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datasets available to search
ShareScore release 0.9.0
Dataset results
32 results for “Data source files”
Bubble/Foam Simulations for Malej et al. 2023, source codes, input files, matlab files, data files
<p><i>.F are source codes, *.m are matlab scripts for analysis and postprocessing, .txt are data files including bathymetry and data from sensitivity tests</i></p>
Source data files for manuscript "Closed Magnetic Topology in the Venusian Magnetotail and Ion Escape at Venus"
<p>The zip file contains source data files for all figures in the manuscript "Closed Magnetic Topology in the Venusian Magnetotail and Ion Escape at Venus" published in Nature Communications. DOI: 10.1038/s41467-024-50480-0.</p>
uncropped western blots for analysis of RPN13 ubiquitylation and NRF1 activation by protein aggregates, as well as source data for qPCR plots and flow cytometry gating and FCS files for agDD-GFP in HeLa or HEK cells
<p>This entry contains uncropped blots for Fig 4D and Fig S4C, Fig. 5B, Fig S5 and Fig S6, and the raw FCS files for Flow Cytometry data in doi.org/10.1101/2024.08.30.610524.</p>
Upslope migration of snow avalanches in a warming climate: data and model source files
<p>Complete data and model source files corresponding to:</p> <p>Giacona, F., Eckert, N., Corona, C., Mainieri, R., Morin, S., Stoffel, M., Martin, B., Naaim, M. (2021). Upslope migration of snow avalanches in a warming climate. Proceedings of the National Academy of Sciences America, Nov 2021, 118 (44) e2107306118; DOI: 10.1073/pnas.2107306118</p>
Data Files of "A Multi-Year Photopolarimetric Study of the Semi-Regular Variable V CVn and Identification of Analogue Sources"
<p>The semi-regular variable star V Canum Venaticorum (V CVn) is well-known for its unusual linear polarization position angle (PA).<br> Decades of observing V CVn reveal a nearly constant PA spanning hundreds of pulsation cycles. This phenomenon has persisted<br> through variability that has ranged by 2 magnitudes in optical brightness and through variability in the polarization amplitude over<br> 0.3% and 6.9%. Additionally, the polarization fraction of V CVn varies inversely with brightness.<br> This paper presents polarization measurements obtained over three pulsation cycles. We find that the polarization maximum does<br> not always occur precisely at the same time as the brightness minimum. Instead, we observe a small lead or lag in relation to the<br> brightness minimum, spanning a period of a few days up to three weeks. Furthermore, the PA sometimes exhibits a non-negligible<br> rotation, especially at lower polarization levels.<br> To elucidate the unusual optical behavior of V CVn, we present a list of literature sources that also exhibit polarization variability<br> with a roughly fixed PA.We find this correlation occurs in stars with high tangential space velocities, i.e., “runaway” stars, suggesting<br> that the long-term constant PA is related to how the circumstellar gas is shaped by the star’s high-speed motion through the interstellar<br> medium.</p>
Anonymized source data files for figures in: Recurrent processes support a cascade of hierarchical decisions
<p>Perception depends on a complex interplay between feedforward and recurrent processing. Yet, while the former has been extensively characterized, the computational organization of the latter remains largely unknown. Here, we use magneto-encephalography to localize, track and decode the feedforward and recurrent processes of reading, as elicited by letters and digits whose level of ambiguity was parametrically manipulated. We first confirm that a feedforward response propagates through the ventral and dorsal pathways within the first 200 ms. The subsequent activity is distributed across temporal, parietal and prefrontal cortices, which sequentially generate five levels of representations culminating in action-specific motor signals. Our decoding analyses reveal that both the content and the timing of these brain responses are best explained by a hierarchy of recurrent neural assemblies, which both maintain and broadcast increasingly rich representations. Together, these results show how recurrent processes generate, over extended time periods, a cascade of decisions that ultimately accounts for subjects' perceptual reports and reaction times.</p>
Remote near infrared identification of pathogens with multiplexed nanosensors - source data file for Nißler et al. 2020 (Nat. Commun.)
<p>source data file for Nißler et al. 2020 (Nat. Commun.)</p> <p>entitled: </p> <p>Remote near infrared identification of pathogens with multiplexed nanosensors</p>
Source Data File – Dual role of the peptide loading complex as proofreader and limiter of MHC-I presentation – PNAS 2023-21600
<p>Source Data Files</p>
CytofIn_Source_Data_Files
<p>Source Data Files for the article "CytofIn enables integrated analysis of public mass cytometry datasets using generalized anchors" published at Nature Communications.</p>
Source Data files for: Primary cilia and SHH signaling impairments in human and mouse models of Parkinson's disease
<p>Parkinson’s disease (PD) as a progressive neurodegenerative disorder arises from multiple genetic and environmental factors. However, underlying pathological mechanisms remain poorly understood. Using multiplexed single-cell transcriptomics, we analyze human neural precursor cells (hNPCs) from sporadic PD (sPD) patients. Alterations in gene expression appear in pathways related to primary cilia (PC). Accordingly, in these hiPSC-derived hNPCs and neurons, we observe a shortening of PC. Additionally, we detect a shortening of PC in <em>PINK1</em>-deficient human cellular and mouse models of familial PD. Furthermore, in sPD models, the shortening of PC is accompanied by an increased SHH signal transduction. Inhibition of this pathway rescues the alterations in PC morphology and mitochondrial dysfunction. Thus, increased SHH activity due to ciliary dysfunction is needed for the development of pathoetiological phenotypes observed in sPD, like mitochondrial dysfunction. In sum, altered PC function is part of early PD pathoetiology and inhibiting the overactive SHH signaling is a potential neuroprotective therapy.</p>
LaMEM source code and input files corresponding to Present‐day upper‐mantle architecture of the Alps: Insights from data‐driven dynamic modelling
<p>This repository contains LaMEM source code and input files for the models presented in Kumar, A., Cacace, M., Scheck-Wenderoth, M., Götze, H.-J., & Kaus, B. J. P. (2022). Present-day upper-mantle architecture of the Alps: Insights from data-driven dynamic modeling. Geophysical Research Letters, 49, e2022GL099476. https://doi. org/10.1029/2022GL099476</p>
Source data files
<p>Source data files for: "Alternative transcription cycle for bacterial RNA polymerase"</p> <p>Timothy T. Harden<sup>1</sup>, Karina S. Herlambang<sup>2†</sup>, Mathew Chamberlain<sup>1†</sup>, Jean-Benoît Lalanne­<sup>3,4</sup>, Christopher D. Wells<sup>5</sup>, Gene-Wei Li<sup>3</sup>, Robert Landick<sup>6</sup>, Ann Hochschild<sup>5</sup>, Jane Kondev<sup>1</sup>, and Jeff Gelles<sup>2</sup></p> <p>Departments of <sup>1</sup>Physics and <sup>2</sup>Biochemistry, Brandeis University, Waltham, MA 02454, USA</p> <p>Departments of <sup>3</sup>Biology and <sup>4</sup>Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA</p> <p><sup>5</sup>Department of Microbiology, Blavatnick Institute, Harvard Medical School, Boston, MA, 02115 USA</p> <p><sup>6</sup>Department of Biochemistry and Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA</p> <p>†These authors contributed equally and are listed in the order determined by a coin toss.</p>
Source Data file for Weiss et al., Nature Communications 10, 4772 (2019).
<p>Source Data file for Weiss et al., "Controlled Creation of a Singular Spinor Vortex by Circumventing the Dirac Belt Trick", Nature Communications <strong>10</strong>, 4772 (2019); containing data for all relevant figures.</p>
Supplemental Dataset Excel files and Source Data Excel file for "START domains generate paralog-specific regulons from a single network architecture"
<p>Supplemental Dataset Excel files and Source Data Excel file for "START domains generate paralog-specific regulons from a single network architecture" in Nat Comms</p>
Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
<p>The germ line produces gametes that transmit genetic and epigenetic information to the next generation. Maintenance of germ cells and development of gametes require germ granules—well-conserved membraneless and RNA-rich organelles. The composition of germ granules is elusive owing to their dynamic nature and their exclusive expression in the germ line. Using <i>C. elegans</i> germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions. An RNAi-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two putative LOTUS-domain proteins. Loss of <i>eggd-1</i> and <i>eggd-2</i> results in separation of P granules from the nuclear envelope, germline atrophy and reduced fertility. We show that intrinsically disordered regions of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote perinuclear localization of P granules. Together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.</p>
Source data file for "Vibrational signature of hydrated protons confined in MXene interlayers"
<p>Source data file for the manuscript entitled: "Vibrational signature of hydrated protons confined in MXene interlayers"</p>
Source code and data files for the fetal kick simulator developed in the Biomechatronics Lab at Imperial College London, UK
<p>This repository holds the code for Fetal Kick Simulator</p> <p>Copyright (c) 2020, Imperial College London All rights reserved.</p> <p>Authors: Abhishek Kumar Ghosh, Ravi Vaidyanathan, Niamh C Nowlan. Imperial College London.</p> <p>This program is a free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.</p> <p>This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.</p> <p>Acknowledgements: If this software is helpful, then Please consider acknowledging or referencing the authors.</p> <p>Publication: Link for the publication related to this repository is <a href="https://www.mdpi.com/1424-8220/20/21/6020">https://www.mdpi.com/1424-8220/20/21/6020</a></p>
Anonymized source data files for figures in: Recurrent processes support a cascade of hierarchical decisions
Open the record for dataset details and reuse information.
Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
Open the record for dataset details and reuse information.
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>
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.