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Figure 7 from: Steinbeck C, Koepler O, Bach F, Herres-Pawlis S, Jung N, Liermann JC, Neumann S, Razum M, Baldauf C, Biedermann F, Bocklitz TW, Boehm F, Broda F, Czodrowski P, Engel T, Hicks MG, Kast SM, Kettner C, Koch W, Lanza G, Link A, Mata RA, Nagel WE, Porzel A, Schlörer N, Schulze T, Weinig H-G, Wenzel W, Wessjohann LA, Wulle S (2020) NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany. Research Ideas and Outcomes 6: e55852. https://doi.org/10.3897/rio.6.e55852
Figure 7 Existing services forming the nucleus of the envisioned federation of repositories as part of the NFDI4Chem infrastructure.
Figure 11 from: Steinbeck C, Koepler O, Bach F, Herres-Pawlis S, Jung N, Liermann JC, Neumann S, Razum M, Baldauf C, Biedermann F, Bocklitz TW, Boehm F, Broda F, Czodrowski P, Engel T, Hicks MG, Kast SM, Kettner C, Koch W, Lanza G, Link A, Mata RA, Nagel WE, Porzel A, Schlörer N, Schulze T, Weinig H-G, Wenzel W, Wessjohann LA, Wulle S (2020) NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany. Research Ideas and Outcomes 6: e55852. https://doi.org/10.3897/rio.6.e55852
Figure 11 TA6 will manage the synergies and interfaces to other NFDI consortia and the NFDI as a whole. It will ensure that cross-cutting topics such as NFDI-wide services are properly addressed and their results incorporated into NFDI4Chem.
Figure 10 from: Steinbeck C, Koepler O, Bach F, Herres-Pawlis S, Jung N, Liermann JC, Neumann S, Razum M, Baldauf C, Biedermann F, Bocklitz TW, Boehm F, Broda F, Czodrowski P, Engel T, Hicks MG, Kast SM, Kettner C, Koch W, Lanza G, Link A, Mata RA, Nagel WE, Porzel A, Schlörer N, Schulze T, Weinig H-G, Wenzel W, Wessjohann LA, Wulle S (2020) NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany. Research Ideas and Outcomes 6: e55852. https://doi.org/10.3897/rio.6.e55852
Figure 10 The cultural change in chemical RDM is supported through training and community involvement in TA5 as well as by the NFDI4Chem infrastructure.
Dataset for Event-based architecture for enabling multi-modal reasoning on loosely coupled Linked Data services
<p>Dataset with the raw UNIX timestamps for start/stop time points for each sample of each evaluated configuration as well as produced plots.</p>
Data from: Canalisation in the wild: effects of developmental conditions on physiological traits are inversely linked to their association with fitness
Ecological conditions affect fitness, but mechanisms causing such effects are not well known, while evolved responses to environmental variation may depend on the underlying mechanisms. Consequences of environmental conditions vary strongly between traits, but a framework to interpret such variation is lacking. We propose that variation in trait response may be explained by differential canalisation, with traits with larger fitness effects showing weaker responses to environmental perturbations due to preferential resource allocation to such traits. We tested the canalisation hypothesis using brood size manipulation in wild jackdaw nestlings in which we measured eight physiological traits (mainly oxidative stress markers), and two feather traits. For each trait, we estimated manipulation response and association with fitness (over-winter survival). As predicted, a strong negative correlation emerged between manipulation response and association with fitness (r=-0.76). We discuss the consequences of differential trait canalization for the study of mechanisms mediating environmental effects on fitness.
Data from: Meiotic drive influences the outcome of sexually antagonistic selection at a linked locus
Most meiotic drivers, such as the t-haplotype in Mus and the segregation distorter (SD) in Drosophila, act in a sex-specific manner, gaining a transmission advantage through one sex although suffering only the fitness costs associated with the driver in the other. Their inheritance is thus more likely through one of the two sexes, a property they share with sexually antagonistic alleles. Previous theory has shown that pairs of linked loci segregating for sexually antagonistic alleles are more likely to remain polymorphic and that linkage disequilibrium accrues between them. I probe this similarity between drive and sexual antagonism and examine the evolution of chromosomes experiencing these selection pressures simultaneously. Reminiscent of previous theory, I find that: the opportunity for polymorphism increases for a sexually antagonistic locus that is physically linked to a driving locus; the opportunity for polymorphism at a driving locus also increases when linked to a sexually antagonistic locus; and stable linkage disequilibrium accompanies any polymorphic equilibrium. Additionally, I find that drive at a linked locus favours the fixation of sexually antagonistic alleles that benefit the sex in which drive occurs. Further, I show that under certain conditions reduced recombination between these two loci is selectively favoured. These theoretical results provide clear, testable predictions about the nature of sexually antagonistic variation on driving chromosomes and have implications for the evolution of genomic architecture.
Data from: Positive cytoplasmic UCHL5 tumor expression in gastric cancer is linked to improved prognosis
Gastric cancer is the second most common cause of cancer-related mortality worldwide. Accurate prediction of disease progression is difficult, and new biomarkers for clinical use are essential. Recently, we reported that the proteasome-associated deubiquitinating enzyme UCHL5/Uch37 is a new prognostic marker in both rectal cancer and pancreatic ductal adenocarcinoma. Here, we have assessed by immunohistochemistry UCHL5 tumor expression in gastric cancer. The study cohort comprised 650 patients, who underwent surgery in Helsinki University Hospital, Finland, between 1983 and 2009. We investigated the association of cytoplasmic UCHL5 tumor expression to assess clinicopathological parameters and patient survival. Positive cytoplasmic UCHL5 tumor immunoexpression is linked to increased survival of patients with small (<5 cm) tumors (p = 0.001), disease stages I-II (p = 0.025), and age 66 years or older (p = 0.037). UCHL5 is thus a potential marker in gastric cancer with new prognostic relevance.
Data from: Rapid local adaptation linked with phenotypic plasticity
<p>Models of 'plasticity-first' evolution are attractive because they explain the rapid evolution of new complex adaptations. Nevertheless, it is unclear whether plasticity can facilitate rapid microevolutionary change between diverging populations. Here we show how plasticity may have generated adaptive differences in fecundity between neighbouring wild populations of burying beetles <i>Nicrophorus vespilloides</i>. These populations occupy distinct Cambridgeshire woodlands that are just 2.5km apart and that probably originated from a common ancestral population c. 1000-4000 years ago. We find that populations are divergently adapted to breed on differently-sized carrion. Adaptive differences in clutch size and egg size are associated with divergence at loci connected with oogenesis. The populations differ specifically in the elevation of the reaction norm linking clutch size to carrion size (i.e. genetic accommodation), and in the likelihood that surplus offspring will be lost after hatching. We suggest that these two processes may have facilitated rapid local adaptation on a fine-grained spatial scale.</p>
Data from: Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity. Many common TE variants were associated with significantly altered expression of nearby genes, and a major fraction of inter-accession DNA methylation differences were associated with nearby TE insertions. Overall, this demonstrates that TE variants are a rich source of genetic diversity that likely plays an important role in facilitating epigenomic and transcriptional differences between individuals, and indicates a strong genetic basis for epigenetic variation.
Data from: Genome scan reveals selection acting on genes linked to stress response in wild pearl millet
Uncovering genomic regions involved in adaption is a major goal in evolutionary biology. High-throughput sequencing now makes it possible to tackle this challenge in nonmodel species. Yet, despite the increasing number of methods targeted to specifically detect genomic footprints of selection, the complex demography of natural populations often causes high rates of false positive in gene discoveries. The aim of this study was to identify climate adaptations in wild pearl millet populations, Cenchrus americanus ssp. monodii. We focused on two climate gradients, one in Mali and one in Niger. We used a two-step strategy to limit false-positive outliers. First, we considered gradients as biological replicates and performed RNA sequencing of four populations at the extremities. We combined four methods—three based on differentiation among populations and one based on diversity patterns within populations—to identify outlier SNPs from a set of 87 218 high-quality SNPs. Among 11 155 contigs of pearl millet reference transcriptome, 540 exhibited selection signals as evidenced by at least one of the four methods. In a second step, we genotyped 762 samples in 11 additional populations distributed along the gradients using SNPs from the detected contigs and random SNPs as control. We further assessed selection on this large data set using a differentiation-based method and a method based on correlations with environmental variables based. Four contigs displayed consistent signatures between the four extreme and 11 additional populations, two of which were linked to abiotic and biotic stress responses.
Data from: Linked morphological changes during palate evolution in early tetrapods
We examined the shapes and sizes of dermal bones of the palate of selected Palaeozoic tetrapods in order to identify the ancestral states of palatal bone morphologies in the earliest tetrapods, to learn how the composition of the palate varies within and among early tetrapod radiations, and recognize evolutionary correlations among the size and shapes of skeletal elements in this important group of animals. We find that whereas the palatal bones themselves and their arrangements are usually conserved, considerable correlated evolutionary change occurs in the shapes and sizes of the bones. Some of the changes in the bones are allometrically linked to overall palate size, which varies more than 100-fold among the taxa in our sample. Often, these allometries were only hinted at in traditional independent contrasts-based regressions of log transformed data, particularly because many allometries are subtle, their slopes may vary among subclades, and the scatter around some trendlines is high. Rather, the allometries showed up in analyses of size-standardized palatal bone dimensions investigated using independent contrasts, bivariate phylomorphospace plots, and mirrored character reconstructions on the phylogenetic tree. We find negative allometry for parasphenoid lengths and widths essentially across the entire tree of Palaeozoic tetrapods, but with different trajectories characterizing the two largest clades, the temnospondyls and the lepospondyls. The lengths of several other elements may show positive allometries, either across the entire tree or in just a subclade. One possible positive allometry exists for the ectopterygoid, which appears to allometrically shorten in temnospondyls that evolve small body and palate size, and, as in Doleserpeton can be lost altogether. Both shortening and loss could be by the same developmental change, paedomorphosis, a form of heterochrony. Paedomorphosis might also account for evolution of relatively large parasphenoids in both lepospondyls and diminutive temnospondyls, but does not seem to explain evolution of ectopterygoid loss in lepospondyls. A regularity observed across nearly all taxa in our study set is an inverse correlation between the lengths of the vomer and pterygoid, bones that lie adjacent to one another along the long palatal axis. Further work is needed to learn whether such correlated evolution might be due to adaptation and/or to developmental bias, and particularly, to learn how correlations and allometries themselves evolve.
Data from: A selfish genetic element linked to increased lifespan impacts metabolism in female house mice
Gene drive systems can lead to the evolution of traits that further enhance the transmission of the driving element. In gene drive, one allele is transmitted to offspring at a higher frequency than the homologous allele. This has a range of consequences, which generally include a reduction in fitness of the carrier of the driving allele, making such systems <i>selfish</i>. The t haplotype is one such driver, found in house mice. It is linked to a reduction in litter size in matings among heterozygous animals, but also to increased lifespan in wild females that carry it. Here, we tested whether carrying the t haplotype was associated with altered resting metabolic rate (RMR). We show that females carrying the t haplotype decrease RMR as they increase in size, compared to wildtype females or males of either genotype. Our study elucidates a plausible mechanism by which a selfish genetic element increases lifespan.
Data from: CLIP test: a new fast, simple and powerful method to distinguish between linked or pleiotropic quantitative trait loci in linkage disequilibria analysis
An important question arises when mapping quantitative trait loci (QTLs) for genetically correlated traits: is the correlation due to pleiotropy (a single QTL affecting more than one trait) and/or close linkage (different QTLs that are physically close to each other and influence the traits)? In this article, we propose the Close Linkage versus Pleiotropism (CLIP) test, a fast, simple and powerful method to distinguish between these two situations. The CLIP test is based on the comparison of the square of the observed correlation between a combination of apparent effects at the marker level to the minimal value it can take under the pleiotropic assumption. A simulation study was performed to estimate the power and alpha risk of the CLIP test and compare it to a test that evaluated whether the confidence intervals of the two QTLs overlapped or not (CI test). On average, the CLIP test showed a higher power (68%) to detect close-linked QTLs than the CI test (43%) and a same alpha risk (4%).
Data from: Testing the link between phenotypic evolution and speciation: an integrated paleontological and phylogenetic analysis
1. The punctuated equilibrium model predicts that phenotypic change is concentrated into pulses associated with speciation, with little change otherwise accruing in established lineages. Paleontological tests of this model have generally lacked an adequate phylogenetic and modeling framework, whereas tests relying on extant populations lack direct constraints on the evolutionary dynamics within lineages. 2. The present study extends a modeling approach developed in comparative studies and applies it to a clade with a rich fossil record, the deep-sea ostracode genus Poseidonamicus. Using a phylogenetic framework and an independent set of shape traits plus body size, a model was fit that allows estimation of anagenetic (within-lineage) evolution, cladogenetic (speciational) change, and geographic variation within species. 3. Maximum-likelihood parameter estimates suggested dominantly speciational change for only one or two shape traits, depending on model assumptions. For the remaining shape traits and body size, the contribution of anagenesis was always substantial. Confidence limits on these solutions were quite broad (though narrower when multiple traits were analyzed jointly), with most traits consistent with both strongly anagenetic and strongly cladogenetic change. 4. Whereas uncertainty about phylogenetic topology and species limits has little influence on the conclusions, assuming stasis instead of Brownian motion within lineages shifted support to solutions in which speciational change was more dominant, although several traits remained dominantly explained by anagenetic evolution. 5. These results suggest that for the traits and taxa examined, anagenesis contributes substantially to long-term divergence. The uncertainty in the results highlights the analytical difficulty of decomposing anagenetic and cladogenetic sources of phenotypic evolution, even with fossil constraints. When model uncertainty is taken into account, the task of doing so using observations from entirely extant populations is even more daunting.
Data from: Pupil-linked arousal determines variability in perceptual decision making
Decision making between several alternatives is thought to involve the gradual accumulation of evidence in favor of each available choice. This process is profoundly variable even for nominally identical stimuli, yet the neuro-cognitive substrates that determine the magnitude of this variability are poorly understood. Here, we demonstrate that arousal state is a powerful determinant of variability in perceptual decision making. We measured pupil size, a highly sensitive index of arousal, while human subjects performed a motion-discrimination task, and decomposed task behavior into latent decision making parameters using an established computational model of the decision process. In direct contrast to previous theoretical accounts specifying a role for arousal in several discrete aspects of decision making, we found that pupil diameter was uniquely related to a model parameter representing variability in the rate of decision evidence accumulation: Periods of increased pupil size, reflecting heightened arousal, were characterized by greater variability in accumulation rate. Pupil diameter also correlated trial-by-trial with specific patterns of behavior that collectively are diagnostic of changing accumulation rate variability, and explained substantial individual differences in this computational quantity. These findings provide a uniquely clear account of how arousal state impacts decision making, and may point to a relationship between pupil-linked neuromodulation and behavioral variability. They also pave the way for future studies aimed at augmenting the precision with which people make decisions.
Data from: Matching-centrality decomposition and the forecasting of new links in networks
Networks play a prominent role in the study of complex systems of interacting entities in biology, sociology, and economics. Despite this diversity, we demonstrate here that a statistical model decomposing networks into matching and centrality components provides a comprehensive and unifying quantification of their architecture. The matching term quantifies the assortative structure in which node makes links with which other node, while the centrality term quantifies the number of links that nodes make. We show, for a diverse set of networks, that this decomposition can provide a tight fit to observed networks. Then we provide three applications. First, we show that the model allows very accurate prediction of missing links in partially known networks. Second, when node characteris- tics are known, we show how the matching-centrality decomposition can be related to this external information. Consequently, it offers a simple and versatile tool to explore how node characteristics ex- plain network architecture. Finally, we demonstrate the efficiency and flexibility of the model to forecast the links that a novel node would create if it were to join an existing network.
Data from: Coevolutionary dynamics of polyandry and sex-linked meiotic drive
Segregation distorters located on sex chromosomes are predicted to sweep to fixation and cause extinction via a shortage of one sex, but in nature they are often found at low, stable frequencies. One potential resolution to this long-standing puzzle involves female multiple mating (polyandry). Because many meiotic drivers severely reduce the sperm competitive ability of their male carriers, females are predicted to evolve more frequent polyandry and thereby promote sperm competition when a meiotic driver invades. Consequently, the driving chromosome's relative fitness should decline, halting or reversing its spread. We used formal modeling to show that this initially appealing hypothesis cannot resolve the puzzle alone: other selective pressures (e.g. low fitness of drive homozygotes) are required to establish a stable meiotic drive polymorphism. However, polyandry and meiotic drive can strongly affect one another's frequency, and polyandrous populations may be resistant to the invasion of rare drive mutants.
Data from: Heterozygosity is linked to the costs of immunity in nestling great tits (Parus major)
There is growing evidence that heterozygosity–fitness correlations (HFCs) are more pronounced under harsh conditions. Empirical evidence suggests a mediating effect of parasite infestation on the occurrence of HFCs. Parasites have the potential to mediate HFCs not only by generally causing high stress levels but also by inducing resource allocation tradeoffs between the necessary investments in immunity and other costly functions. To investigate the relative importance of these two mechanisms, we manipulated growth conditions of great tit nestlings by brood size manipulation, which modifies nestling competition, and simultaneously infested broods with ectoparasites. We investigated under which treatment conditions HFCs arise and, second, whether heterozygosity is linked to tradeoff decisions between immunity and growth. We classified microsatellites as neutral or presumed functional and analyzed these effects separately. Neutral heterozygosity was positively related to the immune response to a novel antigen in parasite-free nests, but not in infested nests. For nestlings with lower heterozygosity levels, the investments in immunity under parasite pressure came at the expenses of reduced feather growth, survival, and female body condition. Functional heterozygosity was negatively related to nestling immune response regardless of the growth conditions. These contrasting effects of functional and neutral markers might indicate different underlying mechanisms causing the HFCs. Our results confirm the importance of considering marker functionality in HFC studies and indicate that parasites mediate HFCs by influencing the costs of immune defense rather than by a general increase in environmental harshness levels.
Data from: A role for migration-linked genes and genomic islands in divergence of a songbird
Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently there has been a debate around the role of "genomic islands of divergence" (i.e. blocks of outlier loci) in facilitating the process of speciation-with-gene-flow. The Swainson's thrush, Catharus ustulatus, is a migratory songbird with two genetically-distinct subspecies that differ in a number of traits known to be involved in reproductive isolation in birds (plumage coloration, song, and migratory behavior), despite contemporary gene flow along a secondary contact zone. Here we use RAD-PE sequencing to test emerging hypotheses about the process of divergence at the level of the genome and identify genes and gene regions involved in differentiation in this migratory songbird. Our analyses revealed distinct genomic islands on 15 of the 23 chromosomes and levels of differentiation that were 2-3 orders of magnitude higher on the sex chromosomes than the autosomes. Further, an analysis of loci linked to pigmentation, song, and migratory behavior showed that genes linked to migration are significantly more differentiated then expected by chance, but that these genes lie primarily outside of the genomic islands. Overall, our analysis supports the idea that genes linked to migration play an important role in divergence in migratory songbirds, but we find no compelling evidence that the observed genomic islands are facilitating adaptive divergence in migratory behavior.
Data from: Joined at the hip: linked characters and the problem of missing data in studies of disparity
Paleontological investigations into morphological diversity, or disparity, are often confronted with large amounts of missing data. We illustrate how missing discrete data effects disparity using a novel simulation for removing data based on parameters from published datasets that contain both extinct and extant taxa. We develop an algorithm that assesses the distribution of missing characters in extinct taxa, and simulates data loss by applying that distribution to extant taxa. We term this technique 'linkage'. We compare differences in disparity metrics and ordination spaces produced by linkage and random character removal. When we incorporated linkage among characters, disparity metrics declined and ordination spaces shrank at a slower rate with increasing missing data, indicating that correlations among characters govern the sensitivity of disparity analysis. We also present and test a new disparity method that uses the linkage algorithm to correct for the bias caused by missing data. We equalized proportions of missing data among time bins before calculating disparity, and found that estimates of disparity changed when missing data were taken into account. By removing the bias of missing data, we can gain new insights into the morphological evolution of organisms and highlight the detrimental effects of missing data on disparity analysis.
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.