into infrared and visible bands (IR x VI) and assigning the average absorption coefficients to each band. These coefficients are pre-calculated based on detailed line-by-line radiative transfer calculations. The correlated-k method is an economic alternative to the line-by-line method, making it possible to accurately and rapidly compute atmospheric radiation.</p> <p> </p>
Correlated-k table for CO2 dominated atmospheres for 3D Climate Modelling
<p>Correlated-k table for CO2 dominated atmospheres with a variable amount of water vapour built by incorporating absorption data files from the HITRAN database and using the exo\_k code by J.Leconte. This correlated-k tables are created to use with Generic-PCM model to simulate the atmospheres of CO2 dominated planets.</p> <p>The calculation of radiative transfer can be performed using the correlated-k method, which efficiently determines net radiative fluxes by categorizing spectral lines into infrared and visible bands (IR x VI) and assigning the average absorption coefficients to each band. These coefficients are pre-calculated based on detailed line-by-line radiative transfer calculations. The correlated-k method is an economic alternative to the line-by-line method, making it possible to accurately and rapidly compute atmospheric radiation.</p> <p> </p>
Limits of the Habitable Zone for H2 atmosphere with 3D climate Modelling
<p>Water is crucial for life, regardless of the environment. That's why in search of extraterrestrial life, we focus on planets in the habitable zone (HZ), where liquid water can exist. The size of this zone depends on factors like the star type and planet size. Using the Generic PCM model (https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/Overview_of_the_Generic_PCM), we've defined the limits of the HZ for atmospheres dominated by H2 in 3D for the first time. You can access the dataset from the simulations in ".nc" file format. Temporal evolution of variables such as surface temperature, surface pressure, water vapour, liquid water, ice etc. are in a 3D grid for different orbital distances and with different surface pressures are present in the dataset. We have used the correlated-k table published in Zenodo for the simulations (https://doi.org/10.5281/zenodo.10978762).</p>
Transcriptomic characterization of 2D and 3D human induced pluripotent stem cell-based in vitro models as New Approach Methodologies for developmental neurotoxicity testing
<p><strong>Abstract:</strong> The safety and developmental neurotoxicity (DNT) potential of chemicals remain critically understudied due to limitations of current in vivo testing guidelines, which are low throughput, resource-intensive, and hindered by species differences that limit their relevance to human health. To address these issues, robust new approach methodologies (NAMs) using deeply characterized cell models are essential. This study presents the comprehensive transcriptomic characterization of two advanced human-induced pluripotent stem cell (hiPSC)-derived models: a 2D adherent and a 3D neurosphere model of human neural progenitor cells (hiNPCs) differentiated up to 21 days. Using high-throughput RNA sequencing, we compared gene expression profiles of 2D and 3D models at three developmental stages (3, 14, and 21 days of differentiation). Both models exhibit maturation towards post-mitotic neurons, with the 3D model maturing faster and showing a higher prevalence of GABAergic neurons, while the 2D model is enriched with glutamatergic neurons. Both models demonstrate broad applicability domains, including excitatory and inhibitory neurons, astrocytes, and key endocrine and especially the understudied cholinergic receptors. Comparison with human fetal brain samples confirms their physiological relevance. This study provides novel in-depth applicability insights into the temporal and dimensional aspects of hiPSC-derived neural models for DNT testing. The complementary use of these two models is highlighted: the 2D model excels in synaptogenesis assessment, while the 3D model is particularly suited for neural network formation as observed as well in previous functional studies with these models. This research marks a significant advancement in developing human-relevant, high-throughput DNT assays for regulatory purposes.</p> <p><strong>This data sets contains:</strong></p> <p><strong>Tab. S1</strong> - Significant genes results</p> <p><strong>Tab. S2</strong> - Enriched pathways_GO_Biological Processes</p> <p><strong>Tab. S3</strong> - Enriched pathways_GO_Cellular Components</p> <p><strong>Tab. S4</strong> - Enriched pathways_GO_Molecular Function</p> <p><strong>Tab. S5</strong> - Enriched pathways_KEGG</p> <p><strong>Tab. S6</strong> - EnrichEnriched pathways_Panther</p> <p><strong>Tab. S7</strong> - Enriched pathways_Reactome</p> <p><strong>Tab. S8</strong> - Gene counts</p> <p><strong>Tab. S9</strong> - Gene selection for targeted analysis</p>
3D Models of yellow coffins in the Musée du Louvre
<p>3D Models of yellow coffin lids in <a href="https://collections.louvre.fr/en/recherche?advanced=1&collection%5B0%5D=3" target="_blank" rel="noopener"><strong>the Musée du Louvre</strong></a></p> <p>The 3D models consider only the external upper part of coffin lids as far down as the lower part of the crossed forearms. </p> <p><br>The dataset contains .zip file of each coffin with:</p> <ol> <li>.zip files with the 3D models generated with the software Agisoft Metashape 1.8.3 (.jpg; .mtl; .obj);</li> <li>.tif files with the orthophtgraphs of the coffins textured and not textured;</li> <li>. PDF file with processing report of 3D models (.pdf);</li> <li>.pdn file with the overlapped layers (orthophotographs textured and not textured, drawings and points) generated with the open source paint. net</li> </ol> <p>The dataset is part of the results of the <a href="https://facesrevealed.museoegizio.it/" target="_blank" rel="noopener"><strong>Faces Revealed Project.</strong></a> The project has received funding from the European Union’s Horizon 2020 research and innovation programme under the <strong>Marie Skłodowska-Curie grant agreement No 895130</strong></p> <p><strong>If you publish material based on datasets contained in this archive, then, in your acknowledgements, please cite the original source, referring to it through the following DOI: 10.5281/zenodo.11063613</strong></p> <p>Thanks to the Director of the Département des Antiquités Égyptiennes of the Musée du Louvre Paris, Vincent Rondot, and the Curators Hélène Guichard, Paticia Rigault-Deon and Caroline Thomas and the entire staff of the Museum </p> <p>Photographs courtesy of the © Musée du Louvre, Département des Antiquités Égyptiennes.</p>
3D model of a small piece of Baltic amber (KM 8) containing four different ant species.
<p>Video S1 of 3D model of a small piece of Baltic amber (KM 8) containing four different ant species. S<span><span><span>pecimen is kept in the collection </span></span><span><span>of the Kaliningrad Amber Museum, Kaliningrad, Russia</span></span></span></p>
Modeling polar bear (Ursus maritimus) snowdrift den habitat on Alaska's Beaufort Sea coast using SnowDens-3D and ArcticDEM data
<p>Pregnant polar bears (<em>Ursus maritimus</em>) excavate maternal dens in seasonal snowdrifts during fall along Alaska's Beaufort Sea coast to shelter their altricial young during birth and development. With recent sea ice decreases, bears are denning more frequently on land. Each year, the weather and blowing-snow conditions control the creation of snowdrifts across the landscape, and the available snowdrift den habitat can vary widely from one year to the next, depending on the late fall and early winter air temperature, snowfall, and wind speed and direction. We implemented a physics-based, spatiotemporal, polar bear snowdrift den habitat model (SnowDens-3D) across the eastern Alaska Beaufort Sea coast (an area of approximately 17,000 km^2^). High-resolution (2.0 m) topography data were provided by the ArcticDEM, and daily meteorological forcings were provided by NASA's MERRA-2 reanalysis. A 21-year (2000–2020) SnowDens-3D simulation was performed, and model outputs were compared with 91 historical polar bear den locations. The year-specific simulations produced viable den habitat for 98% of the observed den locations. The interannual variation in den habitat area over the 21-year period increased by approximately a factor of three from the minimum year (2001; 554 km^2^) to the maximum year (2017; 1,566 km^2^). This data archive provides the key den and den-habitat datasets produced, used, and analyzed by this project.</p>
Electron Physics in 3D Two-Fluid Ten-Moment Modeling of Ganymede's Magnetosphere
<p>The dataset is produced for the manuscript "Electron Physics in 3D Two-Fluid Ten-Moment Modeling of Ganymede's Magnetosphere" accepted by the JGR - Space Physics. The script mirdip.lua was used to perform the simulation by the Gkeyll multi-fluid high-moment code. The simulation produced output files in the HDF5 format following the VizSchema description, both are open-source. The output file can be visualized by free, open-source toolkit ParaView. In the file mirdip_q_10.h5, the state quantities are stored in the 4d array "StructGridField" in the layout of NZ * NY * NX * NCOMP, where NX, NY, and NZ are cell numbers in each direction, and NCOMP = 28 is the number of state quantities in the order of ten electron moment terms, ten ion moment terms, six electromagnetic field terms and two correction potential terms.</p>
DirtyGrid: 3D dust radiative transfer modeling of spectral energy distributions of dusty stellar populations
<p>Output global SEDs of a large grid of 3D stellar+dust radiative transfer models spanning the range of star formation and dust contents of regions of galaxies.</p> <p>Paper describing the DirtyGrid is Law, Gordo, & Misset (2018, ApJ, submitted)</p> <p>Code to make to access this data at: https://github.com/karllark/pydirtygrid</p>
Lithosphere removal (delamination) following continental collision: shape and complexity of observables predicted from 3D numerical models
<p>Upload contains most essential data files from the manuscript. The raw data amount to several TB and cannot be uploaded.</p> <p><strong>1 Model data</strong></p> <p><em>1.1 Models covered</em></p> <p>Relatively frequent output is available for the reference model (<em>R</em> in paper, see Table S2), prefixed <em>dp10</em>. Limited output is uploaded for models with geometric variations (<em>OSM -> dp19, TSM->dp26</em>).</p> <p><em>1.2 Types of data</em></p> <p>Most files are visualisation files (ending *.<em>vtr</em>). These are intended for loading into the visualisation software Paraview. Files starting with <em>comp_</em> contain the lithological composition field; other visualisation files hold the fields of selected physical parameters. Note that as of the design of the study, the maximum file size allowed for loading into Paraview is ca. 2 GB. This limits the number of fields available according to model size - larger models (geometrical variations) hold therefore less fields.</p> <p>Binary files with ending *.<em>prn</em> are saved model states, from which programs can be rerun.</p> <p>Time information mapping step numbers to years is provided in <em>times...txt</em>.</p> <p> </p> <p><strong>2 Software for reproduction</strong></p> <p>The numerical code is not in the public domain, and its use is restricted. A pre-compiled binary is provided and allows reproduction of the main/reference model. We present the input files; however, these cannot be changed freely (equivalent to software distribution), and changes will lead to termination of the program.</p> <p><em>2.1 Requirements, preparation and use</em></p> <p>The code is compiled on CentOS with gcc 4.8.2. There is no library dependency, apart from the intrinsic OpenMP and glibc (>= 2.17). The following requirements <em>must</em> be satisfied in order to run it:</p> <ul> <li>Linux OS (tested on CentOS and Fedora)</li> <li>> 160 GB shared memory</li> </ul> <p>The following provisions are recommended:</p> <ul> <li>16 cores</li> <li>high bandwidth storage</li> <li>storage space <em>O</em>(TB)</li> </ul> <p>To prepare, simply unzip the provided snapshot <em>clsd_reproduce_gcc_CentOS.zip</em> in an appropriate directory (cluster). The input file <em>init.t3c</em> sets the initial conditions; the input file <em>mode.t3c </em>controls solver and file output. <em>file.t3c</em> is the pointer to the last output step; if a model snapshot is available as binary dump (*.prn file), setting the pointer to its number allows restarting.</p> <p>For normal usage, create initial condition with executable <em>in3mg</em>, and subsequently run <em>i3mg</em>. This will create snapshots and *.vtr visualisation files.</p> <p> </p> <p>High-performance computing facilities, runtime (months), proper software environment, and training in use of the code, or in the use of the visualisation software, are not provided.</p> <p> </p>
The OpenEar library of 3D models of the human temporal bone based on computed tomography and micro-slicing
<p>The OpenEar Dataset provides a library consisting of eight three-dimensional models of the human temporal bone to enable surgical training including color data. Each dataset is based on a combination of multimodal imaging including Cone Beam Computed Tomography (CBCT) and micro-slicing. 3D reconstruction of micro-slicing images and subsequent registration to CBCT images allowed for relatively efficient multimodal segmentation of inner ear compartments, middle ear bones, tympanic membrane, relevant nerve structures, blood vessels and the temporal bone. Raw data from the experiment as well as voxel data and triangulated models from the segmentation are provided in full for use in surgical simulators or any other application which relies on high quality models of the human temporal bone.</p>
3D models experimental cores
<p>290 3D models (.ply files) of cores made in quartzite (15 bifacial multipolar centripetal cores and 15 unifacial unipolar cores) from a sequential experiment. Each core was scanned at ten different moments of the reduction. In total, there are 30 3D models of cobbles and 260 3D models of cores. </p>
Constructing stable 3D hydrodynamical models of giant stars
<p>MESA inlist associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2017A&A...599A...5O">Ohlmann et al. (2017)</a>. MESA version 6208.</p> <p>Publication DOI: <a href="https://doi.org/10.1051/0004-6361/201629692">10.1051/0004-6361/201629692</a></p>
Audio from: 'Modeling Voiced Stop Consonants using the 3D Dynamic Digital Waveguide Mesh Vocal Tract Model'
<p>Audio files associated with the paper 'Modeling Voiced Stop Consonants using the 3D Dynamic Digital Waveguide Mesh Vocal Tract Model', presented at the International Congress of Phonetic Sciences 2019, Melbourne, Australia.</p>
Computational model results for "Uncertainties of Glacial Isostatic Adjustment model predictions in North America associated with 3D structure"
<p>The mean GIA signals of RSL, u-dot and g-dot with 1σ, 2σ and 3σ uncertainties in North America. </p>
Topography Response to Horizontal Slab Tearing and Oblique Continental Collision: 3D Thermomechanical Numerical Modelling
<p>This repository submission provides the 3D thermo-mechanical numerical modelling code I3ELVIS developed by the workgroup of Prof. Taras Gerya (ETH Zürich). The code is based on finite-difference and marker-in-cell methods (Gerya & Yuen, 2003, 2007; Gerya, 2019). The code solves the momentum, continuity, and energy equations on the fixed Eulerian grid and transports the physical properties by Lagrangian markers using the velocity field. The code also accounts for the major phase transitions in the Earth’s mantle and internal heat sources arising from adiabatic, radiogenic, and frictional heating. Partial melting and melt extraction processes are neglected for the sake of simplicity. A more detailed description of the code, including the governing equations and the adopted rheological model can be found in various published literature (Andrić-Tomašević et al., 2023; Boonma et al., 2023; Maiti et al., 2024). Interested users are recommended to contact Prof. Taras Gerya (taras.gerya@erdw.ethz.ch). </p> <p>The repository also provides input and output files to run and reproduce model results and manuscript figures of Maiti et al., 2024 (JGR Solid Earth). Paraview States for processing .vtr result files and visualizing the model output data. Matlab script to visualise the topography from .grd files. </p>
EMS3D-KITTI-Synthetic: A Synthetic 3D Dataset in KITTI Format with Balanced EMS Vehicle Distribution for Autonomous Driving AI Model Training
<p>A 3D synthetic dataset in KITTI format, focused on emergency vehicles such as ambulances and police cars. The dataset was generated across 8 towns within the CARLA simulator and converted into the KITTI format, ensuring compatibility for direct use in AI model training for autonomous driving applications.</p>
Wood - barrel 3D model
<p>Wood - barrel 3D model</p>
Truth Tables for consistency-checking 3D geological models
<p>The Microsoft Excel and PDF representations of the Truth Tables and geo-feature relation exampels are provided as supplementary information to the GMD publication: </p> <p><strong>Consistency-Checking 3D Geological Models</strong></p> <p><strong>Marion N. Parquer, Eric A. de Kemp, Boyan Brodaric and Michael J. Hillier</strong></p> <p> </p>
The High-resolution 3D QP Model of the China Seismic Experiment Site
<p><span>The CSES-Q1.0 is the highest resolution 3D <em>Q</em><sub>P</sub> model in the CSES to date.The first column of the file represents longitude, the second column represents latitude, the third column represents depth, and the fourth column represents QP values.</span></p>
ScienceDex guides
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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.