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235 results for “Redundancy”
Functional redundancy of non-volant small mammals increases in human-modified habitats
<p>This repository hosts all R codes, data and output supporting the findings of the study "Functional redundancy of non-volant small mammals increases in human-modified habitats", by André L. Luza (UFRGS, BR), Catherine H. Graham (WSL, CH), Sandra M. Hartz (UFRGS, BR), and Dirk, N. Karger (WSL, CH).</p> <p>The only data that are not here are the Ecoregions of WWF. These data can be found in the webpage of WWF.</p>
A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog - Supporting Data
<p><strong>Description </strong></p> <p>The following files are available : </p> <ul> <li>Simulated non-redundant Gene Catalog (SGC) composed of 128267 genes;</li> <li>Gene abundance profiles across 40 samples: raw read counts, gene length normalized base counts, depth file computed by the jgi_summarize_bam_contig_depth script provided by MetaBAT;</li> <li>Gold Standard (GS) and Gold Standard Single Assignment (GS_SA) binning results;</li> <li>Binning results obtained on the SGC with nine binning methods: MSPminer, MGS-canopy, DAS Tool, MaxBin2, MetaBAT2, SolidBin, CONCOCT, COCACOLA and MyCC.</li> </ul> <p><strong>License</strong></p> <p>These files are licensed under a <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p>
Efficient PCA denoising of spatially correlated redundant MRI data
<p>MRI data used for the study: "Henriques, Ianus, Novello, Jovicich, Jespersen, Shemesh. Efficient PCA denoising of spatially correlated redundant MRI data. Imaging Neuroscience (In Press)."</p><p><strong>Preclinical scanner data</strong></p><p>All animal experiments for the collection of these datasets were preapproved by the institutional and national authorities and carried out according to European Directive 2010/63.</p><p>A mouse brain (C57BL/6J) was extracted via transcardial perfusion with 4% Paraformaldehyde (PFA), immersed in 4% PFA solution for 24 h, washed in Phosphate-Buffered Saline (PBS) solution for at least 24 h, and then placed on a 10 mm NMR tube filled with Flourinert (Sigma Aldrich, Lisbon, PT), which was sealed using paraffin film. </p><p>The MRI experiments were performed on a 16.4 T Bruker Aeon Ascend scanner (Bruker, Karlsruhe, Germany), interfaced with an Avance IIIHD console, and equipped with a gradient system capable of producing up to 3000 mT/m in all directions. A constant temperature of 37oC was maintained throughout the experiments using the probe's variable temperature capability. </p><p>Two distinct diffusion-weighted datasets were then acquired using Bruker's standard "Diffusion Tensor Imaging EPI":</p><ul><li><i>Dataset1 </i>(<strong>MB_exp1.nii</strong> and its brain mask<strong> MB_exp1_mask.nii</strong>): For this dataset, we modulated the amount of spatial correlations by acquiring EPI datasets with parameters optimized to mitigate noise spatial correlations, particularly avoiding k-space undersampling acquisition during EPI's gradient ramps and without using partial Fourier, which minimize regridding.</li><li><i>Dataset2 </i>(<strong>MB_exp2.nii</strong> and its brain mask<strong> MB_exp2_mask.nii</strong>): The second dataset was acquired with identical resolution, number of acquisitions, etc., but with large factors inducing spatial correlations, including k-space sampling during gradient ramps (default Bruker's acquisition and reconstruction procedures for acquisition speed) and with a significant phase partial Fourier factor of 6/8 (note for partial Fourier acquisitions, EPI data is reconstructed with zero-padding, according to the default reconstruction procedures by Bruker's pre-clinical reconstruction software Paravision 6.0.1).</li></ul><p>All datasets are acquired for the following diffusion-weighted parameters: 30 gradient directions for b-values 1, 2 and 3 ms/μm2 (Δ = 15 ms, δ = 1.5 ms), and 20 consecutive b-value=0 acquisitions - b-values and diffusion gradient directions are saved in files: <strong>MB.bval</strong> / <strong>MB.bvec</strong>.</p><p>Other acquisition parameters: TR/TE = 3000/50 ms, 9 coronal slices, Field of View = 12×12 mm2, matrix size 80×80, in-plane voxel resolution of 150×150 μm2, slice thickness = 0.7 mm, number of averages = 2, number of segments = 1, double sampling acquisition.</p><ul><li><i>Gold standard acquisitions for dataset 2 </i>(<strong>MB_exp2_20averages.nii</strong>): For a gold standard reference, the second dataset was also repeated for 20 averages. Note, since this dataset is aligned to <strong>MB_exp2.nii</strong> you can use <strong>MB_exp2_mask.nii </strong>for its brain mask.</li></ul><p>For all datasets, Spatial drifts in the image domain were first corrected using a sub-pixel registration technique (Guizar-Sicairos et al., 2008).</p><p> </p><p><strong>Clinical scanner data</strong></p><p>Experiments were approved by the Ethical Committee of the University of Trento and the participant signed an informed consent. </p><p>MRI data was a acquired for a healthy control (male, 54 years) using a 3T MAGNETOM PRISMA scanner (Siemens Healthcare, Erlangen, Germany) equipped with a 64-channel head-neck RF receive coil. </p><p>Diffusion MRI data was acquired using a monopolar single diffusion encoding EPI PGSE (Feinberg et al., 2010; Moeller et al., 2010; Xu et al., 2013) along 30 diffusion gradient directions for five non-zero b-values = 1, 2, 3, 4.5 and 6 ms/μm2 (Δ = 39.1 ms, δ = 26.3 ms) and 17 interspersed b-value=0 acquisitions. b-values and diffusion gradient directions are saved in files: <strong>HB.bval</strong> / <strong>HB.bvec</strong>. Note, only the masked version of these dataset (<strong>HB_masked.nii</strong> and its brain mask <strong>HB_mask.nii</strong>) is provided to guarantee that data privacy standards are met. For noise maps covering all FOV, the noise maps computed as the std of the 5 first repeating unmasked b = 0 acquisitions are provided in file <strong>stdS0i.nii.</strong></p><p>Other acquisition parameters were the following: TR/TE = 4000/80 ms, 63 axial slices, Field of View = 220×220 mm2, matrix size 110×110, isotropic resolution of 2 mm, 6/8 phase partial Fourier, parallel imaging with GRAPPA 2, simultaneous multi-slice factor 3. All diffusion MRI data was reconstructed using zero-padding, which is the default procedure for data acquired with partial Fourier above 70%. </p>
COInr a comprehensive, non-redundant COI database from NCBI-nt and BOLD
<p>COInr is a non-redundant, comprehensive database of COI sequences extracted from NCBI-nt and BOLD. It is not limited to a taxon, a gene region, or a taxonomic resolution. Sequences are dereplicated between databases and within taxa.</p> <p>Each taxon has a unique taxonomic Identifier (taxID), fundamental to avoid ambiguous associations of homonyms and synonyms in the source database. TaxIDs form a coherent hierarchical system fully compatible with the NCBI taxIDs allowing creating their full or ranked linages.<br> <br> COInr is a good starting point to create custom databases according to the users’ needs using mkCOInr scripts available at <a href="https://github.com/meglecz/mkCOInr">https://github.com/meglecz/mkCOInr</a> <br> It is possible to select/eliminate sequences for a list of taxa, select a specific gene region, select for minimum taxonomic resolution, add new custom sequences, and format the database for BLAST, QIIME, RDP classifiers.</p> <p> </p>
Data for: A fundamental tradeoff among resilience, resistance, efficiency, and redundancy in tidal wetlands
<p>We filtered the raw NASA-MODIS (MOD13Q1) Enhanced Vegetation Index (EVI) dataset to only inlcude pixels with high tidal wetland class purity and Quality Assurance (QA) reliability scores. We filtered 782,693 tidal wetland pixels with coverage spanning the entire contiguous United States to only include those with greater than 90% tidal wetland class purity. We then further filtered these pixels to only include those where data dropouts in the EVI or QA layer occured fewer than 10% of the time. In the end, we used 145,871 pixels in our analysis. Tidal wetland GPP was calculated by pixel for the dates 3/5/2000 to 12/2/2020 at 16-day intervals using the algorithms published in: </p> <p>R. A. Feagin, I. Forbrich, T.P. Huff, J.G. Barr, J. Ruiz-plancarte, J.D Fuentes, R.G. Najjar, R. Vargas, A. Vazquez-lule, L. Windham-Myers, K. Kroeger, E.J. Ward, G.W. Moore, M. Leclerc, K.W. Krauss, C.L. Stagg, M. Alber, S.H. Knox, K.V.R. Schafer, T.S., Bianchi, J.A. Hutchings, H.B. Nahrawi, A. Noormets, B. Mitra, A. Jaimes, A.L. Hinson, B. Bergamaschi, J. King, and G. Miao., Tidal wetland gross primary production across the continental United States, 2000–2019. Global Biogeochemical Cycles 34, e2019GB006349 (2020).</p> <p>The file named "SWR_90percentFinal.csv" contains the filtered SWR database used to calculate GPP. File named "temp_90percentFinal_rounded.csv" contains the filtered air temperature database used to calculate GPP. The file named "EVI(gapped_filled)_90percentFinal.csv" contains the final gap-filled EVI time series database used to calculate GPP. File named "QA_90%Final.csv" contains the filtered quality assurance (QA) values. Dates in the EVI database where QA = 3 were determined to be of poor quality, removed from the database, and replaced with "NA". Single NA gaps in the EVI database were gap-filled by taking the mean of the dates flanking the NA gap. File named "myGPP(gap_filled)_FINAL.csv" contains the calculated GPP estimates used throughout the study analysis. </p> <p>File named "rawEVI.csv" contains the raw EVI database prior to filtering and gap-filling. File named "rawSWR.csv" contains the raw SWR database prior to filtering. File named "rawAirTemp.csv" contains the air temperature database prior to filtering. File named "rawQA.csv" contains the QA layer of the MOD13 satellite product prior to filtering. These files contain the raw data for all 782,693 tidal wetland pixel locations. These raw files can also be accessed at daac.ornl.gov. </p>
Data for: Functional redundancy of weed seed predation is reduced by intensified agriculture
<p>Intensive agriculture, a driver of biodiversity loss, can diminish ecosystem functions and their stability. Biodiversity can increase functional redundancy and is expected to stabilize ecosystem functions. Few studies however have explored how agricultural intensity affects functional redundancy and its link with ecosystem function stability. Here, within a continent-wide study, we assess how the functional redundancy of seed predation is affected by agricultural intensity and landscape simplification. By combining carabid abundances with molecular gut content data, functional redundancy of seed predation was quantified for 65 weed genera across 60 fields in four European countries. Across weed genera, functional redundancy was reduced with high field management intensity and simplified crop rotations. Moreover, functional redundancy increased the spatial stability of weed seed predation within fields. We found that ecosystem functions are vulnerable to disturbance in intensively managed agroecosystems, providing empirical evidence of the importance of biodiversity for stable ecosystem functions across space.</p>
Towards a reproducible interactome: semantic-based detection of redundancies to unify protein-protein interaction databases
<p>Protein-protein interactions (PPIs) play an ubiquitous and fundamental role in all biological processes. Information on PPIs described in the literature is annotated and made available by several protein-interaction databases. Because most databases have their own curation rules and priorities, they often annotate overlapping sets of publications, which leads to redundancies. We developed a semantic-based approach which enables to accurately detect redundancies within PPI datasets from multiple databases. We applied this approach to assemble a "reproducible interactome", with PPIs supported by at least two methods or publications.</p>
UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells
<p>Source data for the publication: UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells.<br> Includes raw image data (e.g. agarose gels, western blots, northern blots), quantifications, qPCR raw Ct values and other supporting material.</p>
Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more
<p>S1 Data</p> <p>Dataset including the discovered CRISPR spacers, direct repeats, protospacers, co-occurrence-based spacer clustering results, predicted protein sequences, built HMMs, database comparison results, phylogenetic analysis results, predicted targeting hosts, and CRISPR-targeted TR sequences.</p>
Supplementary material: Does functional redundancy determine the ecological severity of a mass extinction event?
<p>Many authors have noted the apparent "decoupling" of the taxonomic and ecological severity of mass extinction events, with no widely accepted mechanistic explanation for this pattern having been offered. Here we test between two key factors that potentially influence ecological severity: biosphere entropy (a measure of functional redundancy), and the degree of functional selectivity (in terms of deviation from a pattern of random extinction with respect to functional entities). While theoretical simulations suggest that the Shannon entropy of a given community prior to an extinction event determines the expected outcome following a perturbation of a given magnitude, actual variation in Shannon entropy between major extinction intervals is insufficient to explain the observed variation in ecological severity. Within this information-theoretic framework, we show that it is the degree of functional selectivity which is expected to primarily determine the ecological impact of a given perturbation when levels of functional redundancy are not substantially different.</p>
Kuempel et al. (2024) Quantifying global redundant fisheries trade to streamline seafood supply chains
<p>Species trade data to accompany the publication "Quantifying global redundant fisheries trade to streamline seafood supply chains" by Kuempel et al. (2024) and the associated github repository https://github.com/cdkuempel/Redundant_fisheries_trade</p> <p> </p>
A Truly-Redundant Aerial Manipulator System With Application to Push-and-Slide Inspection in Industrial Plants
<p>This folder contain the data relative to the contact based pipe inspection presented on M. Tognon et al. "A Truly-Redundant Aerial Manipulator System With Application to Push-and-Slide Inspection in Industrial Plants." IEEE Robotics and Automation Letters 4.2 (2019): 1846-1851.</p>
Reinforcement-based processes actively regulate motor exploration along redundant solution manifolds
<p>From a baby's babbling to a songbird practicing a new tune, exploration is critical to motor learning. A hallmark of exploration is the emergence of random walk behaviour along solution manifolds, where successive motor actions are not independent but rather become serially dependent. Such exploratory random walk behaviour is ubiquitous across species, neural firing, gait patterns, and reaching behaviour. Past work has suggested that exploratory random walk behaviour arises from an accumulation of movement variability and a lack of error-based corrections. Here we test a fundamentally different idea—that reinforcement-based processes regulate random walk behaviour to promote continual motor exploration to maximize success. Across three human-reaching experiments, we manipulated the size of both the visually displayed target and an unseen reward zone, as well as the probability of reinforcement feedback. Our empirical and modelling results parsimoniously support the notion that exploratory random walk behaviour emerges by utilizing knowledge of movement variability to update intended reach aim towards recently reinforced motor actions. This mechanism leads to active and continuous exploration of the solution manifold, currently thought by prominent theories to arise passively. The ability to continually explore muscle, joint, and task redundant solution manifolds is beneficial while acting in uncertain environments, during motor development, or when recovering from a neurological disorder to discover and learn new motor actions.</p>
Data from: Dominant species stabilize pollination services through response diversity, but not cross-scale redundancy
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Phylogeny explains why less therapeutically redundant plant species are not necessarily facing greater use pressure
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Data for: Functional redundancy of weed seed predation is reduced by intensified agriculture
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Reinforcement-based processes actively regulate motor exploration along redundant solution manifolds
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Conditionally deleterious mutation load accumulates in genomic islands but can be purged with sufficient genotypic redundancy
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Supplementary material: Does functional redundancy determine the ecological severity of a mass extinction event?
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Data from: Multi-modal defenses in aphids offer redundant protection and increased costs likely impeding a protective mutualism
1.The pea aphid, Acyrthosiphon pisum, maintains extreme variation in resistance to its most common parasitoid wasp enemy, Aphidius ervi, which is sourced from two known mechanisms: protective bacterial symbionts, most commonly Hamiltonella defensa, or endogenously encoded defenses. We have recently found that individual aphids may employ each defense individually, occasionally both defenses together, or neither. 2.In field populations, Hamiltonella-infected aphids are found at low to moderate frequencies and while less is known about the frequency of resistant genotypes, they show up less often than susceptible genotypes in field collections. To better understand these patterns, we sought to compare the strengths and costs of both types of defense, individually and together, in order to elucidate the selective pressures that maintain multi-modal defense mechanisms or that may favor one over the other. 3.We experimentally infected five aphid genotypes (two lowly and three highly resistant), each with two symbiont strains, Hamiltonella-APSE8 (moderate protection) and Hamiltonella-APSE3 (high protection). This resulted in three sublines per genotype: uninfected, +APSE8, and +APSE3. Each of the fifteen total sublines was first subjected to a parasitism assay to determine its resistance phenotype and in a second experiment a subset were chosen to compare fitness (fecundity and survivorship) in presence and absence of parasitism. 4.In susceptible aphid genotypes, parasitized sublines infected with Hamiltonella generally showed increased protection with direct fitness benefits, but clear infection costs to fitness in the absence of parasitism. In resistant genotypes, Hamiltonella infection rarely conferred additional protection, often further reduced fecundity and survivorship when enemy challenged, and resulted in constitutive fitness costs in the absence of parasitism. We also identified strong aphid-genotype X symbiont-strain interactions, such that the best defensive strategy against parasitoids varied for each aphid genotype; one performed best with no protective symbionts, the others with particular strains of Hamiltonella. 5.This surprising variability in outcomes helps explain why Hamiltonella infection frequencies are often intermediate and do not strongly track parasitism frequencies in field populations. We also find that variation in endogenous traits, such as resistance, among host genotypes may offer redundancy and generally limit the invasion potential of mutualistic microbes in insects.
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.