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.
1,956
datasets available to search
ShareScore release 0.9.0
Dataset results
1,956 results for “test data”
Data from: Impact of a novel community testing pathway for people with suspected COVID-19 in Wales: a cost-minimisation analysis
<p><b>Objective: </b>To compare NHS organisations testing pathways for patients with suspected COVID-19 in the community versus standard hospital testing practices</p> <p><b>Perspective</b>: NHS commissioners and services</p> <p><b>Methods</b>: During the containment phase of the Covid-19 pandemic we developed a community model pathway for Covid-19 testing in Wales with testing teams undertaking swabbing for Covid-19 in individuals usual place of residence. We undertook a cost-minimisation analysis comparing the costs to the NHS in Wales of community testing for COVID-19 versus standard hospital testing practices and ambulance conveyancing. We analysed data from patients with suspected COVID-19 between January and February 2020 and applied assumptions of costs from national contractual and reference costs for ambulances, staffing and transportation with market costs at the time of publication.</p> <p><b>Results</b>: 177 patients with suspected COVID-19 underwent community testing via local NHS organisations between January and February 2020 with a mean age of 46.1 (IQR 27.5-56.3). This was 92% of total patients who were tested for Covid-19 during this period. We estimate, compared to standard hospital testing practices cash savings in improved productivity for the NHS of £152,190 during this time period, in addition to further non-monetised benefits for hospital and ambulance flow.</p> <p><b>Conclusions</b>: Community testing for COVID-19 in Wales is now an established pathway and continues to bring benefits for patients, local healthcare organisations and the NHS. Further application of this model in other settings and to other infectious diseases may herald promising returns.</p>
Assigning occurrence data to cryptic taxa improves climatic niche assessments: biodecrypt, a new tool tested on European butterflies
<p><b><span>Aim</span></b><br> <span>Occurrence data are fundamental to macroecology, but accuracy is often compromised when multiple units are lumped together (e.g. in recently separated cryptic species or citizen science records). Using amalgamated data leads to inaccuracy in species mapping, to biased beta-diversity assessments and to potentially erroneous</span><span>ly</span><span> predicted responses to climate change. We provide a set of R functions (biodecrypt) to objectively attribute undetermined occurrences to the most probable taxon based on a subset of identified records.</span></p> <p><b><span>Innovation</span></b><br> <span>Biodecrypt assumes </span><span>that unknown occurrences can only be attributed at certain distances from </span><span>areas of </span><span>sympatry. </span><span>The </span><span>function draws concave hulls based on the subset of identified records; subsequently, based on hull geometry, it attributes (or not) unknown records to a given taxon. Concavity can be imposed with an alpha value and sea or land areas can be excluded. A cross-validation function tests attribution reliability and another function optimizes the parameters (alpha, buffer, distance ratio between hulls). We applied the procedure to 16 European butterfly complexes recently separated into 33 cryptic species for which most records were amalgamated. We compared niche similarity and divergence between cryptic taxa, and we re-calculated and </span><span>contributed </span><span>updated </span><span>CLIMBER variables for climatic preferences</span><span>.</span></p> <p><b><span>Main conclusions</span></b><br> Biodecrypt showed a cross-validated correct attribution of known records always ≥98% and attributed more than 80% of unknown records to the most likely taxon in parapatric species. The functions determined where records can be assigned even for largely sympatric species, and highlighted areas where further sampling is required. All the cryptic taxa <span>showed significantly diverging climatic niches, </span>reflected in different values of mean temperature and precipitation compared to the values originally provided in the CLIMBER database. The substantial fraction of cryptic taxa existing across different taxonomic groups and their divergence in climatic niches highlights the importance of using reliably assigned occurrence data in macroecology.</p>
Convective Differential Rotation in Stars and Planets II: Observational and Numerical Tests - Supporting Data
<p>Contains all scripts and data used in the analysis in the paper 'Convective Differential Rotation in Stars and Planets II: Observational and Numerical Tests'. Includes inputs to and output from MESA models.</p>
Data for 'Slip-hydride interactions in Zircaloy-4: Multiscale mechanical testing and characterisation'
<p>This is the data bundle for 'Slip-hydride interactions in Zircaloy-4: Multiscale mechanical testing and characterisation'</p> <p>Arxiv: https://arxiv.org/abs/2003.13610</p> <p>Acta Materialia: https://doi.org/10.1016/j.actamat.2020.09.038</p> <p>Authors: <br> Siyang Wang, Finn Giuliani, T. Ben Britton<br> Department of Materials, Royal School of Mines, Imperial College London, London, SW7 2AZ, UK</p> <p>This data bundle consists of three folders:<br> 'DIC' contains the raw SEM images and the data from DIC analysis;<br> 'EBSD' contains the .ctf files from EBSD experiments;<br> 'Mech_curves' contains the data from mechanical tests.</p> <p>Any queries please contact Dr. Siyang Wang (siyang.wang15@imperial.ac.uk).</p>
Data from: A test of the niche variation hypothesis in a ruminant herbivore
<p class="MsoPlainText">1. Despite the shared prediction that the width of a population's dietary niche expands as food becomes limiting, the Niche Variation Hypothesis (NVH) and Optimal Foraging Theory (OFT) offer contrasting views about how individuals alter diet selection when food is limited.</p> <p class="MsoPlainText">2. Classical OFT predicts that dietary preferences do not change as food becomes limiting, so individuals expand their diets as they compensate for a lack of preferred foods. In contrast, the NVH predicts that among-individual variation in cognition, physiology, or morphology create functional trade-offs in foraging efficiency, thereby causing individuals to specialize on different subsets of food.</p> <p class="MsoPlainText">3. To evaluate (a) the predictions of the NVH and OFT and (b) evidence for physiological and cognitive-based functional trade-offs, we used DNA microsatellites and metabarcoding to quantify the diet, microbiome, and genetic relatedness (a proxy for social learning) of 218 moose (Alces alces) across six populations that varied in their degree of food limitation.</p> <p class="MsoPlainText">4. Consistent with both the NVH and OFT, dietary niche breadth increased with food limitation. Increased diet breadth of individuals—rather than increased diet specialization—was strongly correlated with both food limitation and dietary niche breadth of populations, indicating that moose foraged in accordance with OFT. Diets were not constrained by inheritance of the microbiome or inheritance of diet selection, offering support for the little-tested hypothesis that functional trade-offs in food use (or lack thereof) determine whether populations adhere to the predictions of the NVH or OFT.</p> <p class="MsoPlainText">5. Our results indicate that both the absence of strong functional trade-offs and the digestive physiology of ruminants provide contexts under which populations should forage in accordance with OFT rather than the NVH. Also, because dietary niche width increased with increased food limitation, OFT and the NVH provide theoretical support for the notion that plant-herbivore interaction networks are plastic rather than static, which has important implications for understanding interspecific niche partitioning. Lastly, because population-level dietary niche breadth and calf recruitment are correlated, and because calf recruitment is a proxy for food limitation, our work demonstrates how diet data can be employed to understand a populations' proximity to carrying capacity.</p>
Data from: Genetics of adaptation: experimental test of a biotic mechanism driving divergence in traits and genes
The genes underlying adaptations are becoming known, yet the causes of selection on genes -- a key step in the study of the genetics of adaptation -- remains uncertain. We address this issue experimentally in a threespine stickleback species pair showing exaggerated divergence in bony defensive armor in association with competition-driven character displacement. We used semi-natural ponds to test the role of a native predator in causing divergent evolution of armor and two known underlying genes. Predator presence/absence altered selection on dorsal spines and allele frequencies at the Msx2a gene across a generation. Evolutionary trajectories of alleles at a second gene, Pitx1, and the pelvic spine trait it controls, were more variable. Our experiment demonstrates how manipulation of putative selective agents help to identify causes of evolutionary divergence at key genes, rule out phenotypic plasticity as a sole determinant of phenotypic differences, and eliminate reliance on fitness surrogates. Divergence of predation regimes in sympatric stickleback is associated with coevolution in response to resource competition, implying a cascade of biotic interactions driving species divergence. We suggest that as divergence proceeds, an increasing number of biotic interactions generate divergent selection, causing more evolution in turn. In this way, biotic adaptation perpetuates species divergence through time during adaptive radiation in an expanding number of traits and genes.
Data from: Testing eco-evolutionary predictions using fossil data: Phyletic evolution following ecological opportunity
Fossil sequences provide observations of phenotypes within a lineage over time and represent essential data for increasing our understanding of phyletic evolution beyond microevolutionary timescales. I investigate if fossil times-series of the diatom Stephanodiscus niagarae/yellowstonensis follow evolutionary dynamics compatible with hypotheses for how the adaptive landscape changes when a population enters a new environment. The lineage – which has a remarkably detailed stratigraphic record – invaded Yellowstone Lake immediately after recession of ice from the basin 14,000 years ago. Several phyletic models portraying different types of evolutionary dynamics – both compatible and not compatible with changes in the adaptive landscape following ecological opportunity – were fitted to the fossil times-series of S. niagarae/yellowstonensis. Different models best describe the three analyzed traits. Two of the models (a new model of decelerated evolution and an Ornstein-Uhlenbeck model) capture trait dynamics compatible with an event of ecological opportunity, while the third model (random walk) does not. Entering a new environment may accordingly affect trait dynamics for thousands of years, but the effects can vary across phenotypes. However, tests of model adequacy reveal shortcomings in all three models explaining the trait dynamics, suggesting model development is needed to more fully understand the phyletic evolution in Stephanodiscus niagarae/yellowstonensis.
I am a test data
<p>Hey, I am a test data. Only for test purpose.</p>
Data from: Are human natal sex ratio differences across the world adaptive? A test of Fisher's principle
<p>Fisher's principle states that natural selection favours an equal number of male and female births at the population level, unless there are sex differences in rearing costs or sex differences in mortality before the end of the period of parental investment. Sex differences in rearing costs should be more pronounced in low- than in high-resource settings. We, therefore, examined whether human development index and sex differences in child mortality contribute to the natural variation in human sex ratio at birth across the globe. As predicted by Fisher's principle, the proportion of male births increased with both increasing male-biased childhood mortality and level of development of each country. However, these relationships were absent after accounting for spatial autocorrelation in the residuals, which our inference is conditioned on. This work shows how the failure to account for residual spatial autocorrelation can lead to incorrect conclusions regarding support for predictions from sex allocation theory.</p>
Test data for MITOS
<p>Test data for a Galaxy tutorial of MITOS</p>
test data for crustal architecture
<p>test data for crustal architecture</p>
Data from: Evaluating the role of inbreeding depression in heterozygosity-fitness correlations: how useful are tests for identity disequilibrium?
Heterozygosity-fitness correlations (HFCs) have been observed for several decades, but their causes are often elusive. Tests for identity disequilibrium (ID, correlated heterozygosity between loci) are commonly used to determine if inbreeding depression is a possible cause of HFCs. We used computer simulations to determine how often ID is detected when HFCs are caused by inbreeding depression. We also used ID in conjunction with HFCs to estimate the proportion of variation (r2) in fitness explained by the individual inbreeding coefficient (F). ID was not detected in a large proportion of populations with statistically significant HFCs (sample size = 120 individuals) unless the variance of F was high (σ2(F) ≥ 0.005) or many loci were used (100 microsatellites or 1000 SNPs). For example, with 25 microsatellites, ID was not detected in 49% of populations when HFCs were caused by six lethal equivalents and σ2(F) was typical of vertebrate populations (σ2(F) ≈ 0.002). Estimates of r2 between survival and F based on ID and HFCs were imprecise unless ID was strong and highly statistically significant (P ≈ 0.01). These results suggest that failing to detect ID in HFC studies should not be taken as evidence that inbreeding depression is absent. The number of markers necessary to simultaneously detect HFC and ID depends strongly on σ2(F). Thus the mating system and demography of populations, which influence σ2(F), should be considered when designing HFC studies. ID should be used in conjunction with HFCs to estimate the correlation between fitness and F, because HFCs alone reveal little about the strength of inbreeding depression.
Data from: Test collections for EHR-based clinical information retrieval
Objectives: To create test collections for evaluating clinical Information Retrieval (IR) systems and advancing clinical IR research. Materials and Methods: Electronic Health Records (EHR) data, including structured and free text data, from 45,000 patients who are a part of the Mayo Clinic Biobank cohort was retrieved from the clinical data warehouse. The clinical IR system indexed 42 million free-text EHR documents. The search queries consisted of 56 topics developed through a collaboration between Mayo Clinic and Oregon Health & Science University. We described the creation of test collections, including a to-be-evaluated document pool using five retrieval models, and human assessment guidelines. We analyzed the relevance judgment results in terms of human agreement and time spent, and results of three levels of relevance, and reported performance of five retrieval models. Results: The two judges had a moderate overall agreement with a Kappa value of 0.49, spent a consistent amount of time judging the relevance, and were able to identify easy and difficult topics. The conventional retrieval model performed best overall on most topics while a concept-based retrieval model had better performance on the topics requiring conceptual level retrieval. Discussion: Information Retrieval can provide an alternate approach to leveraging clinical narratives for patient information discovery as it is less dependent on semantics. Our study showed the feasibility of test collections as well as challenges. Conclusion: The conventional test collections for evaluating the IR system show potential for successfully evaluating clinical IR systems with a few challenges to be investigated.
Data from: Body height and immune efficacy: testing body stature as a signal of biological quality
According to the good genes hypothesis and energy allocation theory, human adult body height may reflect biological quality. An important aspect of this quality is immune system functioning (ISF). The aim of this study was to evaluate the relationship between ISF and body height in healthy people. The ISF was determined by several important innate (total complement and lysozyme activity, neutrophils function) and adaptive immune parameters (lymphocytes, IgA and IgG, and response to flu vaccine). Overall, 96 males and 97 females were subjected to flu vaccination, and of these 35 males and 34 females were subjected to tetanus. Blood samples were collected before and 4 weeks after vaccination. Immunomodulatory factors: participant's age, body fat and free testosterone levels, were controlled. There was no association between body height and all analysed immune parameters for both sexes. That might suggest that in western society, a women's preference for taller men is not related to "good genes for immune competence". We propose the novel Immunity Priority Hypothesis that explains the lack of relationship between adult body stature and ISF. This hypothesis, however, does not contradict the signalling role of a man's body height as a morphological marker of biological quality.
Data from: Testing mechanisms of Bergmann's rule: phenotypic but no genetic change in body size in three passerine bird populations
Bergmann's rule predicts a decrease in body size with increasing temperature and has much empirical support. Surprisingly, we know very little about whether 'Bergmann size clines' are due to a genetic response or is a consequence of phenotypic plasticity. Here we use data on body size (mass and tarsus length) from three long-term (1979-2008) study populations of great tits (Parus major), in which there has been a temperature increase, to examine mechanisms behind Bergmann's rule. We show that adult body mass decreased over the study period in all populations and that tarsus length increased in one population. Both body mass and tarsus length were heritable and under weak positive directional selection, predicting an increase, rather than decrease, in body mass. There was no support for micro-evolutionary change and thus the observed declines in body mass were a result of phenotypic plasticity. Interestingly, this plasticity was not in direct response to temperature changes but seemed to be due to changes in prey dynamics. Our results caution against interpreting recent phenotypic body size declines as an adaptive evolutionary response to temperature changes and highlight the importance of considering alternative environmental factors when testing size clines.
Data from: Herbivore effect traits and their impact on plant community biomass: an experimental test using grasshoppers
1. Using trait-based approaches to study trophic interactions may represent one of the most promising approaches to evaluate the impact of trophic interactions on ecosystem functioning. To achieve this goal, it is necessary to clearly identify which traits determine the impact of one trophic level on another. 2. Using functionally contrasting grasshopper species, we tested the ability of multiple traits (morphological, chemical and biomechanical) to predict herbivore impact on the biomass of a diverse plant community. We set up a cage experiment in an old species rich grassland field and evaluated how multiple candidate grasshopper effect traits mediated herbivore impact on plant biomass. 3. Grasshoppers had different impact on plant community biomass (consuming up to 60 % of plant community biomass). Grasshopper impact was positively correlated with their incisive strength while body size or grasshopper C:N ratio exhibited low predictive ability. Importantly, the strong relationship between the incisive strength and the impact was mediated by the grasshopper feeding niche, which was well predicted in our study by two simple plant traits (leaf dry matter content, leaf C:N ratio). Feeding niche differences between grasshoppers were explained by differences in incisive strength, highlighting the fundamental linkage between grasshopper effect traits and their niche. 4. Our study contributes to the development of the trait-based approach in the study of trophic interactions by providing a first experimental test of the relationship between herbivore effect traits, their impact on plant community biomass, and in a larger extent on ecosystem functioning. By comparing the relative importance of multiple interacting grasshopper traits, our study showed that incisive strength was a key effect trait which determined grasshopper feeding niche and its relative impact on plant community biomass.
Data from: Phylogeny of Lichen- and Non-Lichen-Forming Omphalinoid Mushrooms and the Utility of Testing for Combinability among Multiple Data Sets
As an initial step toward developing a model system to study requirements for and consequences of transitions to mutualism, the phylogeny of a group of closely related lichenized and nonlichenized basidiomycetes (Omphalina) was reconstructed. The phylogenetic analyses are based on four data sets representing different regions of the nuclear ribosomal repeat unit (ITS1, 5.8S, ITS2, and 25S) obtained from 30 species of Omphalina and related genera. The resulting phylogenetic trees from each of these four data sets, when analyzed separately, were not identical. Testing for the combinability of these four data sets suggested that they could not be combined in their entirety. The removal of ambiguous alignments and saturated sites was sufficient, after reapplying the combinability test on the pruned data sets, to explain the topological discrepancies. In this process, the first of two complementary tests developed by Rodrigo et al. (1993, N.Z. J. Bot. 31:257--268) to assess whether two data sets are the result of the same phylogenetic history was found to be biased, rejecting the combinability of two data sets even when they are samples of the same phylogenetic history. Combining the four pruned data sets yielded phylogenies that suggest the five lichen-forming species of Omphalina form a monophyletic group. The sister group to this symbiotic clade consists mostly of dark brown Omphalina species intermixed with species from the genera Arrhenia and Phaeothellus. The genera Omphalina and Gerronema are shown to be polyphyletic. The lichen-forming species O. ericetorum and the nonmutualistic species O. velutipes, O. epichysium, and O. sphagnicola are the best candidates for experimental work designed to gain a better understanding of mechanisms involved in symbiotic interactions and the role symbiosis has played in the evolution of fungi.
Data from: Testing for ecological limitation of diversification: a case study using parasitic plants
Imbalances in phylogenetic diversity could be the result of variable unbounded diversification rates, differing limits on diversity, or a combination of the two. We propose an approach to distinguish between rates and limits as the primary cause of phylogenetic imbalance, using parasitic plants as a model. With sister-taxon comparisons, we show that parasitic plant lineages are typically much less diverse than their autotrophic sisters. We then use age estimates for taxa used in the sister-taxon comparisons to test for correlations between clade age and diversity. We find that parasitic plant diversity is not significantly correlated with the age of the lineage, whereas there is a strong positive correlation between the age and diversity of autotrophic sister lineages. The Ericaceae sister-pair Monotropoideae (parasitic) and Arbutoideae (autotrophic) are sufficiently well samples at the species level to allow more parametric comparisons of diversification patterns. Model-fitting for this group supports ecological limitation in Monotropoideae and unconstrained diversification in Arbutoideae. Thus, differences in diversity between parasitic plants and their autotrophic sisters might be caused by a mixture of ecological limitation and unbounded diversification. A combination of sister-taxon comparisons of diversity and age, coupled with model-fitting of well-sampled phylogenies of focal taxa, provides a powerful test of likely causes of asymmetry in the diversity of lineages.
Data from: Evaluating modularity in morphometric data: challenges with the RV coefficient and a new test measure
Modularity describes the case where patterns of trait covariation are unevenly dispersed across traits. Specifically, trait correlations are high and concentrated within subsets of variables (modules), but the correlations between traits across modules are relatively weaker. For morphometric data sets, hypotheses of modularity are commonly evaluated using the RV coefficient, an association statistic used in a wide variety of fields. In this article, I explore the properties of the RV coefficient using simulated data sets. Using data drawn from a normal distribution where the data were neither modular nor integrated in structure, I show that the RV coefficient is adversely affected by attributes of the data (sample size and the number of variables) that do not characterize the covariance structure between sets of variables. Thus, with the RV coefficient, patterns of modularity or integration in data are confounded with trends generated by sample size and the number of variables, which limits biological interpretations and renders comparisons of RV coefficients across data sets uninformative. As an alternative, I propose the covariance ratio (CR) for quantifying modular structure and show that it is unaffected by sample size or the number of variables. Further, statistical tests based on the CR exhibit appropriate type I error rates and display higher statistical power relative to the RV coefficient when evaluating modular data. Overall, these findings demonstrate that the RV coefficient does not display statistical characteristics suitable for reliable assessment of hypotheses of modular or integrated structure and therefore should not be used to evaluate these patterns in morphological data sets. By contrast, the covariance ratio meets these criteria and provides a useful alternative method for assessing the degree of modular structure in morphological data.
Data from: Validation of a non-invasive method for the early detection of metabolic syndrome: a diagnostic accuracy test in a working population
Objectives. A non-invasive method for the early detection of Metabolic Syndrome (NIN-MetS) using only Waist to Height Ratio (WHtR) and Blood Pressure (BP) has recently been published, with fixed cut-off values for gender and age. The aim of this study was to validate this method in a large sample of Spanish workers. Design. A diagnostic test accuracy to assess the validity of the method was performed. Setting. Occupational Health Services. Participants. The studies were conducted in 2012-2016 on a sample of 60,799 workers from the Balearic Islands (Spain). Interventions. The NCEP-ATP III criteria were used as the gold standard. NIM-MetS has been devised using classification trees (the CHAID, Chi-squared Automatic Interaction Detection method). Main outcome measures. Anthropometric and biochemical variables to diagnose MetS. Sensitivity, specificity, validity index and Youden Index were determined to analyse the accuracy of the diagnostic test (NIM-MetS). Results. Regarding the validation of the method, sensitivity was 54.7%, specificity 94.9% and validity index 91.2%. The cut-off value for WHtR was 0.54, ranging from 0.51 (lower age group) to 0.56 (higher) in the age groups. Variables more closely associated with MetS were WHtR (AUC=0.85; 95% CI: 0.84-0.86) and Systolic Blood Pressure (AUC=0.79; 95% CI: 0.78-0.80). The final cut-off values for the non-invasive method were WHtR≥0.56 and BP≥128/80 mmHg, which includes four levels of MetS risk (very low, low, moderate and high). Conclusions. The analysed method has shown a high validity index (higher than 91%) for the early detection of MetS. It is a non-invasive method easy to apply and interpret in any health care setting. This method provides a scale of MetS risk which allows a more accurate detection and a more effective intervention.
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.