Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
23,351
datasets available to search
ShareScore release 0.9.0
Dataset results
23,351 results for “Comparative”
PlanetProfile Python version outputs compared to models of Vance et al. (2018)
<p>Plain text outputs, associated input files, and comparison figures for hydrosphere properties for PlanetProfile models analogous to those studied by Vance et al. (2018), for Europa, Ganymede, Callisto, Enceladus, and Titan. PlanetProfile is an open-source geophysical modeling framework available at https://github.com/NASA-Planetary-Science/PlanetProfile. The inputs and outputs are from and created by the v2.3.17 release, with default settings. Output files list bulk properties in header lines at the top, then physical properties of each spherically symmetric layer along with depth and radius, beginning at the surface and continuing to the center of the body.</p> <p>Vance et al. (2018) is available at: <a href="https://doi.org/10.1002/2017JE005341">https://doi.org/10.1002/2017JE005341</a></p>
A Benchmark Analytical Solution for Variable Viscosity Flow in Fractured Media: Development and Comparative Analysis with Numerical Simulations
<p>This data is associated with <strong>(a) Figure 3.</strong> Comparison between the velocities obtained through analytical calculations and those estimated numerically, and <strong>(b) Figure 4.</strong> Comparison of the BTCs obtained through analytical calculations and those estimated numerically.</p>
How important is budding speciation for comparative studies?
<p><span><span>The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with three or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be interpreted together whereas after the split lineages are expected to change independently. This clever realization has shaped decades of research. Here we discuss one element of the comparative method often ignored or assumed as unimportant: if nodes of a phylogeny represent the dissolution of the ancestral lineage into two new ones or if the ancestral lineage can survive speciation events (i.e., budding). Budding speciation is often reported in paleontological studies, due to the nature of the evidence for budding in the fossil record, but it is surprisingly absent in comparative methods. Here we show that many PCMs assume that divergence happens as a symmetric split, even if these methods don't explicitly mention this assumption. We discuss the properties of trait evolution models for continuous and discrete traits and their adequacy under a scenario of budding speciation. We </span></span><span><span>discuss</span></span><span><span> the effects of budding speciation under a series of plausible evolutionary scenarios and show when and how these can influence our estimates. We also propose that long-lived lineages that have survived through a series of budding speciation events and given birth to multiple new lineages can produce evolutionary patterns that challenge our intuition about the most parsimonious history of trait changes in a clade. We hope our discussion can help bridge comparative approaches in paleontology and neontology as well as foster awareness about the assumptions we make when we use phylogenetic trees.</span></span></p>
Developing Kalanchoë blossfeldiana as a resource for comparatively studying C3 and crassulacean acid metabolism
<p>Reviewer Link</p> <p> </p> <p> </p> <p> </p> <p> </p>
Phylogeography of Limia vittata (Cyprinodontiformes: Poeciliidae): geographical distribution of mitochondrial haplotypes is comparable to other Cuban poeciliids
<p>This is the supplementary material associated with the article "Phylogeography of <em>Limia vittata</em> (Cyprinodontiformes: Poeciliidae): geographical distribution of mitochondrial haplotypes is comparable to other Cuban poeciliids", published by the Biological Journal of the Linnean Society (<a href="https://doi.org/10.1093/biolinnean/blad040">https://doi.org/10.1093/biolinnean/blad040</a>). The following documents (pdf format) are included:</p> <p><strong>Supporting Information 1 </strong></p> <p><strong>Table S1.</strong> Sampling size (n) and haplotype (<em>COI</em>+<em>CR</em>) information for each sampling locality of <em>L. vittata</em> included in this study. Numbers correspond to those indicated in Figure 1. A star (*) represents a new locality record for <em>L. vittata</em>. ANC: acronym of the Acuario Nacional de Cuba Collection, La Habana, Cuba.</p> <p><strong>Supporting Information 2</strong></p> <p><strong>Table S1.</strong> Prior distribution of parameters used for the analysis of the <em>L. vittata</em> data based on the ABC approach using DIYABC v.2.1.0 (<a href="#CIT0008">Cornuet <em>et al</em>., 2014</a>). Time is in generations. W-PR: Western Pinar del Río population, W-C: Western-Central population, C-E: Central-Eastern population.</p> <p><strong>Table S2.</strong> Summary statistics between <em>L. vittata</em> haplogroups for each scenario based on 3 × 10<sup>6</sup> simulated datasets. NHA: number of alleles, NSS: number of segregating sites, MPD: mean of pairwise differences, VPD: variance of pairwise differences, MP2: mean pairwise differences within samples, MPB: mean pairwise differences between samples, HST: F<sub><em>ST</em></sub> between samples.</p> <p><strong>Table S3.</strong> Posterior distributions of the parameters based on scenario B for <em>L. vittata</em>. Data were obtained from 1% of the simulated dataset (1 × 10<sup>6</sup>). Time is in generations. W-PR: Western Pinar del Río population, W-C: Western-Central population, C-E: Central-Eastern population. RMAE: relative median of absolute error.</p> <p><strong>Figure S1.</strong> PCA of the summary statistics of the observed dataset and the dataset generated from the prior distribution of parameters to evaluate the three biogeographic scenarios explaining the current distribution of <em>L. vittata</em>. The analysis was performed using DIYABC v.2.1.0 (<a href="#CIT0008">Cornuet <em>et al.</em>, 2014</a>).</p> <p><strong>Figure S2.</strong> Posterior probability of the biogeographic scenarios tested to explain the current distribution of <em>L. vittata</em>. Logistic regression was used to compute the posterior probability using the ABC approach as implemented in DIYABC v.2.1.0 (<a href="#CIT0008">Cornuet <em>et al.</em>, 2014</a>).</p> <p><strong>Supporting Information 3</strong></p> <p><strong>Figure S1.</strong> Bayesian tree depicting the relationships of 160 partial <em>COI</em>+<em>CR</em> sequences of <em>L. vittata</em>. The red dots depict samples from eastern localities (Yateras, Sabanalamar, and Yacabo Abajo) sharing the W-C haplogroups (H9 and H10). Bootstrap support (≥ 93) and Bayesian posterior probabilities (≥ 0.95) are shown for the main clades.</p> <p><strong>Supporting Information 4</strong></p> <p><strong>Figure S1.</strong> Mismatch distribution of pairwise haplotype differences from partial <em>COI</em> and <em>CR</em> sequences for the three haplogroups recovered in <em>L. vittata</em>. Dashed lines represent the distribution of the observed pairwise nucleotide differences, whereas solid lines represent the values expected after a population growth or decline model.</p> <p><strong>Supporting Information 5</strong></p> <p><strong>Figure S1.</strong> Maximum Likelihood tree and haplotype network of <em>Girardinus falcatus</em>, <em>Girardinus metallicus,</em> and the <em>Gambusia punctata</em> species complex based on <em>cytb</em> partial sequences. Each colour represents a geographic region in Cuba. Green: westernmost Cuba, blue: western Cuba, orange: central Cuba, red: eastern Cuba. Numbers on tree branches are bootstrap values ≥ 95% and hatch marks on the networks are the number of mutations. n: number of individuals, H: number of haplotypes, <em>h</em>: haplotype diversity, π: nucleotide diversity, SD: standard deviation.</p> <p><strong>Table S1.</strong> Sampling size (n), GenBank accession numbers, and studies that made available the sequences of cytochrome <em>b</em> used for the phylogeographic comparisons of the different poeciliids in Cuba.</p>
Comparative modeling of Vickery's faceted classification and the œuvre of S. R. Ranganathan...
<p> In an effort to make sense of both Ranganathan’s work and Vickery’s we modeled the<br> process involved in classification using the IDEF0 (Integrated Definition for Function<br> Modeling) formalism. This allows us to see five distinct parts of the classification process:<br> actions, inputs, outputs, mechanisms, and constraints. </p>
Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids
<p>Introgression is a potential source of valuable genetic variation and interspecific introgression lines are important resources for plant breeders to access novel alleles. Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from natural interspecific hybridization and provide opportunities to study the nature and transmission pattern of donor chromatin in recipient genomes. Here, we analyze transmission of donor chromatin in reciprocal backcrosses between <em>G. hirsutum</em> and <em>G. barbadense</em>. Across the genome, recurrent backcrossing in both backgrounds yielded donor chromatin at slightly higher frequencies than the Mendelian expectation in BC<sub>5</sub>F<sub>1</sub> plants, while the average frequency of donor alleles in BC<sub>5</sub>F<sub>2</sub> segregating families was less than expected. In the two subgenomes of polyploid cotton, the rate of donor chromatin introgression was similar. Although donor chromatin was tolerated over much of the recipient genomes, 21 regions recalcitrant to donor alleles were identified. Only limited correspondence is observed between the recalcitrant regions in the two backgrounds, suggesting the effect of species background on introgression of donor segments. Genetic breakdown was progressive, with floral abscission and seed inviability ongoing during backcrossing cycles. Regions of either high or low introgression tended to be in terminal chromosomal regions that are generally rich in both genes and crossover events, with long stretches around the centromere having limited crossover activity resulting in relatively constant low introgression frequencies. Constraints on fixation and selection of donor alleles highlights the challenges of utilizing introgression breeding in crop improvement.</p>
Dataset from: Eccentricity driven comparative analysis of GW sources detection with LISA
<p>The data set used in the study: <strong>Eccentricity driven comparative analysis of GW sources detection with LISA</strong></p> <p>Contents:</p> <ul> <li><strong>variable_eccentricity_dataset.zip</strong> <ul> <li>Contains the final DCO files with SNR > 7 detections for binaries with variable ZAMS eccentricity. </li> </ul> </li> <li><strong>variable_eccentricity_dataset_maxDistance.zip</strong> <ul> <li>Contains .npy files with information about the maximum distance up to which the corresponding DCO can be seen with LISA for variable ZAMS eccentricity dataset.</li> </ul> </li> <li><strong>zero_eccentricity_dataset.zip</strong> <ul> <li>Contains the final DCO files with SNR > 7 detections for binaries with zero ZAMS eccentricity.</li> </ul> </li> <li><strong>zero_eccentricity_dataset_maxDistance.zip</strong> <ul> <li>Contains .npy files with information about the maximum distance up to which the corresponding DCO can be seen with LISA for zero ZAMS eccentricity dataset.</li> </ul> </li> </ul>
Data from: A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture
<p><span>Promoters regulate both the amplitude and pattern of gene expression—key factors needed for optimization of many synthetic biology applications. Previous work in <em>Arabidopsis</em> found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters which lack any known promoter elements, thus designated as Coreless, tend to be expressed more ubiquitously. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression stability. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.</span></p>
Metabolic activity of aggregatibacter on Ti-based bulk metallic glass compared with Ti6Al4V
<p>Metabolic activity of aggregatibacter on Ti40Zr10Cu36Pd14 bulk metallic glass compared with T6Al4V (used as a control and therefore all values are considered as 100). </p>
A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods
<p>This repository contains all the datasets used for benchmarking drug repositioning methods based on heterogeneous networks, including drug-drug similarity, disease-disease similarity, and drug-disease associations.</p> <p>The repository consists of:</p> <ol> <li>Name or keyword information for drugs and diseases information contained in the dataset</li> <li>Inputs needed for different drug repositioning methods: multiple drug similarity matrices,multiple disease similarity matrices, and drug-disease associations matrices.</li> </ol> <p> </p> <p> </p> <blockquote> <p><strong>Please cite us :</strong><br>Yinghong Li, Yinqi Yang, Zhuohao Tong, Yu Wang, Qin Mi, Mingze Bai, Guizhao Liang, Bo Li, Kunxian Shu, A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods, <em>Briefings in Bioinformatics</em>, Volume 25, Issue 3, May 2024, bbae172, <a href="https://doi.org/10.1093/bib/bbae172">https://doi.org/10.1093/bib/bbae172</a></p> </blockquote>
Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes
<p>Dataset used to reproduce the analysis performed in "Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes" publication. The directory structure is the following:</p> <ul> <li>Gene_models - directory containing gene models (.gtf or .gff3 files) used for feature length comparisons across species</li> <li>intermediate_data - directory containing intermediate results from various scripts, the main purpose is to speed up the reproducibility of some longer running scripts <ul> <li>batch_adjusted_normalised_gene_expression_matrix.tsv - gene expression matrix used for evolutionary model fitting</li> <li>fc.tsv - fold change matrix used for evolutionary model fitting</li> <li>dated_species_tree.tre - species tree used throughout the model fitting step (newick format)</li> <li>DGE_script_enviorment.RData - saved R environment from differential gene expression analysis</li> <li>downregulated_IDs.RDS - gene IDs which undergo down-regulation throughout maternal-to-zygotic transition</li> <li>maternal_IDs.RDS - gene IDs which meet the cut-off criteria for being considered as maternally expressed</li> <li>N0_blasted.tsv - orthogroup annotations through blasting to a sequence database</li> <li>N0.tsv - orthogroups inferred from OrthoFinder</li> <li>OG_categories.tsv - classification of orthogroups based on them (I) having genes with maternal expression, but no significant down regulation, (II) having genes with maternal expression and significant down regulation throughout maternal-to-zygotic transition or (III) no maternal expression</li> <li>OG_presence.tsv - binary matrix coding for which orthogroup which species have gene expression values</li> <li>Paralog_variances.tsv - matrix containing variance metrics for paralogs in each species from before normalization across species</li> </ul> </li> <li>Pannzer2_annotation - directory containing GO annotations for all species from the Pannzer2 tool, used for GO analyses</li> <li>quantification_files - directory containing all salmon quantification outputs</li> <li>transcriptomes - <em>de novo</em> assembled transcriptomes for non-model species</li> </ul>
Dataset for Paul et al., "Revisiting the applicability and constraints of molybdenum and uranium-based paleo redox proxies: comparing two contrasting sill fjords", Biogeosciences, 2023
<p>The datafile contains the solid phase data for Gullmar Fjord (GF-117) and Koljö Fjord (KF-43), presented in Figures 3, 4 and 6 in the publication:</p> <ol> <li>pore water data (SO<sub>4</sub><sup>2-</sup>, ΣH<sub>2</sub>S, Fe, Mn, Mo, and U)</li> <li>solid-phase carbon and nitrogen data (TOC, TN, C/N, OC<sub>terr</sub> and OC<sub>phyt</sub>)</li> <li>solid-phase sequential extraction data (Mo, U, Fe, Mn, Al, Ca, and S)</li> <li>Mo and U-Enrichment Factors (EF)</li> </ol>
Dataset for Effects of coaxial cables on high-voltage lightning impulse measured parameters: A comparative between measurements and simulations
<p>Dataset for publication named: "Effects of coaxial cables on high-voltage lightning impulse measured parameters: A comparative between measurements and simulations".</p>
Supplementary material for: "Missing nurses cause missed care: is that it? Non-Trivial Configurations of Reasons Associated with Missed Care in Austrian hospitals – A qualitative comparative analysis"
<p>Dataset with calibrated data to reproduce the Qualitative Comparative Analysis in our article. </p><p>This dataset was generated by Ana Cartaxo. It contains 81 variables with 401 observations (complete data), which were included in the MISSCARE-Austria Study and were generated using the revised MISSCARE Austria instrument (Cartaxo et al., 2022). The original data were calibrated as described in the article in preparation of performing Qualitative Comparative Analysis – variables regarding contextual factors (Nurse Characteristics, Unit Characteristics, Hospital Characteristics), reasons for missed nursing care (Demand for patient care, Relationship and communication factors, Labor resources allocation, Material resources allocation) and outcomes of missed nursing care are included in the csv. file. </p><p>The R Script (R-Code.R) was created by Ana Cartaxo, João Cartaxo und Johannes Bergmann. It contains the different functions and analysis steps to reproduce the Qualitative Comparative Analysis reported on the article above, using the dataset made available ("Calibrated_Data_Set.csv").</p>
Data from: Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents
<p><span>Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species </span><span>(<em>Ashinkailepas kermadecensis</em>,<em> Imbricaverruca yamaguchii</em>) </span><span>from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481.5 to 1054.6 Mb, with repetitive sequence contents of 21.2 to 50.7%. Concordance rates of orthologs and heterozygosity ratios were between 82.4 and 91.7% and between 1.1 and 2.6, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, <em>CP100A</em>, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesized to be essential for thoracican settlement. Duplicated genes, <em>CP100B</em> and <em>CP100C</em>, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of <em>CP52 </em>genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no <em>CP52</em> genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field.</span></p>
Mind the Gap: Comparing Exploration Effort with Global Biodiversity Patterns and Climate Projections to Determine Ocean Areas with Greatest Exploration Needs- Dive metadata
<p>Meta data for deep submergence dive locations associated with "Mind the Gap: Comparing Exploration Effort with Global Biodiversity Patterns and Climate Projections to Determine Ocean Areas with Greatest Exploration Needs" published in Frontier of Marine Science 2023. </p>
Meakin Mark Comparative Test (Trnio Plus)
One of the tests conducted at the Digital Archaeology Lab lately was to create a model of the same sherd using every application that we had at our disposal, so as to have comparative data. This particular model was made using Trnio Plus, a photogrammetry iPad application. The sherd itself is an ironstone basal sherd from a plate; it features a transferprinted maker's mark indicating that it was made by J. & G. Meakinn (Hanley, Stoke-on-Trent, England). The mark itself features what is referred to as the "modern" Royal Arms and can be used to date this particular sherd to after 1890. If you look closely, you can make out the beginning of the word "Ironstone" and the start of "J. & G. Meakin." Source: Objaverse 1.0 / Sketchfab
Meakin Mark Comparative Test (PhotoCatch)
One of the tests conducted at the Digital Archaeology Lab lately was to create a model of the same sherd using every application that we had at our disposal, so as to have comparative data. This particular model was made using PhotoCatch, a photogrammetry iPad application. The sherd itself is an ironstone basal sherd from a plate; it features a transferprinted maker's mark indicating that it was made by J. & G. Meakinn (Hanley, Stoke-on-Trent, England). The mark itself features what is referred to as the "modern" Royal Arms and can be used to date this particular sherd to after 1890. If you look closely, you can make out the beginning of the word "Ironstone" and the start of "J. & G. Meakin." Source: Objaverse 1.0 / Sketchfab
Population genetics and comparative morphology of two serpentine Phlox species
<p>Hybridization between rare and widespread species can result in loss of genetic integrity for the rarer species, which can have management and conservation implications. One rare species, <em>Phlox hirsuta</em>, is a serpentine endemic in northern California, and it frequently co-occurs with a widespread congener, <em>P. speciosa</em>. Putative hybrids were recognized based on intermediate morphology, so the possibility of hybridization was explored using floral morphological and molecular data. Ninety-eight individuals of <em>P. hirsuta</em> and <em>P. speciosa</em> were collected from each of three populations, and floral features were measured and compared. Eleven microsatellite loci were amplified for species and putative hybrids, and inter- and intraspecific genetic diversity and relationships were investigated with multiple methods. Variation in morphological and molecular data was recognized. Floral variation was greater for <em>P. hirsuta</em> than <em>P. speciosa</em>. Putative hybrids were genetically allied with <em>P. speciosa</em>, but two individuals of <em>P. hirsuta</em> were resolved to have genetic similarity with <em>P. speciosa</em>. While hybridization is possible between the species, it is uncommon and appears to be primarily unidirectional, with <em>P. speciosa</em> as the hypothesized male parent and <em>P. hirsuta</em> as the hypothesized female parent. The small number of recognized hybrids may be due to ineffective interspecific pollination, early acting inbreeding depression, hybrids being less fit than parents, and/or small sample sizes. Reinforcement does not appear to play a role in secondary contact between species. Both microsatellite loci and floral morphology varied across the small geographic range of <em>P. hirsuta</em>, suggesting local differentiation and adaptation are possible over short distances.</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.