Find research datasets worth reusing

KeyRecs: Keystroke Dynamics Dataset

KeyRecs is a keystroke dynamics dataset that can be used to train, validate, and test machine learning models for anomaly detection and robust typing pattern recognition, as well as the clustering and classification of users that present a similar behavior. It contains fixed-text and free-text samples of user typing behavior, obtained in a study with 100 participants of 20 different nationalities performing password retype and transcription exercises. The samples consist of inter-key latencies computed by measuring the time between each key press and release during an exercise, following a digraph model. Additionally, the participants were also asked to provide their demographic information regarding age, gender, handedness, and nationality. KeyRecs can be valuable to enhance the recognition of authorized users and prevent illegal logins in biometric authentication software, and can be combined with additional data recordings to create more extensive datasets and improve the generalization of machine learning models. If you use this dataset, please cite the primary data article: <a href="https://doi.org/10.1016/j.dib.2023.109509">https://doi.org/10.1016/j.dib.2023.109509</a>

Dataset for "A computational fluid dynamics—Population balance equation approach for evaporating cough droplets transport"

Dataset for figures and tables of the article "A computational fluid dynamics—Population balance equation approach for evaporating cough droplets transport" submitted to "International Journal of Multiphase Flow".

Extreme dynamics of a small molecule in its bound state with an intrinsically disordered protein

These data support the manuscript entitled "Extreme dynamics of a small molecule in its bound state with an intrinsically disordered protein" by Heller, Shukla, Figueiredo, and Hansen.This data should be used with the code provided on GitHub at https://github.com/hansenlab-ucl/R2_IDP_small_mol. Once downloaded, this directory should be extracted using the following command:    tar -xzvf Data.tar.gzThe directory should be saved with the name 'Data' placed in the same directory as the GitHub README.md file.This dataset contains:  Nuclear Magnetic Resonance (NMR) spectroscopy data files (.ft2 format) including: * 1H 1D ligand-detected chemical shift titration of 5-fluoroindole (50 uM) with increasing concentrations of the protein, non-structural protein 5A, domains 2 and 3 (NS5A-D2D3), in 1H_1D_ft2_data/* 1H pseudo-2D Diffusion Ordered SpectroscopY (DOSY) data of 5-fluoroindole (50 uM) with and without NS5A-D2D3 (75 uM) in 1H_DOSY_data/* 1H-15N Heteronuclear Single Quantum Coherence (HSQC) measurements of NS5A-D2D3 (40 uM) in the absence and presence of 5-fluoroindole (160 and 320 uM) in 1H_15N_HSQC_ft2_and_metadata/* 19F 1D ligand-detected chemical shift titration of 5-fluoroindole (50 uM) with increasing concentrations of NS5A-D2D3 in 19F_1D_ft2_data/* 19F pseudo-2D ligand-detected longitudinal (spin-lattice, R1,eff) relaxation titration data of 5-fluoroindole (50 uM) with increasing concentrations of NS5A-D2D3 in 19F_R1eff_ft2_data/* 19F pseudo-2D ligand-detected longitudinal (spin-spin, R2,eff) relaxation titration data of 5-fluoroindole (50 uM) with increasing concentrations of NS5A-D2D3 in 19F_R2eff_ft2_data/Circular Dichroism (CD) data files (.txt format) including: * CD measurements of NS5A-D2D3 at increasing concentrations in CD_data/no_molecule/* CD measurements of NS5A-D2D3 with and without the small molecule, 5-fluoroindole CD_data/with_molecule/Metadata * Metadata from the Biological Magnetic Resonance Data Bank (https://bmrb.io/) used to determine scaling factors for the calculation of chemical shift perturbations in 1H_15N_HSQC_ft2_and_metadata/

CAELUS: Classification of sky conditions from 1-min time series of global solar irradiance using variability indices and dynamic thresholds

CAELUS, a novel classification algorithm that relies on various thresholds to separate all possible sky conditions into six classes, is presented in Ruiz-Arias and Gueymard (2023, doi: <a href="https://doi.org/10.1016/j.solener.2023.111895">10.1016/j.solener.2023.111895</a>). This dataset was used to develop, validate and benchmark CAELUS. It is made up by 1-min quality-assured observations of global horizontal irradiance (GHI) and diffuse horizontal irradiance at 54 stations of the Baseline Surface Radiation Network (BSRN) archive, which is publicly available (see download instructions in https://bsrn.awi.de/data). The dataset includes 5 years of data per station, except in two of them (Petrolina, Brazil, and Solar Village, Saudi Arabia), combined with other variables that are required to run CAELUS, namely: solar zenith angle (sza), extraterrestrial horizontal solar irradiance (eth), clear-sky GHI (ghics) and GHI in a clean and dry atmosphere (ghicda). In addition, the dataset also provides the sky classification obtained with CAELUS. Further details about CAELUS and the dataset compilation is available in Ruiz-Arias and Gueymard (2023, doi: <a href="https://doi.org/10.1016/j.solener.2023.111895">10.1016/j.solener.2023.111895</a>). A Python implementation of CAELUS is available in https://github.com/jararias/caelus.

Dataset for 'Comment on "Glassy Dynamics in Chiral Fluids" '

Data sets from which figures of Dataset for 'Comment on "Glassy Dynamics in Chiral Fluids" ' were obtained, along with python code for produing the figures (in file 'correlations_matrix.ipynb').

TauBench: A Dynamic Benchmark for Graphics Rendering (Dataset Reference Frames)

TauBench is a dynamic graphics rendering benchmark dataset, targeted especially towards rendering methods relying on the reuse of temporal data. The dataset is available at <a href="https://doi.org/10.5281/zenodo.5729573">https://doi.org/10.5281/zenodo.5729573</a>, and this upload provides path traced reference frames for it in PNG format. The images are rendered with <a href="https://github.com/vga-group/tauray">Tauray</a> at 16384 samples per pixel (spp), at both 1080p and 2160p resolutions. Frame indices start from 0 and are not padded with leading zeroes. More information about TauBench is also available at <a href="https://webpages.tuni.fi/vga/taubench">https://webpages.tuni.fi/vga/taubench</a>.

Data and scripts to reproduce the results shown in "Stability of attractor local dimension estimates in non-Axiom A dynamical systems"

Here we make available all the codes and datasets to reproduce the results of the paper "Stability of attractor local dimension estimates in non-Axiom A dynamical systems" by Flavio Pons, Gabriele Messori and Davide Faranda. The pre-print of the article is available at https://hal.science/hal-04051659/document. Any question/comment can be sent to flavio.pons@gmail.com. License for the codes and simulation/analysis results (*.Rda files): the code is shared under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license, see https://creativecommons.org/licenses/by-nc-sa/4.0/ License and terms of use for the ERA5 data (z500_daily_euro.nc): the ERA5 500 hPa geopotential was downloaded from https://climexp.knmi.nl/start.cgi

Data Analysis files for "Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action"

Data analysis files for the manuscript "Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action", <a href="https://www.nature.com/articles/s41467-023-39493-3#data-availability">Nature Communications 14, 3784 (2023)</a>, or <a href="https://arxiv.org/abs/2210.12443">arXiv:2210.12443 (2022)</a> This contains the raw data, the data analysis files, and the figure generation files of the manuscript, which includes the following three parts, 0. Data preparation The total size of the raw dataset is around 120GB. The raw data is pre-processed via digital down-conversion at 40MHz to obtain the optical/microwave transient response of the electro-optical device in the presence of strong optical pulses at different powers and frequencies. The processed data is adopted for data analysis of the response measurements for convenience. 1. Data Analysis <ul> <li>Detailed data analysis of the electro-optical (microwave and optical) responses in presence of the optical pump pulses for different mode and probing configurations.</li> </ul> 2. Figures for the manuscripts. <ol> <li>Figures for the optical characterizations</li> <li>Figures for the coherent responses for different configurations</li> <li>Figures for the excess back-action</li> <li>Figures for the theoretical curves in the Supplementary Information </li> </ol>

Analysis accompanying "Dynamically regulated transcription factors are encoded by highly unstable mRNAs in the Drosophila larval brain"

This repository documents the raw data processing and figure generation for the article “Dynamically regulated transcription factors are encoded by highly unstable mRNAs in the Drosophila larval brain”, doi: 10.1261/rna.079552.122.

Direct observation of geometric phase in dynamics around a conical intersection

The CSV files contain experimental and theoretical data corresponding to figures 3 and A1 of the paper "Direct observation of geometric phase in dynamics around a conical intersection", available at <a href="http://arxiv.org/abs/2211.07320">arxiv:2211.07320</a>.  The contents of the files are described in README.txt.

Climatic and Anthropogenic Controls on Groundwater Dynamics in the Mekong River Basin

Datasets for the paper (Climatic and Anthropogenic Controls on Groundwater Dynamics in the Mekong River Basin)- <ul> <li>Observed streamflow data from Mekong River Commission (MRC)</li> <li>Groundwater observations from Tiwari et al., (2023; Sci. Data)</li> <li>Groundwater simulation outputs from CLM5 for Mekong River Basin.</li> </ul>

Raw data from: "Thermal mismatches explain consumer-resource dynamics in response to environmental warming".

Data from: Álvarez-Codesal, S, Faillace CA, Garreau, A, Bestion, E, Synodinos, AD, & Montoya, JM. 2023. Thermal mismatches explain consumer-resource dynamics in response to environmental warming. Ecology and Evolution.   Composed of seven associated datasets: - Algae_Net_Photosynthesis.csv - Daphnia_Ingestion.csv - Algae_Respiration.csv - Daphnia_Ingestion.csv - Daphnia_respiration.csv - Interaction_Strength.csv - Energy_Balance_Ratios_dataset.csv   A detailed explanation of the methods is provided in the related Alvarez-Codesal et al. 2023 article, please refer to it for a full understanding of the methods and results. Briefly: our aim was to quantify the impact of warming on consumer-resource interactions, using as consumer Daphnia pulex, and as resources two algae species, Chlamydomonas reinhardtii and Desmodesmus sp. First, we measured thermal dependencies of physiological rates related to energy gain (i.e., ingestion, net photosynthesis) and loss (i.e., respiration) for Daphnia and the algae in basal conditions at eight temperatures. From these, we calculated species energetic balances as net photosynthesis-to-respiration ratio (P/Rr) for resources, or as ingestion-to-respiration ratio (I/Rc) for consumers, using predicted values of each (per capita) rate from the models. We used energetic balances as an indicator of how species respond to increasing temperatures, defining intraspecific energetic mismatches when the energetic balance decreases. Second, we inferred interspecific thermal mismatches (inter-TM) by comparing individual energetic balances for both consumer-resource pairs, and identified the thermal mismatch regions, where: 1) trends of energetic balances contrast between the interacting species; and 2) both species reduce their energetic balance with increasing temperature. The inter-TMs were used to increase our qualitative understanding on the outcomes of thermal dependencies of interaction strength. Third, we calculated the natural logarithm of the consumer-resource energetic balance for each interacting pair as the ratio between consumer energetic balance and the resource energetic balance to get qualitative predictions on the trends of interaction strength with temperature. Finally, we measured experimentally thermal dependencies of interaction strength for each consumer-resource pair and verified if our predictions using the thermal mismatches fitted the trends of interaction strengths across temperatures.

opencc-by-4.0Nov 2022View details →

Spatial transcriptomics of B and T cell receptors uncovers lymphocyte clonal dynamics.

This dataset contains a single zipped folder containing: <ul> <li> data </li> <li> scripts </li> </ul> needed to reproduce the manuscript entitled "Spatial transcriptomics of B and T cell receptors uncovers lymphocyte clonal dynamics". Each folder is organized by tissue type, methodology, and analysis. A readme file accompanies each folder with details on the files/scripts within that folder. Alongside the paper and supplementary materials, it should be possible to reproduce all the figures in the manuscript.

Dynamic Nuclear Polarization of Inorganic Halide Perovskites

NMR, EPR, XRD datasets and SEM image for the research article titled "Dynamic Nuclear Polarization of Inorganic Halide Perovskites". For further details see the readme.txt file.

Supplementary datasets: sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data (Ng et al.)

This repository contains data files from the manuscript Ng et al. "sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data". Directories Please untar the sciCSR-data-files.tar.gz archive. Folder "Simulated_data" <ul> <li>'simulated_IGHC_reads' folder: containing list of simulated data (FASTQ sequence files and aligned BAM files) to test the accuracy of commonly used RNA-seq aligners (STAR, HISAT2) to distinguish sterile and productive heavy-chain transcripts. The code to generate these data is in the repository https://github.com/Fraternalilab/sciCSR-analysis.</li> <li>'simulated_transitions.RData': .RData file containing list of Seurat objects of simulated datasets of different number of cells, to test the robustness of sciCSR-inferred transitions across different dataset sizes.</li> </ul> Folder "Seurat_objects" <ul> <li>'human_Bcells_atlas_IGHC_NMF_rank.rds': Nonnegative matrix factorization (NMF) results to derive isotype signatures from the human B cell atlas (see below).</li> <li>'mouse_Bcells_atlas_IGHC_NMF_rank.rds': NMF results to derive isotype signatures from the mouse B cell atlas (see below)</li> <li>'Human_Bcells_atlas_IGHC.rds': Seurat object containing cells forming the 'human B cell atlas' (i.e. merging data from Stewart et al (https://doi.org/10.3389/fimmu.2021.602539) and King et al (https://doi.org/10.1101/2020.04.28.054775))</li> <li>'mouse_Bcells_atlas_IGHC.rds': Seurat object containing cells forming the 'mouse B cell atlas' (i.e. merging data from Mathew et al (https://doi.org/10.1016/j.celrep.2021.109286) and Luo et al (https://doi.org/10.1186/s13578-022-00795-6))</li> <li>'Stewart_HumanPeripheral_Bcells_IGHC.rds': Seurat object containing cells from the Stewart et al (https://doi.org/10.3389/fimmu.2021.602539) peripheral blood B cell atlas.</li> <li>* 'King_HumanTonsil_Bcells_IGHC.rds': Seurat object containing cells from the King et al. (https://doi.org/10.1101/2020.04.28.054775) human tonsilar B cell atlas.</li> <li>'Kim_Covid_Bcells_IGHC.rds': Seurat object containing cells from the Kim et al. (https://doi.org/10.1038/s41586-022-04527-1) time-course scRNA-seq data on human B cell response to SARS-CoV-2 vaccine.</li> <li>'Gomez_AID_VDJ_IGHC.rds': Seurat object containing cells from the Gómez-Escolar et al. (https://doi.org/10.15252/embr.202255000) Aicda mouse knockout scRNA-seq data.</li> <li>'Hong_IL23_Bcells_IGHC.rds': Seurat object containing cells from the Hong et al. (https://doi.org/10.4049/jimmunol.2000280) Il23 p19 mouse knockout scRNA-seq data.</li> <li>'scIFNg.rds': Seurat object containing scRNA-seq data of time-course in vitro culture of B cells stimulated with interferon gamma generated in this work.</li> </ul>

Molecular dynamics trajectories for "Reservoir-REMD facilitates kinetic rescue from metastable peptide conformations

The molecular dynamics-generated ensemble dataset for cyclo-(cGHHQKLV), used in the manuscript "Reservoir-REMD facilitates kinetic rescue from metastable peptide conformations". The dataset consists of 14 + 6 =20 .dcd files, and one .pdb file for rendering.

Ha-SingleMoleculeLab's data for publication: Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level

This upload is the raw data that support our findings sent to review on Nucleic Acids Research, corresponding to each individual figure. The paper title is " Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level".

opencc-by-4.0Jul 2023View details →

Simulation result from "Simulating Bark Beetle Outbreak Dynamics and their Influence on Carbon Balance Estimates with ORCHIDEE r7791"

Eight locations were selected which represent the range of climatic conditions within the distribution area of spruce in Europe (Picea Abies Karst L.) as shown in Table 4. Half-hourly weather data from the FLUXNET database <a href="https://www.zotero.org/google-docs/?ibBw15">(Pastorello et al., 2020)</a> for these locations were used to drive ORCHIDEE.  Some of these locations (FON, SOR, HES, COL, WET) are not populated with spruce but all are located within the species distribution. For each location, a pure spruce stand was simulated and the available FLUXNET data was looped to simulate a 100-year period. The study did not investigate the effect of species mixture in the simulation experiments. Other inputs, including soil texture, pH and soil color were obtained from the USDA map derived from <a href="https://www.zotero.org/google-docs/?aaWPI6">Eswaran et al. (2003</a>), for the corresponding pixel. The amount of fresh breeding woody substrate inputs used by the bark beetles to breed was controlled by modifying the maximum wind speed of a windthrow event in ORCHIDEE. Seven wind speeds ranging between 19 m/s and 40 m/s were selected (Table 3). This range is justified by the observation that mean wind speeds below 19 m/s could not trigger a windthrow event in ORCHIDEE <a href="https://www.zotero.org/google-docs/?jEqNDm">(Chen et al., 2018)</a> while for wind speeds exceeding 40 m/s, more than 60% of the trees are uprooted, leaving too few living trees to trigger a bark beetle outbreak within the same pixel.  To investigate the impact of windthrow intensity and background climate on bark beetle outbreaks, the study conducted a total of 56 [8 sites x 7 wind speed intensities] simulations as given in table 3. The same 56 simulations were also used to analyze the sensitivity of the carbon balance of spruce forests to windthrow intensity and background climate. Where most land surface models use a turnover time to simulate continuous mortality <a href="https://www.zotero.org/google-docs/?5jGfXF">(Thurner et al., 2014; Pugh et al., 2019)</a>, ecological reality is better described by abrupt mortality events. An idealized simulation experiment was used to qualify the impact of abrupt mortality on net biome productivity by changing from a framework in which mortality is approximated by a constant background mortality to a framework in which mortality occurs in abrupt, discrete events. To test the impact of a change in mortality framework two versions of ORCHIDEE were compared to create an idealized simulation experiment: (1) a version simulating mortality as a continuous process, labeled ”the continuous version”, and (2) the version capable of simulating abrupt mortality from windthrow and subsequent bark beetle outbreaks, labeled ”the abrupt version”. The effect of simulating abrupt mortality was evaluated over 20-, 50-, and 100-year time horizons. The effect of changing the framework of simulating mortality from continuous to abrupt was qualified on the basis of 112 simulations (8 sites x 7 wind speeds x 2 model versions) of 100 years each. The simulations with abrupt mortality were run first. Subsequently, the number of trees killed was quantified and used as a reference value for the continuous mortality set-up. This approach resulted in the same quantities of dead trees at the end of the simulation for both frameworks, which then differed only in the timing of the simulated mortality.  This precaution is necessary to avoid comparing two different mortality regimes where the result would mainly be explained by the intensity of the mortality rather than by its underlying mechanisms.

Dataset of Molecular Dynamics Simulations for the Upregulated Biomarker PSMB8: 3UNF and its G210V Mutant in Experimental Autoimmune Encephalomyelitis

This dataset contains molecular dynamics simulations data generated using GROMACS for the upregulated biomarker 3UNF and its G210V mutant in the context of Experimental Autoimmune Encephalomyelitis (EAE). EAE is a widely studied animal model for multiple sclerosis, and investigating the behavior of biomarkers in this model is crucial for understanding disease progression and potential therapeutic interventions. The dataset includes trajectory files, coordinate files, and relevant parameters used in the simulations. These simulations provide valuable insights into the structural dynamics, conformational changes, and interactions of the PSMB8 biomarker 3UNF and its G210V mutant within the EAE system. The data offers researchers an opportunity to analyze and explore the behavior of these biomarkers at the atomic level, aiding in the identification of potential binding partners, functional sites, and mechanisms associated with disease progression. By sharing this dataset, we aim to contribute to the scientific community by providing a valuable resource for further analysis, validation, and comparison of the molecular behavior of the upregulated biomarker 3UNF and its G210V mutant in Experimental Autoimmune Encephalomyelitis.