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311 results for “function dataset”
Dataset for paper "1-to-1 or 1-to-n? Investigating the effect of function inlining on binary similarity analysis"
<p>This is the dataset constructed and used in the paper "1-to-1 or 1-to-n? Investigating the effect of function inlining on binary similarity analysis". </p> <p>We release it with its ground truth labels to facilitate further research in binary similarity analysis under function inlining. Besides, we also welcome others to find miss-labeling in this dataset and fix them. We hope our dataset could help researchers conduct their studies and improve the binary similarity analysis techniques.</p> <p>Binaries of dataset-I can also be accessed from https://github.com/SoftSec-KAIST/BinKit. It is named the "normal dataset".</p> <p>Any miss-labeling can be reported at https://github.com/island255/TOSEM2022.</p> <p>Using this dataset, please cite our paper, "1-to-1 or 1-to-n? Investigating the effect of function inlining on binary similarity analysis".</p>
dataset How does the balance of metal and acid functions on the benchmark Mo/ZSM-5 catalyst drive the Methane dehydroaromatization reaction
<p>dataset How does the balance of metal and acid functions on the benchmark Mo/ZSM-5 catalyst drive the Methane dehydroaromatization reaction</p>
Supplementary table of PRIDE datasets analyzed for "FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data"
<p>Our proteomics dataset comes from The PRoteomics IDEntifications (PRIDE) database, the world’s largest data repository of mass spectrometry-based proteomics data. Specifically, we used 633 human proteomics project experiments with a total of 32,546 runs and reanalyzed them using ionbot with an FDR threshold of 0.01 [16], resulting in a total of 154,885,151 peptide spectrum matches for 18,846 proteins. Here is the full list of projects, runs, and general statistics.</p>
Dataset from: An intuitive form of the energy functional for resistive plasma perturbations
<p>The energy functional of ideal magnetohydrodynamics (MHD) is extended to the regime of finite resistivity and transformed to an intuitive form, which separates pressure-gradient, current-density drive and stabilizing phenomena, analogously to the ideal version of the functional derived by Johnson and Greene. The resulting resistive energy functional is not in the form of a solvable eigenvalue problem but is intended to analyze the energetic composition of eigenfunctions which were calculated in advance by solving the MHD equations. The new resistive energy functional provides information on the different energetic drives and stabilizing phenomena of an eigenfunction. The new energy functional has been implemented in the CASTOR3D code in general 3D curvilinear coordinates and successfully validated across three different coordinate systems for a numerical test case.</p>
Multimodal dataset: Protein Function Prediction using STRING data & COVID19 Mortality Model by EI
<p>The PFP.zip file contains 1. 5 well-formated GO terms dataset for EI, 2. STRING data 3. GO term annotation. The last two could be merged by the 'generate_data.py' script in https://github.com/GauravPandeyLab/ensemble_integration</p> <p>The covid19_model_built.zip contained the EI model built based on the COVID-19 Mortality dataset, the detail of usage are here:.</p>
A specimen-level dataset of functional traits and DNA barcodes for Chinese bees
<p>The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals, thus we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. </p> <p>We built a novel dataset of traits and DNA barcodes for wild bees in China. An informatics framework was developed for phylogeny-based integration of these data and prediction of traits for any subject barcodes, and compared to two Blast-based methods of trait assignment. </p> <p>Under the specimen-level dataset, rate and accuracy of trait assigned dropped with an increase in distance between the query and its nearest reference member, though phylogenetic assignment was found to perform best under several criteria. For a wider range of compiled traits, conservative life-history traits showing the highest rates of assignment, for example sociality was predicted with confidence at 53%, parasitism at 44%, and nest location at 33%. </p> <p>Bayesian phylogenetic assignment of traits showed particular advantage over distance-based methods in the much lower rate that it would return incorrect state predictions when the query lacked relatives in the reference data. Automated, taxon-independent trait assignment might be applied at scale to either barcodes or metabarcodes in any invertebrates. With the further generation of integrated barcode and trait data, the assignment accuracy of the method is likely to increase. </p>
Dataset: Quantifying cell densities and biovolumes of phytoplankton communities and functional groups using scanning flow cytometry, machine learning and unsupervised clustering
<p>This dataset contains all relevant data for the manuscript (in submission) "<em>Quantifying cell densities and biovolumes of phytoplankton communities and functional groups using scanning flow cytometry, machine learning and unsupervised clustering</em>".</p> <p>Code written to analyse this dataset (which may be adapted for other flow cytometry datasets) is found at https://zenodo.org/record/999747</p> <p>--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</p> <p>Naming convention for raw flow cytometry data files (located in /Script 3. Generating raw data subset/input/):</p> <p>[Allparameters] _ [Year] - [Month] - [Date] [Hour] [u] [Minute] _ [Depth]</p> <p>e.g: Allparameters_2014-07-31 08u08_1.0m</p> <p>The date, time and depth indicate the location and time at which the measurement was taken.</p>
Dataset for publication "Tuning germanane bandgap via cyanoethyl functionalization for cutting-edge photoactive cathodes: photo-enhanced hybrid zinc-ion capacitor evaluation"
<p>This is a dataset for a paper "Tuning germanane bandgap via cyanoethyl functionalization for cutting-edge photoactive cathodes: photo-enhanced hybrid zinc-ion capacitor evaluation". All details about the data are included in the readme file.</p>
Fig. 1 in A dataset on African bats' functional traits
Fig. 1 Graphical workflow of AfroBaT dataset construction.
Synthetic dataset for the testing of local conditioning of regularization function using geological uncertainty.
<p>This companion datasets relates to the model shown supplementary information to the manuscript "<strong>Integration of geological uncertainty into geophysical inversion by means of local gradient regularization</strong>", by J. Giraud, M. Lindsay, V. Ogarko, M. Jessell, R. Martin and E. Pakyuz-Charrier, submitted to Solid Earth. The archive contains the input and output geophysical data, starting and inverted models, probabilistic geological model and conditioning volume derived from the calculation of Shannon's entropy. </p> <p>This description will be updated with the accurate reference to the journal publication and acknowledgement prior to publication. </p>
Assessing key ecosystem functions through soundscapes: a new perspective from coral reefs (Acoustic dataset)
<p>Acoustic dataset associated to "Assessing key ecosystem functions through soundscapes: a new perspective from coral reefs" - article published in Ecological Indicators (2019) <a href="https://doi.org/10.1016/j.ecolind.2019.105623">https://doi.org/10.1016/j.ecolind.2019.105623</a></p> <p>All details about sampling are available in the Material and Methods section.</p> <p>Sound sample names are coded as follows : SITE_acq_hydro_100k_DDMMYY_HHMMSS.wav ; with HHMMSS in Local Time (UTC+3)</p>
Dataset 1. Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II.
<p>This dataset is used in the bioformatic methods of the article <strong>Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II </strong>(doi: 10.1186/s13059-025-03537-2). The corresponding code can be found in the repository https://github.com/descostesn/chromglycomethods.git</p>
Dataset: Catalytic pyrolysis mechanism of lignin moieties driven by aldehyde, hydroxyl, methoxy, and allyl functionalization: the role of reactive quinone methide and ketene intermediates
<p>The derived data is part of a manuscript submitted to the journal Green Chemistry, entitled "Catalytic pyrolysis mechanism of lignin moieties driven by aldehyde, hydroxyl, methoxy, and allyl functionalization: the role of reactive quinone methide and ketene intermediates". [DOI https://doi.org/10.1039/d4gc03143a. This work is supported by the Swiss National Science Foundation (project number 200021_178952)</p> <p>Raw data can be found: https://doi.org/10.16907/1ac46f03-6e1b-4230-b5c0-3df2cec87b5e</p> <p>The raw Photoelectron Photoion Coincidence (PEPICO) data were obtained during catalytic fast pyrolysis of eugenol, vanillin, syringol over H-ZSM-5 and HFAU. The analysis software can be obtained from: https://www.psi.ch/en/sls/vuv/pepico. The folders contain mass spectra and threshold photoelectron raw data at different reactor temperatures.</p>
Dataset for the publication: Synthesis, Characterization and Interconversion of p-Tolylsulfone-Functionalized Norbornadiene/Quadricyclane Couples
<p>Overview of all collected data used for the publication "Synthesis, Characterization and Interconversion of p-Tolylsulfone-Functionalized Norbornadiene/Quadricyclane Couples" in the journal Chemistry - A European Journal.</p>
Supporting Dataset for "Comparing GGA, GGA+U, and Meta-GGA Functionals for Redox-Dependent Binding at Open Metal Sites in Metal−Organic Frameworks"
<p>Supporting Dataset for "Comparing GGA, GGA+U, and Meta-GGA Functionals for Redox-Dependent Binding at Open Metal Sites in Metal−Organic Frameworks"</p>
Supplementary Dataset for Trenner et al. 2022: Evolution and Functions of Plant U-box proteins (PUBs): From protein quality control to signalling
<p>This record contains additional information and a supplementary dataset of sequence alignment files and phylograms that support the publication:</p> <p>Trenner J, Monaghan J, Saeed B, Quint M, Shabek N, Trujillo M. 2022. Evolution and Functions of Plant U-box proteins (PUBs): From protein quality control to signalling. (submitted to Annual Review of Plant Biology)</p> <p>Included files:</p> <p><em>Additional information.pdf</em></p> <p>This file contains Supplementary Methods and References.</p> <p><br> <em>Supp_Fig1_Ubox_full_protein_maximum_likelihood_phylogram_linear.pdf</em></p> <p>A multiple protein sequence alignment by MAFFT of 1121 U-box protein sequences from 21 species and four outgroup sequences containing a RING finger domain (<em>A. thaliana</em> RBX1, <em>A. thaliana</em> RMA1, <em>S. cerevisiae</em> RAD18, <em>Homo sapiens</em> TRAF6 ) was used to infer a phylogenetic tree by maximum likelihood with IQ-TREE. The implemented ultrafast bootstrap approximation, set to 2000 bootstrap samples, was used for branch support. The consensus tree was annotated using iTOL.</p> <p> </p> <p><em>Supp_Fig2_Ubox_domain_maximum_likelihood_phylogram_linear.pdf</em></p> <p>In order to analyse specifically the evolution of the U-box domain, the U-box domain of the final 1121 U-box protein sequences as well as the RING finger domain of the four outgroup sequences were isolated and aligned by MAFFT. The U-box domain alignment was then used to infer a phylogenetic tree by maximum likelihood with IQ-TREE. The implemented ultrafast bootstrap approximation, set to 2000 bootstrap samples, was used for branch support. The consensus tree was annotated using iTOL. This tree was used to interpret the evolutionary history of U-box proteins in the main text.</p> <p> </p> <p><em>MAFFT_alignment _1121seqs_Ubox_full_protein_plus_4seqs_RING_outgroup.fasta</em></p> <p>Multiple protein sequences alignment by MAFFT of 1121 U-box full length protein sequences and four RING finger protein sequences, FASTA formatted.</p> <p> </p> <p><em>MAFFT_alignment _1121seqs_Ubox_domain_plus_4seqs_RING_outgroup.fasta</em></p> <p>Multiple protein sequences alignment by MAFFT of U-box domain sequences of 1121 U-box protein and four RING finger domain sequences of outgroup sequences, FASTA formatted.</p> <p> </p> <p><em>Ubox_protein_sequences_information.xlsx</em></p> <p>Spreadsheet with sequence ID information and source databases.</p>
Dataset for "Supramolecular aggregation control in polyoxometalates covalently functionalized with oligoaromatic groups"
<p>Spectroscopic datasets for "Supramolecular aggregation control in polyoxometalates covalently functionalized with oligoaromatic groups"</p> <p>Acknowledgement and Funding</p> <p>The authors gratefully acknowledge the Deutsche Forschungsgemeinschaft DFG for financial support (projects TRR 234 “CataLight”, project no: 364549901; SPP2102, “Light-controlled reactivity of metal complexes”, project no: 359737763, 494988281). S.K. gratefully acknowledges a LGFG PhD fellowship by the State of Baden-Württemberg.</p>
Training datasets of size 1K, 3K, and 9K for four utility function variants
<p>The datasets include 1K, 3K, and 9K training data points that are used for training utility-change prediction models in systems with ground truth from four different mathematical complexities:</p> <ul> <li>Linear utility function</li> <li>Saturating utility function</li> <li>Discontinuous utility function</li> <li>Combined utility function ( combining the above three variants)</li> </ul>
Datasets used for the publication: UAV-Lidar reveals that canopy structure mediates the influence of edge effects on forest diversity, function and microclimate
<p>Datasets used for the publication: UAV-Lidar reveals that canopy structure mediates the influence of edge effects on forest diversity, function and microclimate.</p> <p>The file "Blanchard_et_al_JoE_2023_data_plot_trees.csv" contains individual tree indentification data for the 46 plots used in the study.</p> <p>The file "Blanchard_et_al_JoE_2023_data_plot_aggregated.csv" contains plot-level aggregated metrics used for the analyses:</p> <p>- distance to the forest edge</p> <p>- diversity indices : the 20-sp rarefied species richness "rar_sp_richness_20" and the 20-sp rarefied Beta diversity "Beta_div" which corresponds to the plos coordinates on the PCoA first axis.</p> <p>- functional indices: the community weighted mean trait values for the four traits used in this study : ,"WD","SLA","LA","LDMC"; the fonctional divergence index "FD_trans.FDiv"; and the synthetic community weigthed mean trait wich corresponds to the postion on plots on the principal component analysis of species trait values "Functional_composition_trans". Note that the SLA and LA values were log-transformed before computing "FD_trans.FDiv" and "Functional_composition_trans".</p> <p>- UAV-LiDAR-dervived metrics: canopy height, gap fraction ("gap_fraction2"), slope, curvature</p> <p>- The estimated plot above graound biomass "agb_plot", and the mean value of the vapor pressure deficit during the drisest month "max_monthly_VPD".</p> <p>- coordinates of the plots in UTM 58S (Coordinate reference system)</p> <p>Please read the material and method section of the article for more informations on this dataset.</p>
Dataset: Imaging the columnar functional organization of human area MT+ to axis-of-motion stimuli using VASO at 7 Tesla
<p>First release upon acceptance of the paper. </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.