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Dataset results
311 results for “function dataset”
Dataset: Predicting T Cell Receptor Functionality against Mutant Epitopes
<p>This upload contains the Datasets and Supplementary Material for "Predicting T Cell Receptor Functionality against Mutant Epitopes" (DOI: https://doi.org/10.1101/2023.05.10.540189) by Felix Drost, Emilio Dorigatti, Adrian Straub, Philipp Hilgendorf, Karolin I. Wagner, Kersten Heyer, Marta López Montes, Bernd Bischl, Dirk H. Busch, Kilian Schober, and Benjamin Schubert.</p>
Dataset related to Deliverable 2.2 - Report on functional, nutritional, and sensory characteristics of three optimized alternative proteins
<p>Dataset related to Deliverable 2.2 - Report on functional, nutritional, and sensory characteristics of three optimized alternative proteins</p>
Dataset related to Deliverable 2.1 - Report on functional, nutritional and sensory characteristics of current three alternative proteins
<p>Dataset related to Deliverable 2.1 - Report on functional, nutritional and sensory characteristics of current three alternative proteins</p>
Dataset of Functionalized MOFs/AuNCs PEC
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Nasal organoids as optimal models for studying structure and function of primary nasal epithelial cell cultures - DIA-MS Dataset
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Example Datasets for Functional Enrichment Analysis
<p>This dataset contains a set of example data for a functional enrichment tutorial.</p>
DataSet - Muscle structure governs joint function: linking natural variation in medial gastrocnemius structure with isokinetic plantar flexor function
<p>Experimental data used in analysis and computational model files for research study 'Muscle structure governs joint function: linking natural variation in medial gastrocnemius structure with isokinetic plantar flexor function'</p>
Dataset 2. Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II
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Dataset for: Temporal trajectories of plant functional traits in mediterranean grasslands under different grazing regimes
<p>The excel file contains three spreadsheets:</p> <ol> <li>the environmental and temporal information about the plot (sample)</li> <li>the plant functional traits of the species (traits)</li> <li>the species composition of the plant communities (species).</li> </ol> <p>These data have been used for the statistical analysis of the manuscript Nour et al., 2024 on Applied Vegetation Science. For more information see the manuscript "Temporal trajectories of plant functional traits in Mediterranean grasslands under different grazing regimes" (Nour et al., 2024).</p>
Dataset for the article "A deep equivariant neural network approach for efficient hybrid density functional calculations"
<p>Dataset files for DeepH-hybrid, containing structures and preprocessed Hamiltonian matrices computed with HSE06 hybrid functional and ABACUS DFT package.</p> <p>Enclosed include:</p> <ol> <li>The four datasets corresponding to the four DeepH-hybrid models mentioned in DeepH-hybrid's paper, each containing material structures and electronic structure properties of </li> <li>Basis set files for the ABACUS DFT package</li> <li>Snapshot of a version of the additional codes utilized to preprocess hybrid DFT Hamiltonians (also available via this <a href="https://github.com/aaaashanghai/DeepH-hybrid">GitHub link</a>)</li> </ol> <p>Note only the additional codes of DeepH-hybrid is provided, and it may be used in combination with DeepH-E3 package for neural-network training. For additional details please refer to the "README" file of the code.</p>
Essential role of N-terminal SAM regions in STIM1 multimerization and function dataset
<p>The single-pass transmembrane protein Stromal Interaction Molecule 1 (STIM1), located in the endoplasmic reticulum (ER) membrane, possesses two main functions:<br>It senses the ER-Ca2+ concentration and directly binds to the store-operated Ca2+ channel Orai1 for its activation when Ca2+ recedes. At high resting ER-Ca2+ concentration, the ER-luminal STIM1 domain is kept monomeric but undergoes di/multimerization once stores are depleted. Luminal STIM1 multimerization is essential to unleash the STIM C-terminal binding site for Orai1 channels. However, structural basis of the luminal association sites has so far been elusive. Here, we employed molecular dynamics (MD) simulations and identified two essential di/multimerization segments, the α7 and the adjacent region near the α9-helix in the sterile alpha motif (SAM) domain. Based on MD results, we targeted the two STIM1 SAM domains by engineering point mutations. These mutations interfered with higher-order multimerization of ER-luminal fragments in biochemical assays and puncta formation in live-cell experiments upon Ca2+ store depletion. The STIM1 multimerization impeded mutants significantly reduced Ca2+ entry via Orai1, decreasing the Ca2+ oscillation frequency as well as store-operated Ca2+ entry. Combination of the ER- luminal STIM1 multimerization mutations with gain of function mutations and coexpression of Orai1 partially ameliorated functional defects. Our data point to a hydrophobicity-driven binding within the ER-luminal STIM1 multimer that needs to switch between resting monomeric and activated multimeric state. Altogether, these data reveal that interactions between SAM domains of STIM1 monomers are critical for multimerization and activation of the protein.</p>
Dataset for structural function recognition
<p>Dataset for structural function recognition</p>
Dataset related to "A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations"
<p>This is an accompanying dataset to the article with the title "A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations" (DOI: <a href="https://doi.org/10.1162/netn_a_00429" target="_blank" rel="noopener">10.1162/netn_a_00429</a>). It contains the resulting data of the manipulated SSCx network model, such as benchmarks, fitted stochastic models, manipulated connectomes, structural validations, as well as simulation data and analysis results.</p> <p>The corresponding repository with code, configuration files, and detailed instructions for reproducing the results in this dataset as well as generating the results figures in the accompanying article is available here: <a href="https://github.com/BlueBrain/sscx-connectome-manipulations" target="_blank" rel="noopener">https://github.com/BlueBrain/sscx-connectome-manipulations</a></p> <p>The underlying <em>Connectome-Manipulator</em> software is available here: <a href="https://github.com/BlueBrain/connectome-manipulator" target="_blank" rel="noopener">https://github.com/BlueBrain/connectome-manipulator</a></p> <p>Additional requirement: Original SSCx network model (DOI: <a href="https://doi.org/10.5281/zenodo.8026353" target="_blank" rel="noopener">10.5281/zenodo.8026353</a>)</p> <p>ℹ️ Disclaimer: Some results may have been produced with an older version of <em>Connectome-Manipulator</em>, so slight differences might be possible when re-running with the latest version.</p> <p><strong>Update 25/09/2024 (v2):</strong> Added benchmark results for assessing strong and weak scaling behavior of connectome rewiring.</p> <blockquote> <p><strong><em>Funding</em></strong></p> <p><em>Funding provided by the Swiss government’s ETH Board to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL).</em></p> </blockquote>
code and datasets for "GP73 reinforces cytotoxic T-cell function by regulating HIF-1α and increasing antitumor efficacy"
<p>We utilized T-cell-specific GP73 knockout mice to establish MC38 and B16 tumor models to investigate the impact of GP73-deficient T cells on tumor growth. Single-cell sequencing was subsequently employed to classify tumor-infiltrating immune cells and assess changes in cytokines and metabolic genes. Through RNA sequencing, real-time quantitative PCR, western blotting, flow cytometry, seahorse analysis, glucose uptake, and lactate secretion assays, we explored how GP73 regulates HIF-1α to influence T-cell antitumor functionality. Furthermore, we established adoptive transfer experiments to study the ability of GP73-overexpressing T cells to combat tumors. Clinical tumor patient blood samples were collected to assess the relationship between immunotherapy efficacy and T-cell GP73 levels.</p>
Dataset for: Multivascular networks and functional intravascular topologies within biocompatible hydrogels
<p>Dataset for:</p> <p>Multivascular networks and functional intravascular topologies within biocompatible hydrogels</p> <p>Bagrat Grigoryan1,∗, Samantha J. Paulsen1,∗, Daniel C. Corbett2,∗, Daniel W. Sazer1, Chelsea L. Fortin2, Alexander J. Zaita1, Paul T. Greenfield1, Nicholas J. Calafat1, John P. Gounley3, Anderson H. Ta1, Fredrik Johansson2, Amanda Randles3, Jessica E. Rosenkrantz4, Jesse D. Louis-Rosenberg4, Peter A. Galie5, Kelly R. Stevens2,†, Jordan S. Miller1,†</p> <p>1Department of Bioengineering, Rice University, Houston, TX 77005, USA 2Department of Bioengineering, University of Washington, Seattle, WA 98195, USA 3Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA 4Nervous System, Somerville, MA 02143, USA 5Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA</p> <p>∗Equal contribution. †Corresponding authors. Email: ksteve@uw.edu (K.R.S.) and jmil@rice.edu (J.S.M.).</p> <p>Solid organs transport fluids through distinct vascular networks that are biophysically and biochemically entangled, creating complex 3D transport regimes that have remained difficult to produce and study. We establish intravascular and multivascular design freedoms with photopolymerizable hydrogels using food dye additives as biocompatible yet potent photoabsorbers for projection stereolithography. We demonstrate monolithic transparent hydrogels produced in minutes comprising efficient intravascular 3D fluid mixers and functional bicuspid valves. We further elaborate entangled vascular networks from space-filling mathematical topologies and explore the oxygenation and flow of human red blood cells during tidal ventilation and distension of a proximate airway. In addition, we deployed structured biodegradable hydrogel carriers in a rodent model of hepatic disease to highlight the potential translational utility of this materials innovation.</p>
dataset for "A location and dispersion effects-based ridge analysis method using desirability functions for multi-response optimization"
<p>dataset and code for “A location and dispersion effects-based ridge analysis method using desirability functions for multi-response optimization”</p>
ActTemp+sMSA dataset of "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"
<p>PDB models generated with the protocol described in "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"</p>
Dataset from: Functional traits explain both seedling and adult plant spatial patterns in gypsum annual species
<p><span>1. </span><span>Ecological processes such as seed dispersal or plant–plant interactions and environmental constraints such as climate or soil heterogeneity are known to influence establishment, and thus the spatial patterns of plant communities and populations. In this study, we hypothesized that key functional traits such as the specific leaf area (SLA), reproductive ratio (reproductive/vegetative biomass), seed mass, and maximum plant height would influence the spatial patterns of individual species in annual, gypsophilous plant communities, and that these effects would be modulated by both the soil surface structure (biocrust) and climate (precipitation) conditions. </span></p> <p><span>2. </span><span>We mapped the spatial patterns of all plants found in six 1 </span><span>x</span><span> 1 m plots (more than 1000 individuals per plot) in both the seedling (autumn) and adult stages (spring) under two biocrust experimental conditions (intact vs disturbed biocrust) during two consecutive years which were contrasted in term of precipitation (dry year and wet year). To assess the spatial patterns of seedlings and adults, we fitted four different spatial point pattern models (i.e., Poisson, inhomogeneous Poisson, Poisson cluster, and inhomogeneous Poisson cluster processes) to each of the 242 populations of the 27 most abundant species that had more than 15 individuals per plot.</span></p> <p><span>3. </span><span>Most seedling populations exhibited clustered spatial patterns that persisted in the adult stage, which suggests that short-distance dispersal is an adaptive trait for soil specialists such as gypsophilous plants. One-third of the populations fitted an inhomogeneous model best, but the physical structure of the biocrust was not related to them. More importantly, we found a connection between the functional strategies of species and the spatial distribution of plants. In particular, during the dry year, irrespective of the biocrust conditions, species with a high SLA and high Rep/Veg mainly exhibited clustered spatial patterns, whereas low SLA and low Rep/Veg were associated with random distributions. Species with heavy and light seed masses had random and clustered patterns, respectively. In both the dry and wet years, species with lower maximum heights had clustered patterns, whereas taller species exhibited random patterns. In addition, species with heavier seeds and greater maximum heights had the largest cluster sizes.</span></p> <p><span>4. </span><span>Our results confirm that the spatial patterns of seedlings and adult plants are significantly determined by the functional strategy of each species.</span></p>
Receiver function data on the Southeastern Tibetan Plateau (Dataset)
<p>The dataset about the study of Crustal Anisotropy Beneath the Southeastern Tibetan Plateau and the lateral Extension of the Plateau</p>
Differences in Scattering Properties of the Shallow Crusts of Earth, Mars, and the Moon Revealed by P-Wave Receiver Functions - Dataset
<p>This version includes three parts. The first part is the seismic data set of Earthquakes, Marsquakes, and Moonquakes used in "Differences in Scattering Properties of the Shallow Crusts of Earth, Mars, and the Moon Revealed by P-Wave Receiver Functions" by Shi et al. (2023). In the data set of Earthquakes and Marsquakes, the direct P wave starts after 120 s. In the data set of Moonquakes, the direct P wave starts after 50 s. The second part is the velocity models used in the article for the Earth, Mars, and Moon. The third part is the code used to reproduce all the figures in the main text.</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.