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1,582 results for “manuscript”
Raw western blot from the manuscript "Paradoxical neuronal hyperexcitability in a mouse model of mitochondrial pyruvate import deficiency"
<p>Uncropped western blot associated with the manuscript "Paradoxical neuronal hyperexcitability in a mouse model of mitochondrial pyruvate import deficiency"</p>
Data for the manuscript "Direct visualization of colloid transport over natural heterogeneous and artificial smooth rock surfaces"
<p>The files contain the data used to produce the figures in the manuscript "<strong>Direct visualization of colloid transport over natural heterogeneous and artificial smooth rock surfaces</strong>" by Borgman, Be'er, and Weisbrod.</p> <p>Included in the data set:</p> <ol> <li>ImageAnalysesAndPlots.m: A MATLAB script to generate the figures from the included images and data files.</li> <li>myCmap.mat: A custom set of colors for the images.</li> <li>LH_btc.csv, LH_b_btc.csv, HH_btc.csv, HH_b_btc.csv: Data for the breakthrough curves.</li> <li>LH_t=360min.czi, HH_t=300min.czi: Final images from the experiments, from which the residual surface fluorescence is calculated.</li> <li>LHSurfTopo.csv, HHSurfTopo.csv: Tables containing the profilometer scan data.</li> <li>LH, HH: Folders containing the images for the colloid displacement front</li> <li>Exp01-Exp04: Images for calculating the dispersion coefficient </li> <li>PlotVelocities2.m: A script for plotting the calculated velocity fields</li> <li>velocity_magnitude_HH_flux_boundary.txt/velocity_magnitude_LH_flux_boundary.txt: The data files for the velocity fields.</li> </ol> <p>For the .czi files, it's necessary to use the Bio-Formats for MATLAB <a href="https://docs.openmicroscopy.org/bio-formats/6.1.0/users/matlab/index.html">package</a>.</p>
Supplemental Datafiles for the manuscript "Crustal structure of northern Borneo from VDSS: Implications for subduction termination and the tectonic reconstruction of SE Asia"
<p>Processed waveform data (windowed/filtered) from the seismic stations for the Virtual Deep Seismic Sounding (VDSS) study in northern Borneo.</p>
Files for Manuscript "A pulmonologist's guide to perform and analyse cross-species single-lung-cell transcriptomics"
<p>Input Files for Manuscript "A pulmonologist’s guide to perform and analyse cross-species single-lung-cell transcriptomic"</p> <p>See https://github.com/GenStatLeipzig/pulmonologists_interspecies_scRNA for details.</p> <p>Manuscript authored by:</p> <p>Peter Pennitz1,2*, Holger Kirsten3*, Vincent D. Friedrich3,4, Emanuel Wyler5, Cengiz Goekeri1,2,6, Benedikt Obermayer7, Gitta A. Heinz8, Mir-Farzin Mashreghi8,9, Maren Büttner10,11 Jakob Trimpert12, Markus Landthaler5,13, Norbert Suttorp2, Andreas C. Hocke1,2, Stefan Hippenstiel2, Mario Tönnies14, Markus Scholz3, Wolfgang M. Kuebler15,16, Martin Witzenrath1,2,16, Katja Hoenzke1,2 and Geraldine Nouailles1,2,# </p> <p> </p> <p>1 Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Pulmonary Inflammation, Berlin, Germany. </p> <p>2 Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany. </p> <p>3 University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany. </p> <p>4 Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig, Germany. </p> <p>5 Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany. </p> <p>6 Cyprus International University, Faculty of Medicine, Nicosia, Cyprus. </p> <p>7 Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Bioinformatics, Berlin, Germany. </p> <p>8 Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), A Leibniz Institute, Therapeutic Gene Regulation, Berlin, Germany. </p> <p>9 Berlin Institute of Health at Charité – Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Berlin, Germany. </p> <p>10 University of Bonn, Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, Bonn, Germany. </p> <p>11 Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Systems Medicine, Bonn, Germany. </p> <p>12 Freie Universität Berlin, Institute of Virology, Berlin, Germany. </p> <p>13 Humboldt-Universität zu Berlin, Institute for Biology, IRI Life Sciences, Berlin, Germany. </p> <p>14 HELIOS Clinic Emil von Behring, Department of Pneumology and Department of Thoracic Surgery, Chest Hospital Heckeshorn, Berlin, Germany. </p> <p>15 Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Physiology, Berlin, Germany. </p> <ol> <li> <p>German Center for Lung Research (DZL), Berlin, Germany. </p> </li> </ol> <p> </p> <p>* Authors contributed equally to this work </p> <p> </p> <p>References for original datasets :</p> <p>Human Charité: Hocke A, Hönzke K, Obermayer B, Baumgardt M, Wyler E, Hippenstiel S, Mache C. Charité Berlin /Berlin Institute of Health. GEO accessions GSM5958267, GSM5958272, GSM5958283, GSM5958285</p> <p>Human Travaglini et al.: published at <a href="https://www.synapse.org/">https://www.synapse.org</a> by Travaglini et al. (<a href="https://doi.org/10.1038/s41586-020-2922-4">https://doi.org/10.1038/s41586-020-2922-4</a>)</p> <p>Monkey: published at <a href="https://www.ncbi.nlm.nih.gov/geo">https://www.ncbi.nlm.nih.gov/geo</a> by Speranza et al. (<a href="https://doi.org/10.1126/scitranslmed.abe8146">https://doi.org/10.1126/scitranslmed.abe8146</a>)</p> <p>Hamster: Charité Berlin, see: <a href="https://doi.org/10.1038/s41467-021-25030-7">https://doi.org/10.1038/s41467-021-25030-7</a></p> <p>Mouse: Pennitz P, Witzenrath, M, Nouailles G, Berlin Charité.</p> <p>Rat and Pig: published at <a href="https://www.ncbi.nlm.nih.gov/geo">https://www.ncbi.nlm.nih.gov/geo</a> by Raredon et al. (<a href="https://doi.org/10.1126/sciadv.aaw3851">https://doi.org/10.1126/sciadv.aaw3851</a>) .</p> <p>Annotation: Ensembl BioMart</p>
Dataset and scripts for manuscript "OpenIFS/AC: atmospheric chemistry and aerosol in OpenIFS 43r3"
<p>This repository contains model output datasets and plotting scripts as used for evaluations and figures presented in the manuscript "OpenIFS/AC: atmospheric chemistry and aerosol in OpenIFS 43r3", submitted to Geosci. Model Dev.</p>
Draft Genome Manuscript for Curtobacterium sp. Isolated from Berries Surfaced in Commercial Cranberry Bogs in Massachusetts, USA
<p>Annotated genome of Curtobacterium sp. MWU13.2055</p>
Draft Genome Manuscript for Pseudomonas sp. Strain MWU13.3659 Isolated from Berries Surfaced in Commercial Cranberry Bogs in Massachusetts, USA
<p>Annotated genome of Pseudomonas sp. MWU13.3659</p>
datacleanr manuscript animated example: Extract Recipe
<p>Animated example (GIF) of datacleanr's capabilities showing the "Extract Recipe" Tab.</p> <p>The software <a href="https://github.com/the-Hull/datacleanr">datacleanr </a>is an R package for reproducible and interactive data processing.</p>
datacleanr manuscript animated example: Visual Cleaning and Annotating
<p>Animated example (GIF) of datacleanr's capabilities showing the "Visual Cleaning and Annotating" Tab.</p> <p>The software <a href="https://github.com/the-Hull/datacleanr">datacleanr </a>is an R package for reproducible and interactive data processing.</p>
datacleanr manuscript animated example: Filtering
<p>Animated example (GIF) of datacleanr's capabilities showing the "Filtering" Tab.</p> <p>The software <a href="https://github.com/the-Hull/datacleanr">datacleanr </a>is an R package for reproducible and interactive data processing.</p>
datacleanr manuscript animated example: Set-Up and Overview
<p>Animated example (GIF) of datacleanr's capabilities showing the "Set-up and Overview" Tab.</p> <p>The software <a href="https://github.com/the-Hull/datacleanr">datacleanr </a>is an R package for reproducible and interactive data processing.</p>
Dataset associated with the manuscript " Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics"
<p>Raw dataset associated with the manuscript " Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics"</p>
Source data and code for manuscript 'An executive network for the control of sequence-behavior in pigeons'
<p>The contents of this folder are part of the submission of the manuscript entitled 'An executive network for the control of sequence-behavior in pigeons', by Lukas Alexander Hahn & Jonas Rose</p> <p>Contact: lukas.hahn@ruhr-uni-bochum.de</p> <p>Data and code have been compressed into a .zip folder each. Unpack the contents of the folders to use the dataset. The dataset is split into two main folders and one Matlab file:</p> <p>'code'<br> contains all analysis code to produce all figures and reported statistics of the manuscript (refer to the<br> MATLAB live script 'manuscriptResultsLiveScript.mlx' to run the analysis, please adjust the path information of where the data is stored on your computer).</p> <p>'RESULTSSTATISTICS.mat'<br> contains all reported statistical values (generated by 'manuscriptResultsLiveScript.mlx')</p> <p>'sourceData'<br> Contains all required source data files (i.e. pre-processed data) required to run the analyses stored in 'code'.</p> <p>Data related to animal behavior was recorded using MATLAB (R2016b). Electrophysiological data was recorded by NeuroNexus microelectrodes and an INTAN RHD2000 headstage on an INTAN USB-Interface board, with a sampling rate of 30 kHz and was subsequently filtered for spike sorting at bandpass 0.5 - 7.5 kHz.</p> <p>Data format is the MATLAB '.mat' type (which can be loaded in by MATLAB, or alternatively by the freely available Octave Software (https://www.gnu.org/software/octave)).<br> Data is organized in MATLAB structures, one file per session for behavioral results, one file per neuron for different alignments and preprocessing conditions (refer to manuscriptResultsLiveScript).<br> Structures contain individual matrices (labelled by a descriptive name) that contain numerical values or character strings.<br> Matrices labelled by the keyword 'Info' contain character strings that give a brief description of the loaded data.<br> Source data contains two separate folders containing data of animal 1 ('P855'), and animal 2 ('T1003').</p> <p>Data was sorted into different subsets, for analysis of individual task phases. Subfolder 'NCL' refers to 'nidopallium caudolaterale', 'NIML' refers to 'nidopallium intermedium mediale pars laterale', the recorded brain regions.</p> <p> </p>
Neural motif discovery manuscript reports
<p>This repository holds the supplementary data for the motif and motif-syntax/grammar discovery tool in the associated manuscript.</p> <p><strong>reports.tar.gz</strong><br> Contains the motif and motif-syntax/grammar analysis reports as HTML files for all analyzed transcription factors (TFs). See included README for more details.</p> <p><strong>models.tar.gz</strong><br> Contains the fine-tuned models. Each TF, this includes the fine-tuned single-task profile model for each task/experiment, and the fine-tuned multi-task profile model over all experiments.</p> <p><strong>motifs.tar.gz</strong><br> Contains the motifs discovered by TF-MoDISco on each profile model, for both the profile and counts heads. This includes the PFM, the CWM, and eCWM. This also includes the motifs that have been merged across the profile/counts heads (i.e. `cpmerged`).</p> <p><strong>motif_hits.tar.gz</strong><br> For each experiment, motif instances were called using FiNeMo on the best-performing model. Motif instances are either called for the profile head, count head, or merged across both heads. Each subdirectory includes: 1) the collapsed and filtered motif instances; 2) the set of peaks for which they come from; 3) a file matching motif instances to their peaks; 4) the co-occurrence of multiple motifs in peaks; and 5) the distance distribution of motif pairs which significantly co-occur. Unless stated otherwise, collapsing is done over all motif patterns.</p>
Computational dataset for the manuscript "Tethered agonist exposure in intact adhesion/class B2 GPCRs through intrinsic structural flexibility of the GAIN domain"
<p>This repository provides url links to the MDsrv sessions for the manuscript: <em>Tethered agonist exposure in intact adhesion/class B2 GPCRs through intrinsic structural flexibility of the GAIN domain<strong>.</strong></em> </p> <p><strong>Link 1</strong>: L1 dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1.ngl </a></p> <p><strong>Link 2</strong>: G1 dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/G1.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/G1.ngl</a></p> <p><strong>Link 3</strong>: E5 static: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5_crevice.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5_crevice.ngl</a></p> <p><strong>Link 4: </strong>E5 dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5.ngl</a></p> <p><strong>Link 5: </strong>E5 +3 static: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5+3.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5+3.ngl</a></p> <p><strong>Link 6: </strong>E5 +6 static: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5+6.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5+6.ngl</a></p> <p><strong>Link 7: </strong>E2 dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E2.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E2.ngl</a></p> <p><strong>Link 8: </strong>L1 Phe+3Lys dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Phe+3Lys.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Phe+3Lys.ngl</a></p> <p><strong>Link 9: </strong>L1 Leu+6Lys dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Leu+6Lys.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Leu+6Lys.ngl</a></p> <p><strong>Link 10: </strong>L1 dynamic (ribbon representation): <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Ribbon.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Ribbon.ngl</a></p> <p> </p> <p> </p>
Data of event list of cold and hot patches for manuscript "The Dependence of Cold and Hot Patches on Local Plasma Transport and Particle Precipitation in Northern Hemisphere Winter"
<p>A database of 4,634 cold patches (high density and low electron temperature) and 4,700 hot patches (high density and high electron temperature) from Defense Meteorological Satellite Program F16 in 2005-2018 winter months.</p>
The datasets used in the manuscript named "Fidelity of Global Tropical Cyclone Activity in a High-Resolution Reanalysis Dataset CRA40 in Comparison with Multiple Other Reanalysis Datasets"
<p>The datasets after tracking the TC events in five reanalyses: ERA5, JRA55, CFSR, MERRA2, CRA40. </p>
Validation Data used for manuscript "Climate Projections over the Great Lakes Region: Using Two-way Coupling of a Regional Climate Model with a 3-D Lake Model"
<p>those are the processed data that used for model-data comparison in the manuscript "Climate Projections over the Great Lakes Region: Using Two-way Coupling of a Regional Climate Model with a 3-D Lake Model", including Lake Surface Temperature and Lake Surface Ice Cover from Great Lakes Surface Environmental Analysis (GLSEA), Surface Air temperature and Precipitation from Climatic Research Unit (CRU). </p>
Data for the manuscript 'Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework'.
<p>This zip file contains the data downloaded from external sources used to produce the results in the manuscript 'Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework'. Note that all of the data contained in this zip file was publicly available at the time of writing.</p> <p>The corresponding Github can be found here:<br> https://github.com/alan-turing-institute/jbc-turing-rss-testdebiasing</p> <p>The publication is available here:<br> https://doi.org/10.1038/s41564-021-01029-0</p>
WRF model configuration and data used for the NHESS manuscript "Droughts in Germany: Performance of Regional Climate Models in reproducing observed characteristics"
<p>The file contains:</p> <ul> <li>the namelist.input document with the description of the WRF model configuration used in Warscher et al. (2019)</li> <li>WRF simulation outputs from the reanalysis run: monthly values for the time period 1980-2009 of precipitation, maximum and minimum temperature (needed for the SPEI calculation) from the innermost (5 km grid resolution) and second innermost (15 km) domain; from both domains the same section, relevant for the study, was taken; the data was bilineraily interpolated to 12.5 km horizontal grid resolution to match the EUR-11 CORDEX format</li> </ul> <p> </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.