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1,582 results for “manuscript”
Benchmarking datasets used in the manuscript "Strain-level metagenomic profiling using pangenome graphs with PanTax"
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Supplementary Information for the manuscript: "Gene expression evolution is predicted by stronger selection at more pleiotropic genes"
<p>This repository contains the supplementary information for the manuscript "<em>Gene expression evolution is predicted by stronger selection at more pleiotropic genes</em>" (<a href="https://doi.org/10.1101/2024.07.22.604294">https://doi.org/10.1101/2024.07.22.604294</a>).</p> <p>The supplementary data "data.tar.gz" is related to the Github repository <a href="https://github.com/charlesrocabert/Koch-et-al-Gene-expression-evolution-is-predictable-and-driven-by-indirect-selection-pressures">https://github.com/charlesrocabert/Koch-et-al-Predictability-of-Gene-Expression</a>.</p> <h2>Content of the repository</h2> <ul> <li><strong>Script S1. </strong>BSFG estimates (50.9 MB).</li> <li><strong>Script S2.</strong> WGCNA analysis and results G1 (99.6 MB).</li> <li><strong>Data S1.</strong> Datasets resulting from the global genomics analysis of the output of the transcriptomics pipeline (5.9 MB).</li> <li><strong>Data S2.</strong> VCF file containing the 566,296 quality-checked SNPs (1.1 GB).</li> <li><strong>Data S3.</strong> VCF file containing the 358,142 SNPs with a call rate higher or equal to 50% (964.3 MB).</li> <li><strong>Data S4.</strong> VCF file containing the imputed genotypes (964.3 MB).</li> <li><strong>Data S5.</strong> Results of the imputation tests (479.5 kB).</li> <li><strong>Data S6.</strong> VCF file containing imputed genotypes where SNPs with a minor allele frequency lower than 0.05 have been filtered out (MAF $\leq$ 0.05) (176.0 MB).</li> <li><strong>Data S7.</strong> List of the 1,273 significant eQTL associations (for gene expression levels or relative fitness as phenotypes) (61.2 kB).</li> <li><strong>Data S8.</strong> List of allele frequency changes (AFCs) for every markers in HD environment, for lines L1, L2, L3, L5, L6, Mx1 and Mx2 (32.4 MB).</li> <li><strong>Data S9.</strong> List of all SNPs indicating if their AFC is significantly higher in each line and their degree of parallelism (2.4 MB).</li> <li><strong>Data S10.</strong> Excel file containing the results of the gene functional enrichment analysis of the hub and eQTL carrier genes (33.7 KB).</li> <li><strong>data.tar.gz.</strong> Dataset mandatory to re-run the genomics analysis (see <a href="https://github.com/charlesrocabert/Koch-et-al-Gene-expression-evolution-is-predictable-and-driven-by-indirect-selection-pressures">https://github.com/charlesrocabert/Koch-et-al-Predictability-of-Gene-Expression</a>) (7.8 GB).</li> </ul> <p> </p>
Dataset for the manuscript 'Orbital-optimized Density Functional Calculations of Molecular Rydberg Excited States with Real Space Grid Representation and Self-Interaction Correction'
<p>Dataset for the manuscript 'Orbital-optimized Density Functional Calculations of Molecular Rydberg Excited States with Real Space Grid Representation and Self-Interaction Correction'</p>
Structural Data for the Antibody Developability Manuscript: Cartography of Developability Landscapes in Native and Human-Engineered Antibodies
<p>Here is the additional structural data (predicted models and MD trajectories) for the "Cartography of the Developability Landscapes of Native and Human-Engineered Antibodies" manuscript. Please cite our paper when referring to and using this data. If you have any questions, please contact Eva Smorodina at ribes.ev@gmail.com. Thank you!</p>
Data in support of manuscript "Tidal intrusion fronts, surface convergence, and mixing in an estuary with complex topography"
<p>North River observational data in support of manuscript "Tidal intrusion fronts, surface convergence, and mixing in an estuary with complex topography". Fieldwork in Oct - Nov 2021. CTD data and ADCP data collected during shipboard surveys at a channel constriction and a bend. CTD data and Aquadopp data collected at multiple mooring sites.</p>
Input files and movie visualizations for convection models discussed in Becker and Fuchs, "Generation of evolving plate boundaries and toroidal flow from visco-plastic damage-rheology mantle convection and continents", manuscript revised for G-Cubed
<p>These input files are for the CitcomS software as available on github.com/geodynamics/citcoms and used in the version under commit 2bda530. They can be used to recreate the models discussed in Becker and Fuchs (revised manuscript submitted to G-Cubed, 11/2023), with model codes discussed and listed in Table 1 of the preprint as provided here. We also provide selected animations of the time dependence of model output, referenced to the same model names.</p>
Supplementary tables for Quartet DNA manuscript
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Enhanced perfusion following exposure to radiotherapy: a theoretical investigation (revised manuscript data)
<p>Dataset and software supporting the revised manuscript: "Enhanced perfusion following exposure to radiotherapy: a theoretical investigation." See the enclosed README and manuscript for further information.</p>
Data associated to the manuscript "Enhanced diffusion of tracer particles in nonreciprocal mixtures"
<p>Contains an example of LAMMPS input file and data used to generate the figures of the article:</p><p><strong>Enhanced diffusion of tracer particles in nonreciprocal mixtures</strong></p><p>Anthony Benois, Marie Jardat, Vincent Dahirel, Vincent Démery, Jaime Agudo-Canalejo, Ramin Golestanian, and Pierre Illien</p><p>https://arxiv.org/abs/2307.05408</p><p>Article published in Physical Review E (2023).</p>
Dataset and code for the manuscript "Plant indirect interactions reduce species richness but increase phylogenetic diversity"
<p>This Zenodo repository contains the original data set and code for replicating the result published in the paper "<strong>Plant indirect interactions reduce species richness but increase phylogenetic diversity</strong>"</p><p> </p><ol><li>The "BD.xlsx" data frame contains the original data. The first column, "ID," is an ID for each one of the patches (i.e., vegetation units containing one or more individuals for the same or different species separated from other patches by bare ground). The second and third columns, "localidad" and "suelo", inform about the location where patches are found. The "species" column identifies the different species present at each patch.</li><li> The "Comb1.xlsx" data frame contains the possible combination of 4 species for each ID (concatenation of "localidad" and "suelo") for all the species found in the sampling. Besides "ID", there is one column for each of the species included in interactions ("spA", "spB", "spC", "spD") that contains the name of the species.</li><li>The "phylo.xlsx" data frame contains the taxonomic information of the species found during the sampling. For each species recorded in column "species" we assign its genus (column "genus") and family (column "family")</li><li> "ALL_IN.xlsx" is a data frame containing for each "ID" (proxy of location), the species involved in interactions ("spA", "spB", "spC" & "spD"), the "interaction sign" indicating if a given interaction is positive or negative (results based on simulation) and "Order" indicating the number of species involved in the interactions(from two to four).</li><li>"Code.R" provides the R code necessary to obtain the results. As statistics is based on simulation, every run can provide slightly different results, although differences do not affect interpretation. Please note that running time can be elevated depending on the computer used.</li></ol><p> </p>
Data Source file for manuscript: Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients
<p>ABSTRACT</p><p>Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) are associated with excess morbidity and mortality. Despite recognition of this immediate impact on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-producing <i>Klebsiella pneumoniae </i>species complex and ESBL-<i>Escherichia coli</i> in individual patients over time, we conducted performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-<i>K. pneumoniae</i> species complex and 284 ESBL-<i>E. coli</i> isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-<i>K. pneumoniae </i>species complex, and 83.6% of patients colonized with ES BL-<i>E. coli</i>. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at a prolonged risk of recurrent infection with colonizing strains.</p><p>DATA SOURCE FILE</p><p>In this Data Source file, you will find access to the raw data, metadata and results obtained during the study: "Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients". Data is organized following the structure of Figures/Tables of the manuscript and Supplementary Material. Additional figures not included in the main manuscript nor in the Supplementary Material are also available.</p><p>All sequencing and sample data from this study can be accessed at the NCBI database under the BioProject number PRJNA910977: <a href="http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977">http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977. </a>No new software was developed during this study. Standard bioinformatics software was used and the commands used can be accessed at the Supplementary Information file.</p>
Dataset for the manuscript: Changes in isotope fractionation during nitrate assimilation by eukaryotic and prokaryotic algae under different pH and CO2 conditions
<p>This is the dataset for the manuscript: Different effects of ocean acidification on isotope fractionation during nitrate assimilation by eukaryotic and prokaryotic algae</p>
Manuscript-Data
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Dataset for the manuscript "Homogeneous microenvironmental conditions under nurses promote facilitation". FUNCTIONAL ECOLOGY
<p>The following directory contains the data necessary to replicate the results obtained in the manuscript entitled '<strong>Homogeneous Microenvironmental Conditions Under Nurses Promote Facilitation</strong>'</p><p>We provided two spreadsheets: 'BD_beneficiaries.xlsx' and 'BD_nurses.xlsx.'</p><p>'BDbeneficiaries.xlsx' contains the data needed to identify beneficiary/non-beneficiary species (sheet: network_<i>data) and the data of functional traits for the tested species (sheet: Beneficiary-Non</i>_beneficiary).</p><p>'BD<i>nurses.xlsx' contains the data needed to identify nurses/non-nurses species (sheet: network_data) and the data of environmental modification provided by nurse/non-nurse species (sheet: nurse-non</i>_nurse effects).</p><p>Both archives contain a metadata sheet describing the meaning of each variable.</p>
Data and code for manuscript ``Insights on the vulnerability of Antarctic glaciers from the ISMIP6 ice sheet model ensemble and associated uncertainty''
<p>Supporting data and code for manuscript:</p><p>Seroussi, H., Verjans, V., Nowicki, S., Payne, A. J., Goelzer, H., Lipscomb, W. H., Abe-Ouchi, A., Agosta, C., Albrecht, T., Asay-Davis, X., Barthel, A., Calov, R., Cullather, R., Dumas, C., Galton-Fenzi, B. K., Gladstone, R., Golledge, N. R., Gregory, J. M., Greve, R., Hattermann, T., Hoffman, M. J., Humbert, A., Huybrechts, P., Jourdain, N. C., Kleiner, T., Larour, E., Leguy, G. R., Lowry, D. P., Little, C. M., Morlighem, M., Pattyn, F., Pelle, T., Price, S. F., Quiquet, A., Reese, R., Schlegel, N.-J., Shepherd, A., Simon, E., Smith, R. S., Straneo, F., Sun, S., Trusel, L. D., Van Breedam, J., Van Katwyk, P., van de Wal, R. S. W., Winkelmann, R., Zhao, C., Zhang, T., and Zwinger, T.: Insights into the vulnerability of Antarctic glaciers from the ISMIP6 ice sheet model ensemble and associated uncertainty, The Cryosphere, 17, 5197–5217, https://doi.org/10.5194/tc-17-5197-2023, 2023.</p><p> </p><p>It contains the code to prepare the datasets, to create the figures and the data for the analysis, and the scalar values computed for the 198 Antarctic glaciers stored by ice flow models.</p><p>The files Glacier_XX contain the data to emulate the results for individual glaciers.</p><p>The files Antarctica and AntarcticaWithCtrl contain the data to emulate the results for the Antarctic runs without and with the ctrl_proj experiment.</p><p>The files GROUP_ICEFLOW contain the ice flow model data for all the experiments recomputed for the 198 glaciers in Antarctica.</p>
Molecular dynamics trajectories related to manuscript: SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle
<p>This dataset contains two folders, each with sequentially numbers coordinates files for all-atom molecular dynamics trajectories related to the manuscript "SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle" by Zimmermann et al. Each folder contains PDB and PSF files specifying the components of each system depicted in Fig. S10 of that manuscript as well as 200 sequentially named DCD files, each containing 5 nanoseconds of a 1 microsecond trajectory.</p>
Stim circuits and collected data for "Error-corrected Hadamard gate simulated at the circuit level" manuscript
<p>The stim circuits which we sampled to obtain logical failure probabilities, and the collected data organised in an excel file.</p>
STORMS_Check_list_for_manuscripts
<p>STORMS (Strengthening The Organization and Reporting of Microbiome Studies) checklist for submitted manuscript</p>
Data and R-Scripts for the manuscript "Arctic tundra ecosystems under fire – potential trajectories for stable state shifts"
Open the record for dataset details and reuse information.
Supplemental movies for Fluids manuscript
<p>Supplemental movies for manuscript "Pipe formation by fluid focalization in bilayered sediments" by A. Gay, G. Tangavelou & V. Vidal, submitted to Fluids (dec. 2023)</p>
ScienceDex guides
Understand access before you commit
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.