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Fig. 2 in First three-dimensional skull of the Middle Triassic mixosaurid ichthyosaur Phalarodon fraasi from Svalbard, Norway
Fig. 2. The segmented model of right lateral side of the skull of mixosaurid ichthyosaur Phalarodon fraasi (Merriam, 1910) PMO 235.393, from the Botneheia Formation, Middle Triassic of the Isfjorden area in Spitsbergen, Svalbard.
Fig. 3 in First three-dimensional skull of the Middle Triassic mixosaurid ichthyosaur Phalarodon fraasi from Svalbard, Norway
Fig. 3. The computed tomography rendered segmentation of rostral elements of mixosaurid ichthyosaur Phalarodon fraasi (Merriam, 1910) PMO 235.393, from the Botneheia Formation, Middle Triassic of the Isfjorden area in Spitsbergen, Svalbard. Right dentary and maxilla in lingual (A1) and labial (A2) views, right dentary (A3) in dorsal view, right maxilla in dorsal (A4) and lateral (A5) views. Note that the dorsal extent of the maxilla is not complete. Scale bars 10 mm.
Experimental data for: "Multi-slice electron ptychographic tomography for three-dimensional phase-contrast microscopy beyond the depth of field limits"
<p>This is the raw experimental data for the paper: "Multi-slice electron ptychographic tomography for three-dimensional phase-contrast microscopy beyond the depth of field limits"</p> <p>Now also including code to recreate figures, and data from alignment and multi-slice ptychography reconstructions.</p> <p>The data is in zarr format and can be read with the zarr python library. It also contains metadata in a dictionary. </p>
Supplementary material: Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules
<p><strong>Supplementary material to the manuscript <em>"Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules"</em> by Terry Mullins, Evangelos T. Karamatskos, Joss Wiese, Jolijn Onvlee, Arnaud Rouzée, Andrey Yachmenev, Sebastian Trippel, and Jochen Küpper, <em>Nat Commun</em> 13, 1431 (2022). <a href="https://doi.org/10.1038/s41467-022-28951-z">https://doi.org/10.1038/s41467-022-28951-z</a>, arXiv: <a href="https://arxiv.org/abs/2009.08157">2009.08157 </a></strong></p> <ul> <li> <em><strong>simulations_part.z*</strong> </em>is split zip archive containing simulations data for indole molecule, such as files with rotational probability density distributions computed at different times <span class="math-tex">\(t=0..1500\)</span> ps during the laser pulse and field-free evolution, and example python scripts for data retrieval.</li> <li><strong><em>rawdata_part.z*</em></strong> is split zip archive containing raw experimental data.</li> <li><strong><em>analysis_scripts.zip</em></strong> is zip archive containing experimental analysis codes.</li> </ul> <p><strong>The <em>simulations_part.zip</em> contains the following files and folders:</strong></p> <ul> <li><em><strong>prob_density_euler_angles</strong></em> contains files <em>rotdens_av_<time>.gz</em> with simulated state-averaged rotational probability density distributions in terms of Euler angles for different times <time>, ranging from the beginning of the alignment laser pulse at <span class="math-tex">\(t=0\)</span> up to <span class="math-tex">\(t=1500\)</span> ps with a time step of 1 ps.<br> Calculations of probability density distributions were done using <a href="https://github.com/CFEL-CMI/richmol">Richmol</a> program.<br> The gzipped ASCII data files <em>rotdens_av_<time>.gz</em> contain in columns the values of the Euler angles <span class="math-tex">\(\phi,\theta,\chi\)</span> followed by the normalized probability density value.</li> <li><em><strong>prob_density_atoms_xyz</strong></em> contains files <em>monte_carlo_av_<time>.h5</em> with state-averaged rotational probability density distributions of all atoms in the indole molecule in terms of their Cartesian coordinates, for different times <time>, ranging from the beginning of the alignment pulse at <span class="math-tex">\(t=0\)</span> up to <span class="math-tex">\(t=1500\)</span> ps with a time step of 1 ps.<br> Structure of <em>monte_carlo_av_<time>.h5</em> HDF5 files:<br> Key Description<br> ----- ----------------<br> 'C10' - Cartesian coordinates of carbon atom no. 10<br> 'C11' - Cartesian coordinates of carbon atom no. 11<br> 'C12' - ...<br> 'C14' - ...<br> 'C3' - ...<br> 'C6' - ...<br> 'C7' - ...<br> 'C9' - ...<br> 'N4' - ...<br> 'H1-C3' - Cartesian coordinates of a vector pointing from carbon atom no. 3 to hydrogen atom no. 1<br> 'H13-C11' - ...<br> 'H15-C12' - ...<br> 'H16-C14' - ...<br> 'H2-N4' - ...<br> 'H5-C7' - ...<br> 'H8-C9' - ...<br> 'ref_vectors' - reference molecular-frame Cartesian coordinates of all atoms<br> 'x' - coordinates of the x-axis of Principal Axes of Inertia Frame<br> 'y' - coordinates of the y-axis of Principal Axes of Inertia Frame<br> 'z' - coordinates of the z-axis of Principal Axes of Inertia Frame<br> 'pol_x' - coordinates of the x-axis of Principal Axes of Polarizability Frame<br> 'pol_y' - coordinates of the y-axis of Principal Axes of Polarizability Frame<br> 'pol_z' - coordinates of the z-axis of Principal Axes of Polarizability Frame</li> <li><em><strong>indole_deflected_states.txt</strong></em> ASCII file contains initial populations of rotational states of indole in the deflected beam.<br> The following data is arranged in columns: <em>m, J</em>, <em>id</em>, <em>energy</em>, <em>normalized population</em>. The <em>J</em> and <em>m</em> are rotational quantum numbers of the total angular momentum and its <em>Z</em>-projection, the <em>id</em> number refers to the state's index in file <em>indole_energies_j0_j20.txt</em> listing rotational states of indole.</li> <li><em><strong>indole_data.py</strong></em> Python module provides basic functions to extract information from HDF5 data files <em>monte_carlo_av_<time>.h5</em>. It can also be used to compute alignment and orientation.</li> <li><em><strong>example_cos.py</strong></em> and <em><strong>example_dens.py</strong></em> Python scripts that demonstrate how to use <em>indole_data.py</em> module for computing and plotting alignment traces and a 2D projection of the probability density distribution, respectively.</li> <li><em><strong>monte_carlo.py</strong></em> Python script that was used to compute through Monte-Carlo sampling probability density distributions for Cartesian positions of atoms in indole (<em>monte_carlo_av_<time>.h5</em> files) using probability density distribution functions in Euler angles (outputs of Richmol program <em>rotdens_av_<time>.gz</em>).</li> </ul> <p><strong>The <em>analysis_scripts.zip</em> contains the following files and folders:</strong></p> <ul> <li><strong><em>H_Plus</em></strong> folder contains codes relevant for the analysis of H<sup>+</sup> ion data. <ul> <li><strong><em>analyse_full_alignment_scans.m</em></strong>: subtracts background and combines delay scan data sets together, takes account of errors.</li> <li><em><strong>calculate_resamped_df.m</strong></em>: called by <em>analyse_full_alignment_scans.m</em> to calculate the frequency sampling.</li> <li><em><strong>unique_mean.m</strong></em>: called by <em>analyse_full_alignment_scans.m</em> when combining data sets. Combines non-unique data points into a single data point.</li> </ul> </li> <li><em><strong>C_Plus2</strong></em> folder contains codes for the analysis of C<sup>2+</sup> ion data. The file descriptions are identical to those in the <em>H_Plus</em> directory.</li> <li><em><strong>intensity/calculate_intensity.m</strong></em>: calculates peak intensity of the laser pulse from measured parameters as well as statistical error.</li> <li><em><strong>intensity/compare_exp_sim.m</strong></em>: fits experimental and theoretical tomography and delay-dependent 2D projection values.</li> <li><em><strong>intensity/nir2hdf5_kHz.py</strong></em>: converts raw data files (from <em>rawdata_part.z*</em> archive<em>)</em> into hdf5 files.</li> </ul>
Raw Data for the article: Changes in the Transcriptome Profiles of Human Amnion-Derived Mesenchymal Stromal/Stem Cells Induced by Three-Dimensional Culture: A Potential Priming Strategy to Improve Their Properties
<p>Mesenchymal stromal/stem cells (MSCs) are believed to function in vivo as a homeostatic tool that shows therapeutic properties for tissue repair/regeneration. Conventionally, these cells are expanded in two-dimensional (2D) cultures, and, in that case, MSCs undergo genotypic/phenotypic changes resulting in a loss of their therapeutic capabilities. Moreover, several clinical trials using MSCs have shown controversial results with moderate/insufficient therapeutic responses. Different priming methods were tested to improve MSC effects, and three-dimensional (3D) culturing techniques were also examined. MSC spheroids display increased therapeutic properties, and, in this context, it is crucial to understand molecular changes underlying spheroid generation. To address these limitations, we performed RNA-seq on human amnion-derived MSCs (hAMSCs) cultured in both 2D and 3D conditions and examined the transcriptome changes associated with hAMSC spheroid formation. We found a large number of 3D culture-sensitive genes and identified selected genes related to 3D hAMSC therapeutic effects. In particular, we observed that these genes can regulate proliferation/differentiation, as well as immunomodulatory and angiogenic processes. We validated RNA-seq results by qRT-PCR and methylome analysis and investigation of secreted factors. Overall, our results showed that hAMSC spheroid culture represents a promising approach to cell-based therapy that could significantly impact hAMSC application in the field of regenerative medicine.</p>
Topological states in superlattices of HgTe class of materials for engineering three-dimensional flat bands
<p>In search of materials with three-dimensional flat band dispersions, using ab-initio computations we investigate how topological phases evolve as a function of hydrostatic pressure and uniaxial strain in two types of superlattices: HgTe/CdTe and HgTe/HgSe. In short-period HgTe/CdTe superlattices, our analysis unveils the presence of isoenergetic nodal lines, which could host strain-induced three-dimensional flat bands at the Fermi level without requiring doping, when fabricated, for instance, as core-shell nanowires. In contrast, HgTe/HgSe short-period superlattices are found to harbor a rich phase diagram with a plethora of topological phases. Notably, the unstrained superlattice realizes an ideal Weyl semimetal with Weyl points situated at the Fermi level. A small-gap topological insulator with multiple band inversions can be obtained by tuning the volume: under compressive uniaxial strain, the material transitions sequentially into a Dirac semimetal to a nodal-line semimetal, and finally into a topological insulator with a single band inversion.</p> <p>The provided repository contains data to reproduce the figures of the corresponding article.</p>
Three-dimensional in-situ imaging of single-grain growth in polycrystalline In2O3:Zr films
<p>Original data</p> <p>Here, we image a single-grain growth during the amorphous-to-polycrystalline transition in technologically relevant transparent conductive oxide (TCO) film of In<sub>2</sub>O<sub>3</sub>:Zr with <em>in-situ</em> Bragg coherent X-ray diffraction imaging.</p> <p>Data was obtained at 34ID-C end-station at Advanced Photon Source, Argonne National Laboratory (USA).</p> <p>Repository contains all raw datasets of the BCDI measurements, .spec files with corresponding meta-data, and .xlsx table with information on scan numbers related to annealing steps of the sample.</p>
Three-dimensional movement of the beak during seed processing in domestic canaries
<p>Many songbird species rely on seeds as a primary food source and the process of picking up, positioning, cracking, dehusking, and swallowing seeds is one of the most sophisticated tasks of the beak. Still, we lack understanding about how granivorous songbirds move their beak during the different phases of seed processing. In this study, we used multi-view high speed imaging to analyze the three-dimensional movement of the beak in feeding domestic canaries. Our analysis focuses on correlation of upper and lower beak, frequency of mandibulation, and direction of mandible movement in 3D space. We show that the correlation of maxilla and mandible movement differs among the phases of seed processing. Furthermore, we found that the beak moves at extremely high frequencies, up to 25 Hz, which resembles previously reported maximal syllable rates in singing canaries. Finally, we report that canaries use specific 3D mandible movements during the different phases of seed processing. Kinematic parameters do not differ between male and female canaries. Our findings provide an important biomechanical basis for better understanding the beak as a functional tool.</p>
Three-dimensional Digital Outcrop Models of the Tullig Sandstone, Western Irish Namurian Basin, Co. Clare, Ireland
<p>Tullig Sandstone is part of the Tullig Cyclothem, Western Irish Namurian Basin, Co. Clare, Ireland. The Tullig Sandstone is a prominent sandstone interval that represents an ancient fluvial-deltaic system. </p> <p>Outcrops of the Tullig Sandstone were surveyed by an unmanned aerial vehicle (UAV, DJI Mavic Pro Platinum™). Three-dimensional digital outcrop models were generated from images collected from UAV using Agisoft Metashape™.</p>
Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts
<p>These files are results obtained in<br><span><span><span><span>Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts</span></span></span></span><br>by Yoshito Hirata, Arisa H. Oda, Chie Motono, Masanori Shiro & Kunihiro Ohta.</p> <p>There are 33 files for the corresponding each reconstruction of three-dimensional chromosomone structures<br>for each cell.<br>There are 3D structures for 15 GM cells and 18 PBMC cells, which are obtained from the single cell Hi-C data of Tan et al. Science (2018).</p> <p>For each file, there are 6 columns:<br>The first column corresponds to the allele (0: maternal, 1: paternal)<br>The second column corresponds to the chromosome (1-22: chromosome's number, 23: X, 24: Y)<br>The third column corrsponds to the base point.<br>The fourth column, the fifth column and the sixth column correspond to x-, y-, and z-axes of our reconstruction.</p>
Three-dimensional surface scans of tooth surfaces of Sika deer from Torihama shell midden site
<p>Three-dimensional surface scans of tooth surfaces of Sika deer remains from Torihama shell midden site are saved in .sur format and surface analyses files in .mnt format, which are analyzed in:</p> <p>Sato, K., and Sato, T., and Kubo, M. O. "Reconstructing diets of hunted sika deer from Torihama shell midden site (ca. 6000 years ago) by dental microwear texture analysis" submitted to Frontiers in Ecology and Evolution. doi: 10.3389/fevo.2022.957038</p> <p>More details can be found in the information published in this paper.</p>
Three-Dimensional Thermoporoelastic Modeling of Hydrofracturing and Fluid Circulation in Hot Dry Rock: EGS Collab Experiment 1
<p>The data regarding the determined natural fractures, locations of monitoring devices, microseismic events, and well trajectories in EGS Collab Experiment 1.</p>
Raw data accompanying the manuscript "Cost-effective high-speed, three-dimensional live-cell imaging of HIV-1 transfer at the T cell virological synapse"
<p>These are the raw datasets used to generate the figures for the manuscript entitled "Cost-effective high-speed, three-dimensional live-cell imaging of HIV-1 transfer at the T cell virological synapse". The data files are 3D image stacks of a custom-built wide field deconvolution fluorescence microscope (.tif) and super-resolution structured illumination microscopy data (.dv) of Jurkat T cells transferring HIV-1 virus particles to previously uninfected primary T cells.</p>
Eddy Duck Data: Measured Three-Dimensional Structure of Surfzone Velocities
<p>This archive contains data from the 2011 EddyDuck experiment. Three-dimensional structure of surfzone velocity fields was measured using 12 horizontally-spaced Nortek Aquadopp current meters, each instrument measuring vertical profiles of water velocity. The experiment was conducted by folks from Washington State University and Oregon State University, with help from staff of the USACE's Duck Field Research Facility.</p> <p>Funding from the US National Sciences Foundation, Award OCE-1061692</p> <p>An in-review JGR-Oceans manuscript “Depth-Dependence of Nearshore Currents and Eddies” discusses the observations.</p> <p> </p> <p>Data are contained in two zip files.</p> <p>File summary.zip unzips to give a folder containing summary data in matlab 2015b format, and a pdf readme file explaining details.</p> <p>Folder full.zip unzips to give a folder containing full time-resolution data in ASCII format, and a readme file explaining details.</p> <p> </p> <p> </p> <p>Questions to steve_henderson@wsu.edu</p>
Data from: In vitro to in vivo extrapolation from three-dimensional hiPSC-derived cardiac microtissues and physiologically based pharmacokinetic modeling to inform next-generation arrythmia risk assessment
<p>Proarrhythmic cardiotoxicity remains a substantial barrier to drug development as well as a major global health challenge. <em>In vitro</em> human pluripotent stem cell-based new approach methodologies have been increasingly proposed and employed as alternatives to existing <em>in vitro</em> and <em>in vivo</em> models that do not accurately recapitulate human cardiac electrophysiology or cardiotoxicity risk. In this study, we expanded the capacity of our previously established three-dimensional human cardiac microtissue model to perform quantitative risk assessment by combining it with a physiologically based pharmacokinetic model, allowing a direct comparison of potentially harmful concentrations predicted <em>in vitro</em> to <em>in vivo</em> therapeutic levels. This approach enabled the measurement of concentration responses and margins of exposure for two physiologically relevant metrics of proarrhythmic risk (<em>i.e.</em>, action potential duration and triangulation assessed by optical mapping) across concentrations spanning three orders of magnitude. The combination of both metrics enabled accurate proarrhythmic risk assessment of four compounds with a range of known proarrhythmic risk profiles (<em>i.e., </em>quinidine, cisapride, ranolazine, and verapamil) and demonstrated close agreement with their known clinical effects. Action potential triangulation was found to be a more sensitive metric for predicting proarrhythmic risk associated with the primary mechanism of concern for pharmaceutical-induced fatal ventricular arrhythmias, delayed cardiac repolarization due to inhibition of the rapid delayed rectifier potassium channel, or hERG channel. This study advances human induced pluripotent stem cell-based three-dimensional cardiac tissue models as new approach methodologies that enable <em>in vitro</em> proarrhythmic risk assessment with high precision of quantitative metrics for understanding clinically relevant cardiotoxicity.</p>
Instantaneous, three-dimensional velocity fields past a bio-prosthetic aortic valve measured in-vitro with tomographic particle image velocimetry.
<p>Each folder contains instantaneous, three-dimensional velocity vector data obtained in a simplified model of the aortic root with a distinct size and geometry (small, medium, large, and sinus-less). The specific geometry of each aortic root model is contained in the corresponding folder.</p> <p>The velocity data is structured in the following way: Two separate folders for velocity data in the "ascending aorta" domain (AAo) and in the "sinus of Valsalva" domain (SOV). Each domain contains velocity datasets for instances t=0.00, 0.03, 0.06, ..., 0.39 s (t000, t003, t006, ..., t039). Each velocity dataset contains N=16 phase-locked instantaneous 3D velocity fields.</p> <p>The data was acquired using tomographic particle image velocimetry and a custom built hydraulic setup capable of replicating normal physiological flow conditions in the human aorta (heart rate = 72 bpm, cardiac output = 4.8 l)</p> <p>Data format:</p> <p>- aortic root geometry: STL (the geometry is provided with respect to the reference frame of the velocity data)</p> <p>- velocity data: NPY (NumPy), shape= (N_nodes, 6), columns contain X, Y, Z, U, V, W data, where U, V, W are the X, Y, Z components of the instantaneous vector field</p>
Micro-CT scans, whole-test meshes, and internal chamber segments of planktonic foraminifera for three-dimensional analysis of inter- and intra-specific variation in ontogenetic growth trajectories
<p> </p> <p>Here, we release tomographic reconstructions of 42 planktonic foraminifera from plankton tows and sediment traps, along with meshes and shrinkwrap meshes the whole tests and internal meshes of segmented chambers. Shrinkwrap meshes are test meshes that have been modified to close all pores and apertures in the test. Additionally, we have provided sample metadata for each specimen and volumetric measurements for the tests and chambers. This dataset was used in a study of ontogenetic growth in planktonic foraminifera and its variation within and among species.</p> <p> The CT-scans and reconstructions were obtained at Naturalis Biodiversity Center in Leiden, the Netherlands with a Zeiss Xradia 520 Versa micro-CT scanner. The meshes and segments were created at Yale University.</p> <ol> <li>Sample_Metadata.csv: Spreadsheet containing information on the sampling localities and dates for all specimens.</li> <li>Scan_data.csv: Spreadsheet containing metadata for all micro-CT scans including current strength, pixel size, voltage, image height, image width, and the number of images taken.</li> <li>Whole_Test_Measurements.csv: Spreadsheet containing measurements of linear dimensions (axis1, axis2, axis 3), total number of chambers, calcite test volume, calcite test surface area, shrinkwrap volumes, and and shrinkwrap surface areas for all specimens.</li> <li>Chamber_Measurements.csv: Spreadsheet containing measurements of individual internal chamber segments, including position from the final chamber (F-chamber), position from the first chamber (Chamber), volume, and surface area.</li> <li>CT_Scan_Stacks.zip: reconstructed micro-CT image stacks (.tif files) for each specimen.</li> <li>Meshes.zip: Meshes of the test calcite, the shrinkwrap, and the internal chamber segments for each specimen (.stl 3D mesh files). Regular test meshes are named with the format “SampleID.stl”, and shrinkwrap meshes are named “SampleID-WRAP.stl”. Chamber meshes are named “SampleID-CH#.stl” and “SampleID-CH#-Wrap.stl”. Chambers are numbered in relation to their position from the final chamber, with “CH1” being the final chamber and “CH2” being the penultimate chamber.</li> </ol> <p>This data is described and analyzed in the manuscript “Three-Dimensional Analysis of Inter- and Intraspecific Variation in Ontogenetic Growth Trajectories of Planktonic Foraminifera” submitted to the journal <em>Marine Micropaleontology.</em></p>
Video supplement: A three-dimensional palaeo-reconstruction of the groundwater salinity distribution in the Nile Delta Aquifer
<p>Videos of validated models. The filenames indicate simulation code, for explanation see accompanying paper, submitted to HESS.</p> <p><strong>Abstract</strong></p> <p>The Nile Delta is an important agricultural area with a fast-growing population. Though traditionally irrigated with surface water, the delta increasingly relies on groundwater. However, saline groundwater extends far land inward, rendering groundwater close to the coastal zone useless for consumption or agriculture. To aid groundwater management decisions, hydrogeologists reconstructed this saline and brackish groundwater zone using variable-density groundwater models with very large dispersivities. However, this approach cannot explain the observed freshening of this zone as observed by hydrogeochemists, who hypothesize that the coastal saline zone is the effect of the Holocene transgression. Here, we investigated physical plausibility of this hypothesis by conducting a palaeo-reconstruction of groundwater salinity for the last 32 ka with a complex 3D variable-density groundwater flow model, using state-of-the-art model code that allows for parallel computation. Several scenarios with different lithologies and hypersaline groundwater provenances were simulated, of which five were selected that showed the best match with the observations. Amongst these selections, total fresh water volumes varied strongly, ranging from 1526 to 2659 km3, mainly due to uncertainties in the lithology offshore and at larger depths. This range is smaller (1511-1989 km3) when we consider the volumes of onshore fresh groundwater within 300 m depth. Regardless of the variance, in all cases the total volume of hypersaline groundwater exceeded that of sea water. We also show that during the last 32 ka, the total fresh groundwater volumes significantly declined, with a factor ranging from 1.9 to 5.4, due to the rising sea-level. Compared to a steady-state solution with present-day boundary conditions, the palaeo-reconstruction improved our validation for the saline zone (5 g/L – 35 g/L TDS). Also, under highly permeable conditions the marine transgression simulated with the palaeo-reconstruction led to a steeper fresh-salt interface compared to its steady-state equivalent, while low permeable clay layers allowed for the preservation of volumes of fresh groundwater. This shows that long-term transient simulations are needed when estimating present-day fresh-salt groundwater distribution in large deltas. The insights of this study are also applicable to other major deltaic areas, given the wide-range of lithological model scenarios used in this study and since many deltas also experienced a Holocene marine transgression.</p>
Data for three-dimensional active nematic turbulence
<p>Selected data from numerical simulation of bulk three-dimensional active nematic turbulence. Data includes nematic Q-tensor and the velocity field. The outer layer of data points is used for allocation of periodic boundary conditions. Symmetric Q-tensor is written in the order (Q<sub>xx</sub>, Q<sub>yy</sub>, Q<sub>zz</sub>, Q<sub>xy</sub>, Q<sub>xz</sub>, Q<sub>yz</sub>). Data points are written with x as the fast coordinate. The data is obtained by numerically solving the Beris-Edwards model for nematic hydrodynamics, generalized by the active stress term [1,2]. The details of the data and the numerical model are available in publication "Spectral energy analysis of bulk three-dimensional active nematic turbulence" [3].</p> <p>Files:</p> <ul> <li>"active_turbulence-135x135x135-0.300.tar" — A timeline of active turbulence including Q-tensor and velocity profile in a box of size (135)<sup>3</sup> at activity 0.3 L/Δx<sup>2</sup>. The timeline includes 26000 steps, relevant fields are written every 50 steps.</li> <li>"active_turbulence-407x407x407-0.025_Q.raw.gz" — Q-tensor profile in a box of size (407)<sup>3</sup> at activity 0.025 L/Δx<sup>2</sup>.</li> <li>"active_turbulence-407x407x407-0.025_u.raw.gz" — velocity profile in a box of size (407)<sup>3</sup> at activity 0.025 L/Δx<sup>2</sup>.</li> <li>"active_turbulence-407x407x407-0.100_Q.raw.gz" — Q-tensor profile in a box of size (407)<sup>3</sup> at activity 0.1 L/Δx<sup>2</sup>.</li> <li>"active_turbulence-407x407x407-0.100_u.raw.gz" — velocity profile in a box of size (407)<sup>3</sup> at activity 0.1 L/Δx<sup>2</sup>.</li> <li>"active_turbulence-407x407x407-0.300_Q.raw.gz" — Q-tensor profile in a box of size (407)<sup>3</sup> at activity 0.3 L/Δx<sup>2</sup>.</li> <li>"active_turbulence-407x407x407-0.300_u.raw.gz" — velocity profile in a box of size (407)<sup>3</sup> at activity 0.3 L/Δx<sup>2</sup>.</li> </ul> <p> </p> <p> </p>
Fig. 11 in Three-dimensional elasto-plastic soil modelling and analysis of sauropod tracks
Fig. 11. Vertical displacement after circular and pressure-shaped curvilinear quadrilateral. A. Vertical displacement after a circular pressure. B. Vertical displacement after a pressure-shaped curvilinear quadrilateral with concave and convex alternate sides.
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.