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1,548 results for “Trajectories”
Choice-dependent delta-band neural trajectory during semantic category decision making in the human brain
<p>The dataset and code provided correspond to Manuscript Number: ISCIENCE-D-23-09408R1, titled "Choice-dependent delta-band neural trajectory during semantic category decision making in the human brain."</p> <p>This dataset comprises delta and alpha filtered data from a total of 19 participants. Each .mat file contains 800 cells, representing the number of trials. Each cell contains a matrix of size 128 x 1750. Here, 128 denotes the number of EEG channels, and 1750 represents the number of time points. Time points are sampled from -1 s to 2.5 s relative to the onset of the first stimulus, with a 2ms interval.<br><br></p> <p>The participants' behavioral data are stored in separate .mat files for each run (or block). Upon loading these files, a struct named "data" is loaded, containing six variables, each representing a 1 x 200 vector:</p> <ol> <li> <p>Cat1: Represents the category of the first stimulus. It takes a value of 1 for animate words and 2 for inanimate words.</p> </li> <li> <p>Cat2: Denotes the category of the second stimulus. It is assigned 1 for animate words and 2 for inanimate words.</p> </li> <li> <p>Same: Indicates the correct response for each trial. A value of 1 signifies a match between the categories of Stimulus 1 and Stimulus 2, while 2 indicates a non-match.</p> </li> <li> <p>Resp: Records the participant's decision for each trial. A value of 1 denotes a match between the categories of Stimulus 1 and Stimulus 2, whereas 2 represents a non-match.</p> </li> <li> <p>RT: Represents the participant's response time in seconds for each trial.</p> </li> <li> <p>Corr: Indicates the correctness of the participant's response. A value of 1 signifies a correct response, while 0 indicates an incorrect response.</p> </li> </ol> <p> </p>
Shift in reproductive strategies in the evolutionary trajectory of a plant lineage
<p>Target loci of The Angiosperms353 gene set (AGS) assembled on Easy353 pipeline for Saxifraga section Irregulares and related taxa.</p>
Supplementary collection of preprocessed and analysed data objects for the paper: "Gene-level alignment of single cell trajectories"
<p>Supplementary collection of h5ad data files containing preprocessed and analysed single-cell reference and query datasets discussed in the case studies of the paper:<em><strong>"Gene-level alignment of single cell trajectories"</strong></em> (<a href="https://doi.org/10.1101/2023.03.08.531713" rel="nofollow">https://doi.org/10.1101/2023.03.08.531713</a>).</p> <p>Our artificial thymic organoid raw sequencing data are available from ArrayExpress (E-MTAB-12720).</p> <p>Below lists the original sources of the literature datasets we downloaded prior to our own preprocessing and trajectory analysis.</p> <ul> <li> <p>Original pan fetal reference data from: Suo, C. et al. (2022) "Mapping the developing human immune system across organs" (<a href="https://doi.org/10.1126/science.abo0510">https://doi.org/10.1126/science.abo0510</a><a href="http://paperpile.com/b/XTpgLG/TQtQ3">), </a>downloaded from <a href="https://developmental.cellatlas.io/fetal-immune">https://developmental.cellatlas.io/fetal-immune</a>.</p> </li> </ul> <ul> <li> <p>Original healthy/IPF data from: Adams, T. S. et al. (2020), "Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis" (<a href="https://doi.org/10.1126/sciadv.aba1983">https://doi.org/10.1126/sciadv.aba1983</a>), downloaded from GEO (GSE136831).</p> </li> </ul> <p>We have run our scripts in <a href="https://github.com/Teichlab/G2G_notebooks">https://github.com/Teichlab/G2G_notebooks</a> to generate new latent embeddings and infer pseudotime trajectories for the above datasets, and used them to model trajectory alignments with our newly developed framework: ‘Genes2Genes’ <a href="https://github.com/Teichlab/Genes2Genes">https://github.com/Teichlab/Genes2Genes</a>. </p>
Replication package for "A Structural Analysis of Mental Health and Labor Market Trajectories"
<p>"A Structural Analysis of Mental Health and Labor Market Trajectories" MS 29076</p> <p>The replication package contains the codes (two folders: code_manip and code_analysis) and data (three folders: data_raw, data_inter and data_analysis) to replicate the paper's results as well as the figure outputs in an output folder and a readme pdf file.</p> <p> </p>
MD simulation trajectories for paper "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms"
<div> <div>The dataset includes the MD simulation trajectories for the paper "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms". </div> <div>Citation: Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y. Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. Mol Cell. 2021 Jan 7;81(1):166-182.e6. PMID: 33238161; PMCID: PMC7796963.</div> </div>
DRAM raw annotations for "Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils" Seitz et al 2024
<p>Additional File 5: <span>Raw DRAM MAG annotations. </span></p>
Global mean sea-level projections from MimiBRICK forced by uncertain emissions trajectories
<p>Model output for Darnell et al (2025), . Output contains csv files for components of GMSLR from 1850--2300, as well as parameter values for the simulations. There are two files: emissions_parameters.zip, which contains the parameter values used to generate the emissions trajectories, and ensemble_output.zip, which contains the model outputs. Rows correspond to ensemble members and columns correspond to years.</p>
Sliding trajectories of strained Graphullerene/graphene and Graphullerene/h-BN heterojunction
<p>This dataset contains the sliding trajectories of strained GF/graphene and GF/<em>h</em>-BN along three directions (including total energy and atomic coordinates in extend xyz format) described in the manuscript "Superlubric Graphullerene" (to be submitted). </p>
Data for the PPSN 2024 article: "Entropy, Trajectories, and Explainability for Frequency Fitness Assignment"
<p>Dataset for the PPSN 2024 article: "Entropy, Trajectories, and Explainability for Frequency Fitness Assignment"</p>
Tracked trajectories Gyrodinium dominans
<p>Datasets containing the traked trajectories for each experimental replicate with<em> Gyrodinium dominans</em> analyzed in the article: <strong>The distinctive chemotactic responses of three marine herbivore protists to DMSP and related compounds.</strong> </p> <p>Nomenclature:</p> <p>G + _ + 1 letter identifying the compound + concentration in uM+ _ + experimental replicate number </p> <p>for example: G_D20_R1 stands for "<em>Gyrodnium domimans</em>, DMSP, 20 uM, third replicate"</p> <p>The compounds are identified with: </p> <p>D --> DMSP, M--> DMS, A --> Acrylate</p> <p>The datasets are saved as Pandas dataframe and can be opened with the library Pickle</p> <p> </p>
5,000 accretion disk trajectories from a double neutron star merger from Sprouse et al. ApJ 962 79 (2024)
<p>This dataset contains 5,000 trajectories from the 1.2 second long accretion disk simulation (with central black hole) of Sprouse et al. ApJ 962 79 (2024). Individual trajectories are contained in a folder labeled "trace_{tid}" where {tid} is the unique name of the trajectory. Each of these folders contains three files.</p> <p>The "initx.dat" file:</p> <ul> <li>The "initx.dat" file provides the initial mass fraction of the ejected material at a prescribed starting temperature and density using the SFHo equation of state.</li> <li>The columns of the "initx.dat" file are: Z (proton number), A (mass number), and X (mass fraction).</li> <li>The last column, X, should sum to unity by definition.</li> </ul> <p>The "metadata.dat" file:</p> <ul> <li>The "metadata.dat" file provides additional information about the ejected material.</li> <li>This file defines the trace id {tid}, the ejected mass, the maximum temperature reach in the simulation, the starting time, temperature, and density used to intialize the "initx.dat" file. </li> <li>The ejected mass associated with the trajectory can be used for the relative weighting of each trajectory.</li> <li>Units of associated quantities are defined in the file header (first line).</li> </ul> <p>The "trajectory.dat" file:</p> <ul> <li>The "trajectory.dat" file provides the time-dependent evolution of temperature (T), density (rho), radius (R) and electron fraction (Ye).</li> <li>This is the primary peace of information needed to run a nucleosynthesis network in post processing to determine the resultant abundances.</li> <li>Units of associated quantities are defined in the file header (first line).</li> </ul>
SHARC Trajectories, Cyclohexenone-BF3
<p>We calculated surface hopping trajectories using for the cyclohex-2-enone-BF3 complex using the SHARC program package and a new SHARC-FermiONs interface. </p> <p>This dataset contains the full trajectory data for the two conformers of cyclohex-2-enone-BF3 in the gasphase and in an explicit dichloromethane solvant.</p>
Trajectories and thresholds of multi-diversities and multi-functions in response to nitrogen enrichment
<p><span>An ecosystem is composed by multiple biota across several trophic levels, which interactively perform multiple ecosystem functions. </span><span>Anthropogenic reactive nitrogen</span><span> is expected to alter these ecosystem attributes including biota diversities and ecosystem functions. </span><span>Here, </span><span>we find that five biota diversities differ substantially in response trajectory and threshold with increasing nitrogen amount, and so do the four examined functions. </span><span>Our study provides a vivid picture of how multi-biota diversities and multiple functions concurrently respond to nitrogen enrichment and suggests that the attribute-specific response trajectories and thresholds should be taken into account in models predicting ecosystem feedbacks to nitrogen deposition.</span></p>
Post-transition state trajectories and transition state structures of 4+2/6+4 cycloadditions | BGAN-EPS outputs
<p>dataset.zip and log.zip are the dataset and outputs for the bidirectional generative adversarial network - entropic path sampling (BGAN-EPS). The source code can be found at https://github.com/rshin1209/bgan_eps.</p> <p>dataset.zip includes post-TS trajectories (xyz format) and transition state structures (pdb format) for the following 4+2/6+4 cycloadditions:</p> <ul> <li>Diene/triene cycloaddition (i.e., dta)</li> <li>Tethered-diene/triene cycloaddition (i.e., dtb)</li> <li>NgnD-catalyzed Diels–Alder reaction (i.e., ngnd)</li> <li>SpnF-catalyzed Diels–Alder reaction (i.e., spnf)</li> </ul> <p>dataset.zip can be unzipped and directly used for the BGAN-EPS method.</p> <p>XXX_r2p_1 refers to 4+2-adduct and XXX_r2p_2 refers to 6+4-adduct.</p> <p>log.zip includes outputs of the BGAN-EPS for the above 4+2/6+4 cycloadditions. The graphing for entropic profiles and entropy decomposition analysis can also be found at Git Hub link.</p>
Molecular dynamics simulation trajectory data for "Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function"
<p>Trajectories and input files corresponding to entries in Supplementary Table S1.</p>
Molecular dynamic trajectory for the article "The Binding Mechanism between Inositol Phosphate (InsP) and the Jasmonate Receptor Complex: A Computational Study"
<p>Molecular dynamic trajectory preparation file of Jasmonate receptor complex. We set up six systems. </p> <p>Each system contains PSF file and PDB file.</p>
Source codes and trajectories for multiscale simulations of barnase/barstar complex association
<p>Source codes and trajectories for multiscale simulations of barnase/barstar complex association</p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: 1e8V/m, 2e8 V/m, 3e8 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p><a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_centered_08.xtc">traj_centered_08.xtc </a>1e8 V/m<br> <a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_centered_3_08.xtc">traj_centered_3_08.xtc </a> 3e8 V/m<br> <a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_ricentrata_2_08.xtc">traj_ricentrata_2_08.xtc </a> 2e8 V/m</p> <p> </p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: no field, 2e7 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p><a href="https://zenodo.org/api/files/81479d2b-9168-43d1-8573-9c979435b8f0/traj_centered_no_field.xtc">traj_centered_no_field.xtc </a> no field</p> <p><a href="https://zenodo.org/api/files/81479d2b-9168-43d1-8573-9c979435b8f0/traj_centered_2_07.xtc">traj_centered_2_07.xtc </a> 2e7 V/m</p> <p> </p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: 1e7V/m, 5e7 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p>t<a href="https://zenodo.org/api/files/cba74eb5-a746-4cdf-80e4-1c06a1ec0462/traj_centered_07.xtc?versionId=62da1fac-7265-4aeb-a239-481088fb396a">raj_centered_07.xtc </a> 1e7 V/m</p> <p><a href="https://zenodo.org/api/files/cba74eb5-a746-4cdf-80e4-1c06a1ec0462/traj_centered_5_07.xtc?versionId=c0b8015d-b977-4eda-b678-9d4b719a90e2">traj_centered_5_07.xtc </a> 5e7 V/m</p> <p> </p> <p><br> <br> <br> </p>
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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.