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.
818
datasets available to search
ShareScore release 0.9.0
Dataset results
818 results for “Neutrality”
Amino sugars and neutral sugars in the biomass of different taxa
<p>Amino sugar and neutra sugar necromass biomarkers in the biomass of archaea, bacteria, fungi and plant species. </p>
A Novel Backtracing Model to Study the Emission of Energetic Neutral Atoms at Titan
<p>Data for the manuscript "A Novel Backtracing Model to Study the Emission of Energetic Neutral Atoms at Titan" by Tippens et al., (2023). See README.txt for a description of the data files included here.</p>
Data and code for 'Pseudogenes act as a neutral reference for detecting selection in prokaryotic pangenomes'
<p>This repository contains the code and files for reproducing the analyses and results reported in 'Pseudogenes act as a neutral reference for detecting selection in prokaryotic pangenomes' by Gavin M. Douglas and B. Jesse Shapiro (<a href="https://doi.org/10.1038/s41559-023-02268-6">https://doi.org/10.1038/s41559-023-02268-6</a>).</p> <p>File organization and descriptions:</p> <ul> <li><strong>code/</strong> - Contains GitHub repository releases of code used in manuscript (the other folders contain datafiles only). This code is provided here as well as on GitHub to ensure long-term access. <ul> <li><strong>handy_pop_gen-1.1.0/</strong> - release v1.1.0 of the convenience repository (used for specific data processing and analysis steps referred to in the manuscript).</li> <li><strong>pangenome_pseudogene_null-1.1.0/ </strong>- Main code repository for manuscript.</li> </ul> </li> </ul> <p> </p> <ul> <li><strong>broad_pangenome_analysis/</strong> <ul> <li><strong>element_info/element_counts.tsv.gz</strong> - Counts of (filtered) pseudogenes and intact genes called per genome accession.</li> <li><strong>element_info/gene_sizes.tsv.gz</strong> - Gene sizes in base-pairs.</li> <li><strong>element_info/pseudogene_sizes.tsv.gz</strong> - Filtered pseudogene sizes in base-pairs.</li> <li><strong>element_info/element_percent_coverage/*tsv.gz</strong> - Tables containing the percent genome coverage of genes and pseudogenes, by accession and averaged over accessions per species separately.</li> <li><strong>example_Mycoplasmopsis_bovis_panaroo_output.csv.gz</strong> - Panaroo output table for <em>Mycoplasmopsis bovis</em>, which was used for an example. Corresponds to the <em>gene_presence_absence.csv</em> file in the raw Panaroo output.</li> <li><strong>focal_and_non.focal_full_to_short.tsv.gz</strong> - Mapfile of full to short (and unique) species ids used in analysis. Primarily to include species ids in cluster names without making them unnecessarily long.</li> <li><strong>genome_info/accessions.tsv.gz</strong> - Genome accessions used for broad pangenome analysis (note that not all genome accessions could be downloaded [and were ignored], which is indicated in the "could_download" column).</li> <li><strong>genome_info/genome_sizes.tsv.gz</strong> - Sizes of all genomes used for the broad pangenome analysis.</li> <li><strong>metrics_additional_subsamples.tsv.gz</strong> - Contains columns also found in the <em>pangenome_and_related_metrics.tsv.gz</em> file below, but based on genome subsamplings of 3 and 20, rather than 9.</li> <li><strong>model_output/pangenome_linear_models.rds</strong> - R Data Serialization files containing the output of R linear model objects (generated by lm and provided as an R list object). There are separate elements in the list for the mean number of genes, genomic fluidity, percentage singletons (si), and si/sp.</li> <li><strong>model_output/linear_model_coef.tsv.gz</strong> - Coefficient summary table for all linear models.</li> <li><strong>pangenome_and_related_metrics.tsv.gz</strong> - Metrics used for broad pangenome analysis across 670 prokaryotic species. Note that this table was filtered down to 668 species after excluding those with < 9 genomes.</li> <li><strong>pangenome_and_related_metrics_filt.tsv.gz</strong> - Filtered table, as described above.</li> <li><strong>taxonomy.tsv.gz</strong> - Taxonomy for all species used for this analysis, taken from GTDB. Row names are species names.</li> </ul> </li> </ul> <p> </p> <ul> <li><strong>indepth_10_species_analysis/</strong> <ul> <li><strong>cluster_breakdown_tables/</strong> - Folder containing tables providing breakdown of how clusters are distributed by element type, pangenome partition, and species. Provided for easy plotting.</li> <li><strong>cluster_COG_annot.tsv.gz</strong> - Mapping of cluster IDs to COG annotations.</li> <li><strong>cluster_filt_lengths_and_additional.tsv.gz</strong> - Metadata on clusters, most pertinently the length of the representative sequence in the cluster (which was used to filter out some clusters, below the cut-off which pseudogenes could not be called).</li> <li><strong>cluster_member_breakdown.tsv.gz </strong>- Table providing information on each element (called pseudogenes and intact genes) and provides information such as what cluster they are part of, what species and genome accession they are found in, etc.</li> <li><strong>cluster_types.rds</strong> - R Data Serialization file containing R list providing breakdown of all clusters into categories (intact/pseudogene/mixed, where mixed means containing both pseudogene and intact elements).</li> <li><strong>COG_enrichment_results/ultra.cloud-COG-gene-enrichments.tsv.gz</strong> - Output file with enrichment test summaries for COG IDs in significant COG categories, which was run for the ultra-cloud pangenome partition model only.</li> <li><strong>element_glmm_input.tsv.gz </strong>- Table containing all information used for fitting generalized linear mixed models.</li> <li><strong>focal_species.txt</strong> - Names of species used for the in-depth analysis.</li> <li><strong>genome_info/ </strong>- Folder containing the genome accessions (and the corresponding genome sizes) for all ten analyzed species.</li> <li><strong>glmm_output/</strong> - Folder containing R Data Serialization files containing output R objects after fitting generalized linear mixed models (only ultra-rare files are present, due to file size constraints).</li> <li><strong>per_genome_element.type_percent_coverages.rds</strong> - R Data Serialization file containing R list providing the percent coverage by intact genes vs pseudogenes per accession (nested by species)</li> </ul> </li> </ul>
Supporting information for prebiotic triose glycolysis promoted by co-catalytic proline and phosphate in neutral water
<p>Supporting information for prebiotic triose glycolysis promoted by co-catalytic proline and phosphate in neutral water</p>
Dataset for the article "Beyond PLFA: Concurrent extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities"
<p>The following are data and code used for statistical analysis and figure plotting in the manuscript</p> <p>Gorka et al. (2023) "Beyond PLFA: Concurrent extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities", Soil Biology and Biochemistry</p> <p>It contains the following files:</p> <p>1. Pure lipid standard data</p> <ul> <li>Total ion chromatogram (TIC) area data (<strong>area.csv</strong>)</li> <li>Assignment of lipids that the measured fatty acids originate from (<strong>LipidClass.csv</strong>)</li> <li>An R script reproducing the calculations and plotting for Fig. 2 and Fig. S1 (<strong>pure_lipids.R</strong>)</li> </ul> <p>2. Microbial pure culture fatty acid data data</p> <ul> <li>TIC area data of the PLFA, NLFA, and GLFA data from pure culture extracts (<strong>area.csv</strong>)</li> <li>Files needed for calculating the data and assigning taxonomic groups in the R code (<strong>weights.csv</strong>, <strong>C_atoms.csv</strong>, <strong>species_list.csv</strong>)</li> <li>An R script reproducing the calculations and plotting for Fig. 3, Fig. 4, Fig. S2, and Fig. S3 (<strong>pure_cultures.R</strong>)</li> </ul> <p>3. Soil fatty acid data</p> <ul> <li>Absolute abundance data in nmol C g<sup>-1</sup> dry weight of the PLFA, NLFA, and GLFA data from soil extracts (<strong>nmolC.csv</strong>)</li> <li>Taxonomic group assignments of fatty acids needed to run the R code (<strong>phylum.csv</strong>)</li> <li>An R script reproducing the calculations and plotting for Fig. 5, and Fig. S4 (<strong>soil.R</strong>)</li> </ul>
Observation of an isotope effect in state-selective mutual neutralization of lithium with hydrogen
<p>The data files found here contain the data as obtained and displayed in : "Observation of an isotope effect in state-selective mutual neutralization of lithium with hydrogen" published in Physical Review A (2023). Each file contains an explanatory header. Header lines start with #.</p> <p> </p>
The relationship between neutral genetic diversity and performance in wild arthropod populations
Open the record for dataset details and reuse information.
Neutral processes related to regional bee commonness and dispersal distances are important predictors of plant-pollinator networks along gradients of climate and landscape conditions
Open the record for dataset details and reuse information.
Neutrality in plant–herbivore interactions
Open the record for dataset details and reuse information.
The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern
Open the record for dataset details and reuse information.
Data for: Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms
Open the record for dataset details and reuse information.
Data from: Competition on a neutral playing field: Invaders still win and size still matters, sometimes
Open the record for dataset details and reuse information.
Improving Neutral Density Predictions Using Exospheric Temperatures Calculated on a Geodesic, Polyhedral Grid
<p>These files provide supplemental data, additional graphs of neutral density predictions, and basic program code and required files, to accompany the paper "Improving Neutral Density Predictions Using Exospheric Temperatures Calculated on a Geodesic, Polyhedral Grid,” published in the journal <em>Space Weather, </em>doi:10.1029/2019SW002355. For more information, refer to the READ_ME.pdf documentation and the journal paper.</p>
Data from: Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine
<p><span><span><span><span><span><span><span><span><span><span><span>It is generally accepted that the spatial distribution of neutral genetic diversity within a species' native range mostly depends on effective population size, demographic history, and geographic position. However, it is unclear how genetic diversity at adaptive loci correlates with geographic peripherality or with habitat suitability within the ecological niche. Using exome-wide genomic data and distribution maps of the Alpine range, we first tested whether geographic peripherality correlates with four measures of population genetic diversity at >17,000 SNP loci in 24 Alpine populations (480 individuals) of Swiss stone pine (<i>Pinus cembra</i>) from Switzerland. To distinguish between neutral and adaptive SNP sets, we used four approaches (two gene diversity estimates, <i>F</i><sub>ST</sub> outlier test, and environmental association analysis) that search for signatures of selection. Second, we established ecological niche models for <i>P. cembra</i> in the study range and investigated how habitat suitability correlates with genetic diversity at neutral and adaptive loci. All estimates of neutral genetic diversity decreased with geographic peripherality, but were uncorrelated with habitat suitability. However, heterozygosity (<i>H</i><sub>e</sub>) at adaptive loci based on Tajima's <i>D</i> declined significantly with increasingly suitable conditions. No other diversity estimates at adaptive loci were correlated with habitat suitability. Our findings suggest that populations at the edge of a species' geographic distribution harbour limited neutral genetic diversity due to demographic properties. Moreover, we argue that populations from suitable habitats went through strong selection processes, are thus well adapted to local conditions, and therefore exhibit reduced genetic diversity at adaptive loci compared to populations at niche margins.</span></span></span></span></span></span></span></span></span></span></span></p>
Positive and negative interspecific interactions between coexisting rice planthoppers neutralize the effects of elevated temperatures
Global warming is often predicted to increase damage to plants through direct effects on insect herbivores. However, the indirect impacts of rising temperatures on herbivores, mediated through interactions with their biotic environment, could dampen these effects. Using a series of reciprocal density experiments with gravid females and developing nymphs, we examined interspecific competition between two coexisting phloem feeders, Nilaparvata lugens (BPH) and Sogatella furcifera (WBPH), on rice at 25°C and 30°C. WBPH performed better (i.e., adults survived longer, nymphs developed faster and grew larger) at 25°C and BPH (i.e., nymphs developed faster) at 30°C. However, contrary to predictions, WBPH had a greater effect in reducing oviposition and nymph performance in BPH at 30°C. A decoupling of resource use by WBPH and its antagonistic effects on BPH at the higher temperature suggests that WBPH feeding induces host defenses that reduce BPH fitness (i.e., interference competition). Meanwhile, BPH facilitated WBPH oviposition at 30°C and facilitated WBPH nymph performance at 25 and 30°C. Greater facilitation of feeding in WBPH nymphs by BPH at high densities suggests that mechanical damage and host responses to damage increased the fitness of the heterospecific nymphs. Although BPH also facilitated egg-laying by WBPH, intra- and interspecific crowding countered this facilitation at both temperatures. Simulated life tables for planthoppers at 25 and 30°C depicted significantly lower offspring numbers on rice infested by WBPH alone and from mixed BPH-WBPH infestations than from infestations by BPH alone. Our results indicate how interference competition – mediated through host plant defenses - can increase ecosystem resilience to the warmer temperatures predicted under global climate change.
Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities
<p>Python Script. Cell count outputs were converted into a standardized spreadsheet using a Python version 3.7.2 script</p> <p>Codes for binomial and lognormal model</p> <p>code to obtain the images from the model results</p> <p>data to run the models, data result from the models</p>
Experimental and numerical data of an article on the prediction of wind load on pylons for a neutral atmospheric boundary layer ow over two successive hills
<p>his deposit contains experimental and numerical data related to the article entitled "Towards prediction of wind load on pylons for a neutral atmospheric boundary layer flow over two successive hills" that will be publised in Journal of Wind Engineering & Industrial Aerodynamics. It consists in post-processed experimental data (turbulence statistics) for flows around 2D hills, measured by PIV, and numerical date of k-epsilon simulations of the same configirations. All data are provided in matlab metadata format. Matlab functions are given to plot all the figures of the article.</p>
Data from: Is MHC diversity a better marker for conservation than neutral genetic diversity? a case study of two contrasting dolphin populations
Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia—one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty‐three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population—for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human‐induced changes to the coastal ecosystem it inhabits.
Neutralization Data and Aligned ENV Sequences for Predicting Antibody Affinities using Artificial Neural Networks
<p>Sample file with neutralization data (IC<sub>50</sub>) for different antibodies and viral strains, adapted from J. Huang, G. Ofek, L. Laub, M. K. Louder, N. A. Doria-Rose, N. S. Longo, H. Imamichi, R. T. Bailer, B. Chakrabarti, S. K. Sharma, S. M. Alam, T. Wang, Y. Yang, B. Zhang, S. A. Migueles, R. Wyatt, B. F. Haynes, P. D. Kwong, J. R. Mascola, and M. Connors, “Broad and potent neutralization of HIV-1 by a gp41-specific human antibody.,” <em>Nature</em>, vol. 491, no. 7424, pp. 406–12, Nov. 2012.</p> <p> </p> <p>Aligned ENV sequences downloaded from the HIV Sequence Database (www.hiv.lanl.gov/content/sequence/HIV/mainpage.html). There are 4907 sequences and the alignment length is 1369.</p>
Scaling of the electron temperature on the expansion ratio with plasma heating by Neutral Beams only (diamonds) and with both Neutral Beams and ECRH (square)
<p>Scaling of the electron temperature on the expansion ratio with plasma heating by Neutral Beams only (diamonds) and with both Neutral Beams and ECRH (square)</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.