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96 results for “Time processing”
Data from: Biogeographic dating of speciation times using paleogeographically informed processes
Standard models of molecular evolution cannot estimate absolute speciation times alone, and require external calibrations to do so, such as fossils. Because fossil calibration methods rely on the incomplete fossil record, a great number of nodes in the tree of life cannot be dated precisely. However, many major paleogeographical events are dated, and since biogeographic processes depend on paleogeographical conditions, biogeographic dating may be used as an alternative or complementary method to fossil dating. I demonstrate how a time-stratified biogeographic stochastic process may be used to estimate absolute divergence times by conditioning on dated paleogeographical events. Informed by the current paleogeographical literature, I construct an empirical dispersal graph using 25 areas and 26 epochs for the past 540 Ma of Earth's history. Simulations indicate biogeographic dating performs well so long as paleogeography imposes constraint on biogeographic character evolution. To gauge whether biogeographic dating may be of practical use, I analyzed the well-studied turtle clade (Testudines) to assess how well biogeographic dating fares when compared to fossil-calibrated dating estimates reported in the literature. Fossil-free biogeographic dating estimated the age of the most recent common ancestor of extant turtles to be from the Late Triassic, which is consistent with fossil-based estimates. Dating precision improves further when including a root node fossil calibration. The described model, paleogeographical dispersal graph, and analysis scripts are available for use with RevBayes.
Dataset for "Time-Resolved Trigger Processes Leading to the Plinian Eruptions at Sakurajima Volcano, Japan"
<p>Dataset 1: Core compositions of plagioclase phenocrysts<br>Dataset 2: Core and rim compositions of orthopyroxene phenocrysts<br>Dataset 3: Core and rim compositions of clinopyroxene phenocrysts<br>Dataset 4: Core compositions of olivine phenocrysts in the 1914–1915 lava<br>Dataset 5: Chemical compositions of microlite-bearing groundmass glass of the 1914 Plinian pumice<br>Dataset 6: Core and rim compositions of magnetite phenocrysts<br>Dataset 7: Compositions of magnetite inclusion and hosting plagioclase<br>Dataset 8: Chemical compositions of magnetite microlites in the 1914 Plinian pumices</p>
rOMT processed data: Cerebral amyloid angiopathy is associated with glymphatic transport reduction and time-delayed solute drainage along the neck arteries
<p>This dataset contains the speed map and Péclet map data processed by regularized optimal mass transport method (<a href="https://zenodo.org/record/5809635#.YczuJy2ZNBw">https://zenodo.org/record/5809635#.YczuJy2ZNBw</a>, <a href="https://github.com/xinan-nancy-chen/rOMT">https://github.com/xinan-nancy-chen/rOMT</a>).</p> <p>All files are in nifty format. This dataset contains in total 55 rat cases which are divided by age (3-month, 6-month and 12-month) and status of health ("WT" for wild-type and "CAA" for those who have developed Cerebral Amyloid Angiopathy).</p>
The timing of spring warming shapes reproductive effort in a warm-water fish: the role of mismatches between hepatic and gonadal processes
Spring-spawning fishes native to northern environments rely on both increasing temperature and lengthening photoperiod to cue reproduction and may thus be particularly sensitive to rapid warming earlier in the year while day lengths remain short. We investigated the reproductive response of pumpkinseed sunfish Lepomis gibbosus to spring warming commencing at a range of day lengths (9 – 15 hours), corresponding to various calendar days (January 10 – May 22). In both the laboratory and field, both male and female fish that experienced early warming while day lengths were <11 hours: 1) failed to initiate reproductive preparation in the liver before gonad development began, and 2) had reduced reproductive allocation. Analysis of published data on temperate fishes suggested that liver development prior to gonad development is widespread across warm-, cool-, and cold-water thermal guilds, though the precise phenology of liver relative to gonad development appears to vary widely among species. Together, our results point toward dampened reproductive preparation as a novel mechanism mediating reduced reproductive output in both warm- and cool-water fish following earlier spring warming.
Timing of blood sample processing affects the transcriptomic and epigenomic profiles in CD4+ T-cells of atopic subjects
<p><span>Optimal</span><span> pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4<sup>+</sup> T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, </span><span>CD4<sup>+</sup></span><span> T-cells were isolated from the first blood sample within 2 hours (immediate) or from the second blood sample after 24 hours storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed </span><span>CD4<sup>+</sup></span><span> T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed </span><span>CD4<sup>+</sup></span><span> T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood </span><span>CD4<sup>+</sup></span><span> T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operating procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended.</span></p>
Reproduction package for the publication "Tidal disruption event AT2020ocn: early-time X-ray flares caused by a possible disc alignment process"
<p>This package contains the data analysed in the paper "Tidal disruption event AT2020ocn: early–time X–ray flares caused by a possible disc alignment process". The software XSPEC (Arnaud 1996) is needed to perform the spectral analysis and reproduce the results shown in the paper.</p> <p>The structure is as follows:</p> <p>./reproduction_ocn/nicer: contains all processed NICER data used in the paper, grouped by their epochs. "speclist-early.dat" lists all the early-time epochs before MJD 59130. "en_range.dat" lists the selected energy range at each epoch during the early-time period for X-ray spectral analysis. Within each epoch-specific folder, "src.fits" and "bkg.fits" are the source+background and background spectra re-binned using the FTOOL "ftgrouppha"; "*.arf" and "*.rmf" are ancillary file and response file for spectral analysis; rest files are direct products of the NICER data reduction process. See the paper for details.</p> <p>./reproduction_ocn/swift: contains all Swift/UVOT data used in the paper, grouped by their observation IDs. "m2.fits", "w1.fits", and "w2.fits" contain the UV lightcurves from three UV filters, produced by Swift task "uvotproduct". "swfxraypclc.dat" is the Swift/XRT lightcurve, produced by the online Swift pipeline: https://www.swift.ac.uk/user_objects/ (Evans et al. 2009). "./reproduction_ocn/MOSFiT-products/" includes MCMC products from the MOSFiT package (Mockler et al. 2019).</p> <p>./reproduction_ocn/xmm: contains the reduced XMM-Newton/EPIC-pn spectra of three epochs used in the paper. "1and2-slim.xcm" is fitting the XMM#1 and XMM#2 spectra using the slim disc model. "3-phenmnlgcl.xcm" and "3-relxillCp.xcm", are fitting the XMM#3 spectrum with, a powerlaw+zbbody model and a slim disc+relxillCp model, respectively.</p>
Dataset for time evolution of classical contact process with 100 sites
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Data from: Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia
Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher-altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.
Data and processing for "Multitone Microwave Frequency Locking to a Noisy Cavity via Real-Time Feedback"
<p>This folder contains all the code and data necessary to produce the figures of the paper titled "Multitone Microwave Frequency Locking to a Noisy Cavity via Real-Time Feedback" written by Jean-Paul van Soest, Clinton A. Potts, Sarwan Peiter, Adrián Sanz Mora and Gary A. Steele.</p>
Real-time fMRI Neurofeedback Training on the Anterior Insula Based on Interoceptive Processing
ClinicalTrials.gov study NCT05260749. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Circadian Timing, Information Processing and Energy Balance Study
ClinicalTrials.gov study NCT04759755. IPD Sharing: YES. Countries: 1. Publications: 1.
Priority Setting and Waiting Time Decision in the Referral Process, How and by Whom?
ClinicalTrials.gov study NCT01976221. IPD Sharing: NO. Countries: 1. Publications: 1.
The Impact of Self-processing on Mental Time Travel
ClinicalTrials.gov study NCT06823193. IPD Sharing: NO. Countries: 1. Publications: 10.
The timing of spring warming shapes reproductive effort in a warm-water fish: the role of mismatches between hepatic and gonadal processes
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Fossilization processes have little impact on tip-calibrated divergence time analyses
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Data from: Biogeographic dating of speciation times using paleogeographically informed processes
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Data from: Estimating field capacity from volumetric soil water content time series using automated processing algorithms
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Data from: Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia
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Timing of blood sample processing affects the transcriptomic and epigenomic profiles in CD4+ T-cells of atopic subjects
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Physical processes determine spatial structure in water temperature and residence time on a wide reef flat
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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.