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.
2,412
datasets available to search
ShareScore release 0.9.0
Dataset results
2,412 results for “independent”
Environment dependent costs and benefits of recombination in independently evolved populations of Escherichia coli
Understanding of the causes by which reproductive isolation arises remains limited. We examine the role of adaptation in driving reproductive isolation among 12 Escherichia coli populations evolved in two different environments. We found that, regardless of whether parents were selected in the same or different environments, the average fitness of recombinants was lower than the expected, consistent with a prevailing influence of incompatibility between independently accumulated mutations. Exceptions to this pattern occurred among recombinants of some parents evolved in different environments. These recombinants were less fit than expected in the selective environment of one parent, but more fit than expected in the selective environment of the other parent. Our results indicate that both parallel and divergent adaptation can quickly lead to intrinsic genetic barriers contributing to the initial stages of speciation and show that these barriers can be complex, for example, depending on the environment in which recombinant offspring are tested.
Data from: Body size variation in aquatic consumers causes pervasive community effects, independent of mean body size
Intraspecific phenotypic variation is a significant component of biodiversity. Body size, for example, is variable and critical for structuring communities. We need to understand how homogenous and variably-sized populations differ in their ecological responses or effects if we are to have a robust understanding of communities. We manipulated body size variation in consumer (tadpole) populations in mesocosms (both with and without predators), keeping mean size and density of these consumers constant. Size-variable consumer populations exhibited stronger antipredator responses (reduced activity), which had a cascading effect of increasing the biomass of the consumer's resources. Predators foraged less when consumers were variable in size, and this may have mediated the differential effects of predators on the community composition of alternative prey (zooplankton). All trophic levels responded to differences in consumer size variation, demonstrating that intrapopulation phenotypic variability can significantly alter interspecific ecological interactions. Furthermore, we identify a key mechanism (size thresholds for predation risk) that may mediate impacts of size variation in natural communities. Together, our results suggest that phenotypic variability plays a significant role in structuring ecological communities.
Adaptation to drought is coupled with slow growth, but independent from phenology in marginal silver fir (Abies alba Mill.) populations
Drought is one of the most important selection pressures for forest trees in the context of climate change. Yet, the different evolutionary mechanisms, and their environmental drivers, by which certain populations become more drought tolerant than others is still little understood. We studied adaptation to drought in 16 silver fir (<i>Abies alba</i> Mill.) populations from the French Mediterranean Alps by combining observations on seedlings from a large scale greenhouse experiment (N=8199) and on adult tress in situ (N=315). In the greenhouse, we followed half-sib families for four growing seasons for growth traits and bud break phenology, and tested their water stress response in a "drought until death" experiment. Adult trees in the field were assessed for δ<sup>13</sup>C, a proxy for water use efficiency and genotyped at 357 SNP loci. SNP data was used to generate a null expectation for trait divergence between populations to detect the signature of selection, and 31 environmental variables to identify the selective environment. We found that seedlings originating from populations with low soil water capacity grew more slowly, attained a smaller stature, and resisted the water stress treatment for a longer period of time in the greenhouse. Additionally, adult trees of these populations exhibited a higher water use efficiency as evidenced by δ<sup>13</sup>C. These results suggest a correlated evolution of the growth-drought tolerance trait complex. Population divergence in bud break phenology was adaptive only in the second growing season, and evolved independently from the growth-drought tolerance trait complex. Adaptive divergence in bud break phenology was principally driven by the inter- and intra-annual variation in temperature at the geographic origin of the population. Our results illustrate the different evolutionary strategies used by populations to cope with drought stress at the range limits across a highly heterogeneous landscape, and can be used to inform assisted migration programs.
Sex-independent senescence in a cooperatively breeding mammal
<p>1. Researchers studying mammals have frequently interpreted earlier or faster rates of ageing in males as resulting from polygyny and the associated higher costs of reproductive competition.</p> <p>2. Yet few studies conducted on wild populations have compared sex-specific senescence trajectories outside of polygynous species, making it difficult to make generalised inferences on the role of reproductive competition in driving senescence, particularly when other differences between males and females might also contribute to sex-specific changes in performance across lifespan.</p> <p>3. Here, we examine age-related variation in body mass, reproductive output and survival in dominant male and female meerkats, <i>Suricata suricatta</i>. Meerkats are socially monogamous cooperative breeders where a single dominant pair virtually monopolize reproduction in each group and subordinate group members help to rear offspring produced by breeders.</p> <p>4. In contrast to many polygynous societies, we find that neither the onset nor the rate of senescence in body mass or reproductive output show clear differences between males and females. Both sexes also display similar patterns of age-related survival across lifespan, but unlike most wild vertebrates, survival senescence (increases in annual mortality with rising age) was absent in dominants of both sexes, and as a result, the fitness costs of senescence were entirely attributable to declines in reproductive output from mid- to late-life.</p> <p>5. We suggest that the potential for intrasexual competition to increase rates of senescence in females – who are hormonally masculinised and frequently aggressive – is offset by their ability to maintain longer tenures of dominance than males, and that these processes combined lead to similar patterns of senescence in both sexes.</p> <p>6. Our results stress the need to consider the form and intensity of sexual competition as well as other sex-specific features of life history when investigating the operation of senescence in wild populations.</p>
Independence Cross – a case
ID no.: MNS-H/4204 Museum: Nowy Sącz District Museum https://muzea.malopolska.pl/en/objects-list/2355 Digitalisation: RDW MIC, Virtual Małopolska project Source: Objaverse 1.0 / Sketchfab
Time independent traces from NAS MPI benchmarks (LU,IS,FT)
<p>Time independent traces from NAS MPI benchmarks (LU,IS,FT) that runs on Grid'5000 testbed on the graphene cluster (node 105 to143) using a dedicated switch (no network contention) and with 1 MPI process per node.</p> <p>These traces are made to be used by a distributed system simulator to replay the jobs executions.</p>
Energy management strategies for ectothermic vertebrates: temperature and heart rate as independent proxies
<p>Filtered data used for analysis of energy management strategies in three different species. R script provides an example of the across- and within-individual analysis. </p>
aFCn for independent cis-eQTLs across 49 tissues in the GTEx v8 release
<p>The aFC-n model is the multi-variant generalization of the aFC approach (<a href="https://github.com/secastel/aFC">https://github.com/secastel/aFC</a>), to estimate the <i>cis</i>-regulatory effect size in genes associated with multiple conditionally independent eQTLs. Notably, aFC-n is the first method that allows for predicting genetically regulated gene expression in a haplotype-specific fashion, paving the way for a future class of genome association studies that can systematically incorporate allele dosage effects.</p><p>This dataset is generated using aFC-n software package (<a href="https://doi.org/10.5281/zenodo.8412460">10.5281/zenodo.8412460</a>) to calculate effect sizes for ~half a million independent <i>cis</i>-eQTLs across 49 tissues in the GTEx v8 release as described in the <a href="https://www.biorxiv.org/content/10.1101/2022.01.28.478116v1">manuscript</a>.</p><p>GTEx_v8_aFCn contains:</p><ul><li>gene_id : Ensembl gene ID</li><li>variant_id : eQTL ID associated to the gene</li><li>log2_aFC : The log2 of eQTL effect sizes measured as allelic Fold Change (aFC).</li><li>log2_aFC_min_95_interv : Lower bound 95% confidence interval</li><li>log2_aFC_plus_95_interv: Upper bound 95% confidence interval</li></ul><p>GTEx_v8<i>_</i>aFCn<i>_</i>combined contains:</p><ul><li>gene_id : Ensembl gene ID</li><li>variant_id : eQTL ID associated to the gene</li><li>rest of the columns : The log2 of eQTL effect sizes measured as allelic Fold Change (aFC) in the tissue specified by the column label capped at ±log2(100) <ul><li>nan = The variant is not an eQTL for the tissue / the effect size is not calculated for variants on chrX</li></ul></li></ul><p> </p>
Combined bioinformatics and machine learning methodologies reveal prognosis-related ceRNA network and propose ABCA8, CAT, and CXCL12 as independent protective factors against osteosarcoma
<p><strong>Supplementary Table 1</strong>. Basic traits of the seven microarray datasets from the Gene Expression Omnibus and The Cancer Genome Atlas.</p><p><strong>Supplementary Table 2</strong>. Basic characteristics of the nine differentially expressed circRNAs</p><p><strong>Supplementary Table 3</strong>. Index of concordance (C-index) and variance inflation factor (VIF) of ABCA8, CXCL12, and CAT.</p><p><strong>Supplementary Table 4.</strong> LASSO and cox analysis of ceRNA with coef/se(coef) < 0.01 and P-value of proportional hazards assumption (PH) > 0.05.</p><p><strong>Supplementary Table 5</strong>. Robust rank aggregation analysis of ABCA8, CXCL12, and CAT. LogFC in the four datasets and RRA score of the three RNAs.</p><p><strong>Supplementary Figure 1.</strong> Competitive endogenous RNA in osteosarcoma.</p><p><strong>Supplementary Figure 2.</strong> Protein–protein interaction (PPI) network of genes in the competitive endogenous RNA network</p><p><strong>Supplementary Figure 3.</strong> Proportional hazards assumption (left) and linearity assumption (right).</p><p><strong>Supplementary Figure 4.</strong> Survival analysis for competitive endogenous RNA in osteosarcoma.</p>
Genomics polymorphisms of Staphylococcus aureus strain NCTC 8325 in the lab stock maintained at TUM (WT), after 30 passes in BHI media (D) and after 30 passes detecting 4 -fold MIC increase to isocyanide -code I16- 3 biological replicates (A,B,C), and 3 independent colonies sequenced per replicate at the end of the experiment.
<p>Genomics polymorphisms of Staphylococcus aureus strain NCTC 8325 in the lab stock maintained at TUM (WT), after 30 passes in BHI media (D) and after 30 passes detecting 4 -fold MIC increase to isocyanide -code I16- 3 biological replicates (A,B,C), and 3 independent colonies sequenced per replicate at the end of the experiment. Determined from Illumina shotgun genomic sequencing datasets, mapping and analyses vs the reference genome of the strain https://www.ncbi.nlm.nih.gov/nuccore/NC_007795.1/</p>
Social experiences shape song preference learning independent of developmental exposure to song
<p>Communication governs the formation and maintenance of social relationships. The interpretation of communication signals depends not only on the signal's content, but also on a receiver's individual experience. Experiences throughout life may interact to affect behavioral plasticity, such that a lack of developmental sensory exposure could constrain adult learning, while salient adult social experiences could remedy developmental deficits. We investigated how experiences impact the formation and direction of female auditory preferences in the zebra finch. Zebra finches form long-lasting pair bonds and females learn preferences for their mate's vocalizations. We found that after two weeks of cohabitation with a male, females formed pair bonds and learned to prefer their partner's song regardless of whether they were reared with ("normally-reared") or without ("song-naïve") developmental exposure to song. In contrast, females that heard but did not physically interact with a male did not prefer his song. In addition, previous work has found that song-naive females do not show species-typical preferences for courtship song. We found that cohabitation with a male ameliorated this difference in preference. Thus, courtship and pair bonding, but not acoustic-only interactions, strongly influence preference learning regardless of rearing experience, and may dynamically drive auditory plasticity for recognition and preference.</p>
Dataset related to the publication "An Invar-based dual Fabry–Perot cavity refractometer for assessment of pressure with a pressure independent uncertainty in the sub-mPa region"
<p>The data set consists of; The published paper, all figures that present measurement or simulation data in .png and .fig format and the underlying data plotted in the figures in text format.<span> </span>The published plots were generated from the fig files. The text files were generated by reading the plotted data from the fig files. The files are named Fig_XX were XX corresponds to the figure number in the publication.<span> </span>The format of the text file is as follows. Before every data set there is a header consisting of; The number of the subplot where the data is plotted (Plot: XX), the number of the data set in the sub plot (DataSet: XX), and the color of the line or marker in the plot (Color: XX). The description of what each color represents can be found in the publication.</p>
Building a realistic, scalable memory model with independent engrams using a homeostatic mechanism
<p>Code and data for our paper:</p> <p><a href="doi.org/10.3389/fninf.2024.1323203">Building a realistic, scalable memory model with independent engrams using a homeostatic mechanism</a><br>Marvin Kaster, Fabian Czappa, Markus Butz-Ostendorf, Felix Wolf</p>
A synthetic moving-envelope metasurface antenna for arbitrary harmonic orders independent control
<p>Raw measured data for the paper "A synthetic moving-envelope metasurface antenna for arbitrary harmonic orders independent control"</p>
Data associated with 'Closing the stellar labels gap: Stellar label independent evidence for [α/M] information in Gaia BP/RP spectra'
<p>We present a stellar label independent model for Gaia BP/RP (XP) spectra, which does not rely on stellar labels to simulate XP spectra. Here, we provide all of the data required to reproduce <a href="https://github.com/AlexLaroche7/xp_vae">our results</a>. All of the data files should be placed in the data folder. Below we brieflty summarize the contents of each:</p> <p>APOGEE/GAIA XP DATA:</p> <ul> <li>xp_apogee_cat.h5: Contains all Gaia XP data and APOGEE stellar labels used in this work.</li> <li>xp_corrs.npz: Contains Gaia XP covariance matrices for a subset of the test data to compute reconstruction errors.</li> </ul> <p>INTERMEDIATE DATA PRODUCTS:</p> <p><em>(All files below can be reproduced with our codebase. We simply include them to speed up runtime for reproducing our results.)</em></p> <ul> <li>lb23_xp_est_labels.npy: <a href="https://ui.adsabs.harvard.edu/abs/2024MNRAS.527.1494L/abstract">Leung & Bovy (2023)</a> XP coeffficient spectra reconstructions (stellar label dependent implementaton)</li> <li>lb23_xp_est_no_labels.npy: Leung & Bovy (2023) XP coeffficient spectra reconstructions (stellar label independent implementaton)</li> <li>xp_wavelength_space.npy: Observed Gaia XP spectra in wavelength space</li> <li>err_wavelength_space.npy: Observed Gaia XP uncertainties in wavelength space</li> <li>apogee_norm.npz: Means and standard deviations which are used to pre-process Gaia XP data before inputting into our model</li> <li>zhang_stellar_params_xmatch.npz: <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524.1855Z/abstract">Zhang, Green, Rix (2023)</a> stellar parameter estimates for subset of XP spectra (to compute reconstructions)</li> <li>vae_wavelength_space.npy: Our model XP coefficient reconstructions in wavelength space</li> </ul> <p>If you have any questions please reach out via email: alex.laroche@mail.utoronto.ca</p>
Null device-independent prepare-and-prepare bipartite dimension test with a single joint measurement
Open the record for dataset details and reuse information.
CRABS CLAW-independent floral nectary development in Penstemon barbatus
<p>Data and Scripts for the "CRABS CLAW-independent floral nectary development in Penstemon barbatus" manuscript.</p> <p> </p> <p>Scripts:</p> <ol> <li>fastp.sh - filter and quality trim reads using fastp on all samples</li> <li>1ribo_detect.sh - detect and filter rRNA. Example script for 1 sample.</li> <li>gffread.sh - convert P. barbatus genome annotation GFF to a GTF for use in STAR</li> <li>star_initalize.sh - initalize STAR for the P. barbatus genome</li> <li>1star_ribo.sh - Example script for aligning reads from 1 sample to the genome.</li> <li>htseq_ribo.sh - counting reads for each sample using HTseq</li> <li>deseq2_code.R - R script for running the transcriptome tissue comparisons in DEseq2 with the output from HTseq.</li> <li>deseq_PCA.R - R script for the generation of the PCA plots for the samples. To be used in conjuction with the deseq2_code.R script.</li> <li>20230321_topGO_script.R - R script for Gene Ontology analyses in topGO.</li> <li>area_perimeter_cor.R - R script for vasculature ANOVAs.</li> </ol> <p> </p> <p>Data:</p> <ol> <li>Genome files <ul> <li>4_LG_2022_maker.all.maker.proteins.fasta - protein sequences for all genes in the P. barbatus genome in Wessinger et al. 2023</li> <li>4_LG_2022_maker.all.maker.noseq.gff - GFF file for all genes in the P. barbatus genome in Wessinger et al. 2023</li> </ul> </li> <li>HTseq output trimmed to only the counts (excludes other log information) - trimmed_htseq_35404342.txt</li> <li>DEseq2 output <br> <ul> <li>Early stage <ul> <li>barb_early_nect_nonect_FDR0.01_LFC0.csv</li> <li>barb_early_nect_nonect_FDR0.01_LFC0.annotated.csv</li> </ul> </li> <li>Late stage <ul> <li>barb_late_nect_nonect_FDR0.01_LFC0.csv</li> <li>barb_late_nect_nonect_FDR0.01_LFC0.annotated.csv</li> </ul> </li> <li>Nectar removal <ul> <li>barb_stage5_6_FDR0.01_LFC0.csv</li> <li>barb_stage5_6_FDR0.01_LFC0.annotated.csv</li> </ul> </li> </ul> </li> <li>Orthofinder output - N0.tsv</li> <li>Vasculature raw data - 20231025_bud_measurements_pbarb.csv</li> <li>Archive_Images directory - contains raw section images stained with either Alcian Blue & Safranin O or </li> </ol>
Electronic supplementary information: Independent and adaptive evolution of phenotypic novelties is driven by coral symbiosis in barnacle larvae
<p class="Standard">The invasion of novel habitats is recognized as a major promotor of adaptive trait evolution in animals. We tested whether similar ecological niches entail independent and adaptive evolution of key phenotypic structures related to larval host invasion in distantly related taxa. We use disparately related clades of coral barnacles as our model system (Acrothoracica: <i>Berndtia</i> and Thoracica: Pyrgomatidae). We analyze the larval antennular phenotypes and functional morphologies facilitating host invasion. Extensive video recordings show that coral host invasion is carried out exclusively by cypris larvae with spear-shaped antennules. These first exercise a series of complex probing behaviors followed by repeated antennular penetration of the soft host tissues, which subsequently facilitates permanent invasion. Phylogenetic mapping of larval form and function related to niche invasion in 99 species of barnacles (Thecostraca) compellingly shows that the spear-phenotype is uniquely associated with corals and penetrative behaviors. These features evolved independently in the two coral barnacle clades and from ancestors with fundamentally different antennular phenotypes. The larval host invasion system in coral barnacles likely evolved adaptively across millions of years for overcoming challenges associated with invading and entering demanding coral hosts.</p> <p class="Standard"> </p> <p class="Standard"><i>Key words: </i>adaptive host invasion, larval phenotypes, coral barnacle, barnacle phylogeny</p>
Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species
<p>The repeated transition from outcrossing to selfing is a key topic in evolutionary biology. However, the molecular basis of such shifts has been rarely examined due to lack of knowledge of the genes controlling these transitions. A classic example of mating system transition is the repeated shift from heterostyly to homostyly. Occurring in 28 angiosperm families, heterostyly is characterized by the reciprocal position of male and female sexual organs in two (or three) distinct, usually self-incompatible floral morphs. Conversely, homostyly is characterized by a single, self-compatible floral morph with reduced separation of male and female organs, facilitating selfing. Here, we investigate the origins of homostyly in <i>Primula vulgaris </i>and its microevolutionary consequences by integrating surveys of the frequency of homostyles in natural populations, DNA sequence analyses of the gene controlling the position of female sexual organs (<i>CYPᵀ</i>), and microsatellite genotyping of both progeny arrays and natural populations characterized by varying frequencies of homostyles. As expected, we found that homostyles displace short-styled individuals, but long-style morphs are maintained at low frequencies within populations. We also demonstrated that homostyles repeatedly evolved from short-styled individuals in association with different types of loss-of-function mutations in <i>CYPᵀ</i>. Additionally, homostyly triggers a shift to selfing, promoting increased inbreeding within and genetic differentiation among populations. Our results elucidate the causes and consequences of repeated transitions to homostyly within species, and the putative mechanisms precluding its fixation in <i>P. vulgaris</i>. This study represents a benchmark for future analyses of losses of heterostyly in other angiosperms.</p>
Data from: Ultra-wideband and polarization-independent RCS reduction based on polarization conversion metasurface
<p>We proposed an ultra-wideband polarization conversion metasurface (PCM). Because it is an anisotropic structure with a pair of mutually perpendicular symmetric axes<i> u</i> and <i>v</i>, and the phase difference between the reflection coefficients under <i>u</i>- and <i>v</i>-polarized incidences is close to 180<sup>°</sup> in an ultra-wide frequency range from 9.5 to 29.5 GHz, it can realize ultra-wideband circular polarization (CP) maintaining reflection and make its co-polarized reflection coefficient under CP incidence close to 1.0 in the ultra-wide band 9.2-29.7 GHz. In addition, when its unit cell structure is rotated by an angle <i>ψ</i>, almost ±2<i>ψ</i> Pancharatnam-Berry (PB) phase will be generated in co-polarized reflection coefficient under CP incidence. Thus, based on the proposed PCM, an ultra-wideband Pancharatnam-Berry (PB) 2-dit coding metasurface is conveniently proposed. The simulation and experimental results show that the coding metasurface can achieve more than 10 dB radar cross section (RCS) reduction in the ultra-wide frequency band 8.7-29.3 GHz with a relative bandwidth of 108.4% under normal incidence with arbitrary polarizations, in addition, when the incident angle is increased to 30<sup>°</sup>, the RCS reduction performance can be kept well. In this data file, the simulation results obtained by commercial software Ansys HFSS and measurement results are listed.</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.