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.
7,378
datasets available to search
ShareScore release 0.9.0
Dataset results
7,378 results for “case”
Grading 600+ students: A Case Study on Peer and Self Grading
<p>The appendix of our "Grading 600+ students: A Case Study on Peer and Self Grading" ICSE JSEET 2021 paper.</p> <p>In case of questions, please contact the first author via e-mail. </p>
Illustrating cases of horizontal head-shaking nystagmus (HSN) in posterior canal benign paroxysmal positional vertigo (PC-BPPV).
<p><strong>Supplementary video 1. </strong>Illustrating case of<strong> </strong>horizontal head-shaking nystagmus (HSN) in left posterior canal benign paroxysmal positional vertigo (PC-BPPV).</p> <p><strong>Supplementary video 2. </strong>Illustrating case of pure downbeat head-shaking nystagmus (HSN) in right posterior canal benign paroxysmal positional vertigo (PC-BPPV).</p> <p><strong>Supplementary video 3. </strong>Illustrating case of torsional downbeat head-shaking nystagmus (HSN) in right posterior canal benign paroxysmal positional vertigo (PC-BPPV).</p>
Data from: Within- and among-genus components of size evolution during mass extinction, recovery, and background intervals: a case study of Late Permian through Late Triassic foraminifera
One of the best-recognized patterns in the evolution of organismal size is the tendency for mean and maximum size within a clade to decrease following a major extinction event and to increase during the subsequent recovery interval. Because larger organisms are typically thought to be at higher extinction risk than their smaller relatives, it has commonly been assumed that size reduction mostly reflects the selective extinction of larger species. However, to our knowledge the relative importance of within- and among-lineage processes in driving overall trends in body size has never been compared quantitatively. In this study, we use a global, specimen-level database of foraminifera to study size evolution from the Late Permian through Late Triassic. We explicitly decompose size evolution into within- and among-genus components. We find that size reduction following the end- Permian mass extinction was driven more by size reduction within surviving species and genera than by the selective extinction of larger taxa. Similarly, we find that increase in mean size across taxa during Early Triassic biotic recovery was a product primarily of size increase within survivors and the extinction of unusually small taxa, rather than the origination of new, larger taxa. During background intervals we find no strong or consistent tendency for extinction, origination, or within- lineage change to move the overall size distribution toward larger or smaller sizes. Thus, size stasis during background intervals appears to result from small and inconsistent effects of within- and among-lineage processes rather than from large but offsetting effects of within- and among-taxon components. These observations are compatible with existing data for other taxa and extinction events, implying that mass extinctions do not influence size evolution by simply selecting against larger organisms. Instead, they appear to create conditions favorable to smaller organisms.
Data from: Telomere attrition and growth: a life-history framework and case study in common terns
The relationship between growth and age-specific telomere length, as a proxy of somatic state, is increasingly investigated, but observed patterns vary and a predictive framework is lacking. We outline expectations based on the assumption that telomere maintenance is costly and argue that individual heterogeneity in resource acquisition is predicted to lead to positive covariance between growth and telomere length. However, canalization of resource allocation to the trait with a larger effect on fitness, rendering that trait relatively invariant, can cause the absence of covariance. In a case study of common tern (Sterna hirundo) chicks, in which hatching order is the main determinant of variation in resource acquisition within broods, we find that body mass, but not telomere length or attrition, varies with hatching order. Moreover, body mass and growth positively predict survival to fledging, whereas telomere length and attrition do not. Using a novel statistical method to quantify standardized variance in plasticity, we estimate between-individual variation in telomere attrition to be only 12% of that of growth. Consistent with the relative invariance of telomere attrition, we find no correlation between age-specific body mass or growth and telomere attrition. We suggest that common tern chicks prioritize investment in long-term somatic state (as indicated by canalization of telomere maintenance) over immediate survival benefits of growth as part of an efficient brood reduction strategy that benefits the parents. As such, inter-specific variation in the growth-telomere length relationship may be explained by the extent to which parents benefit from rapid mortality of excess offspring.
Data from: Complementarity of statistical treatments to reconstruct worldwide routes of invasion: the case of the Asian ladybird Harmonia axyridis
Inferences about introduction histories of invasive species remain challenging because of the stochastic demographic processes involved. Approximate Bayesian computation (ABC) can help to overcome these problems, but such method requires a prior understanding of population structure over the study area, necessitating the use of alternative methods and an intense sampling design. In this study, we made inferences about the worldwide invasion history of the ladybird Harmonia axyridis by various population genetics statistical methods, using a large set of sampling sites distributed over most of the species' native and invaded areas. We evaluated the complementarity of the statistical methods and the consequences of using different sets of site samples for ABC inferences. We found that the H. axyridis invasion has involved two bridgehead invasive populations in North America, which have served as the source populations for at least six independent introductions into other continents. We also identified several situations of genetic admixture between differentiated sources. Our results highlight the importance of coupling ABC methods with more traditional statistical approaches. We found that the choice of site samples could affect the conclusions of ABC analyses comparing possible scenarios. Approaches involving independent ABC analyses on several sample sets constitute a sensible solution, complementary to standard quality controls based on the analysis of pseudo-observed datasets, to minimize erroneous conclusions. This study provides biologists without expertise in this area with detailed methodological and conceptual guidelines for making inferences about invasion routes when dealing with a large number of sampling sites and complex population genetic structures.
Data from: Repurposing population genetics data to discern genomic architecture: a case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)
Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome-wide single nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted re-sampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principle components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex-linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species' genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research.
Data from: Influence of device accuracy and choice of algorithm for species distribution modelling of seabirds: a case study using black-browed albatrosses
Species distribution models (SDM) based on tracking data from different devices are used increasingly to explain and predict seabird distributions. However, different tracking methods provide different data resolutions, ranging from < 10m to >100km. To better understand the implications of this variation, we modeled the potential distribution of black-browed albatrosses Thalassarche melanophris from South Georgia that were simultaneously equipped with a Platform Terminal Transmitter (PTT) (high resolution) and a Global Location Sensor (GLS) logger (coarse resolution), and measured the overlap of the respective potential distribution for a total of nine different SDM algorithms. We found slightly better model fits for the PTT than for GLS data (AUC values 0.958±0.048 vs. 0.95±0.05) across all algorithms. The overlaps of the predicted distributions were higher between device types for the same algorithm, than among algorithms for either device type. Uncertainty arising from coarse-resolution location data is therefore lower than that associated with the modeling technique. Consequently, the choice of an appropriate algorithm appears to be more important than device type when applying SDMs to seabird tracking data. Despite their low accuracy, GLS data appear to be effective for analyzing the habitat preferences and distribution patterns of pelagic species.
Data from: A probable case of incipient speciation in Schizocosa wolf spiders driven by allochrony, habitat use and female mate choice
There is growing evidence that speciation can occur between populations that are not geographically isolated. The emergence of assortative mating is believed to be critical to this process, but how assortative mating arises in diverging populations is poorly understood. The wolf spider genus Schizocosa has become a model system for studying mechanisms of assortative mating. We conducted a series of experiments to identify the factors that control mate pair formation in a Schizocosa population that includes both ornamented and non-ornamented males. We show that the population also includes two previously unrecognised female phenotypes. One female phenotype mates mostly or exclusively with ornamented males, and the other mates mostly or exclusively with unornamented males. Assortative mating within these groups is maintained by differences in maturation time, microhabitat use, and female mate preference. We conclude that the population is not a single species as previously believed, but rather an incipient species pair with multiple overlapping mechanisms of reproductive isolation. The identification of a new incipient species pair in the well-studied and rapidly speciating Schizocosa clade presents new opportunities for the study of speciation without geographic isolation.
Data from: Drift versus selection as drivers of phenotypic divergence at small spatial scales: the case of Belgjarskógur threespine stickleback
Divergence in phenotypic traits is facilitated by a combination of natural selection, phenotypic plasticity, gene flow and genetic drift, whereby the role of drift is expected to be particularly important in small and isolated populations. Separating the components of phenotypic divergence is notoriously difficult, particularly for multivariate phenotypes. Here we assessed phenotypic divergence of threespine stickleback (Gasterosteus aculeatus) across 19 semi-interconnected ponds within a small geographic region (~7.5 km2) using multivariate comparisons of phenotypic divergence (PST) neutral genetic (FST) and environmental (EST) variation. We found phenotypic divergence across the ponds in a suite of functionally relevant phenotypic traits, including feeding, defense and swimming traits and body shape (geometric morphometric). Comparisons of PSTs with FSTs suggest that phenotypic divergence is predominantly driven by neutral or stabilizing selection, whereas phenotypic divergence in defensive traits is in accordance with divergent selection. Comparisons of population pairwise PSTs with ESTs suggest that phenotypic divergence in swimming traits is correlated with prey availability, whereas there were no clear associations between phenotypic divergence and environmental difference in the other phenotypic groups. Overall, our results suggest that phenotypic divergence of these small populations at small geographic scales is largely driven by neutral processes (gene flow, drift), although environmental determinants (natural selection or phenotypic plasticity) may play a role.
Data from: The importance (or lack thereof) of niche divergence to the maintenance of a northern species complex: the case of the long-toed salamander (Ambystoma macrodactylum Baird)
The relative importance of ecological versus non-ecological factors for the origin and maintenance of species is an open question in evolutionary biology. Young lineages—such as the distinct genetic groups that make up the ranges of many northern species—represent an opportunity to study the importance of ecological divergence during the early stages of diversification. Yet, few studies have examined the extent of niche divergence between lineages in previously glaciated regions and the role of ecology in maintaining the contact zones between them. In this study, we used tests of niche overlap in combination with ecological niche models to explore the extent of niche divergence between lineages of the long-toed salamander (Ambystoma macrodactylum Baird) species complex and to determine whether contact zones correspond to (divergent) niche limits. We found limited evidence for niche divergence between the different long-toed salamander lineages, substantial overlap in the predicted distribution of suitable climatic space for all lineages and range limits that are independent of niche limits. These results raise questions as to the importance of ecological divergence to the development of this widespread species complex and highlight the potential for non-ecological factors to play a more important role in the maintenance of northern taxa.
Data from: Determining social and population structures requires multiple approaches: a case study of the desert ant Cataglyphis israelensis
The remarkable diversity of ant social organization is reflected in both their life history and population kin structure. Different species demonstrate a high variation with respect to both social structure and mating strategies: from the ancestral colony type that is composed of a single queen (monogyny), singly inseminated (monoandry), to the more derived states of colonies headed by a multiply inseminated queen (polyandry), to colonies composed of multiple queens (polygyny) that are either singly or multiply inseminated. Moreover, the population structure of an ant species can range from multicoloniality to polydomy to supercoloniality, and Cataglyphis is considered to be a model genus in regard to such diversity. The present study sought to determine the social and population structure of the recently described C. israelensis species in Israel. For this purpose we employed a multidisciplinary approach, rather than the commonly used single approach that is mostly based on genetics. Our study encompassed behavior (nest insularity/openness), chemistry (composition of nestmate recognition signals, cuticular hydrocarbons), and genetics (microsatellite polymorphism). Each approach has been shown to possess both advantages and disadvantages, depending on the studied species. Our findings reveal that C. israelensis colonies are headed by a single, multiply-inseminated queen and that the population structure is polydomous, with each colony comprising one main nest and several additional satellite nests. Moreover, our findings demonstrate that none of the above-noted approaches, when employed individually, is suitable or sufficient in itself for delineating population structure, thus emphasizing the importance of using multiple approaches when assessing such complex systems.
Test cases (input), test scripts (output), and source code
<p>Test cases (input), test scripts (output), and source code used in the paper "NLP-assisted Test Generation Toward Script-free Web Testing" submitted to ICSME2021 NIER track</p>
Data from: Using big data to assess prescribing patterns in Greece: the case of chronic obstructive pulmonary disease
Introduction: Chronic Obstructive Pulmonary Disease (COPD) is one of the top leading causes of death and disability, and its management is focused on reducing risk factors, relieving symptoms, and preventing exacerbations. The study aim was to describe COPD prescribing patterns in Greece by using existing health administrative data for outpatients. Methods: This is a retrospective cross-sectional study based on prescriptions collected by the largest social insurance fund, during the first and last trimester of 2012. Selection criteria were the prescription of specific active substances and a COPD diagnosis. Extracted information included active substance, strength, pharmaceutical form and number of packages prescribed, diagnosis, time of dispensing, as well as insurees' age, gender, percentage of co-payment and social security unique number. Statistical analysis included descriptive statistics and logistic regression. Results: 174,357 patients received medicines for COPD during the study period. Patients were almost equally distributed between male and female, and age above 55 years was strongly correlated with COPD. Most patients received a long-acting beta agonist plus inhaled corticosteroid combination (LABA +ICS), followed by long-acting muscarinic agonist (LAMA). 63% patients belonging in the 35-54 age received LABA+ICS. LAMA was prescribed more frequently among males and was strongly correlated with COPD. Conclusion: The study provides big data analysis of Greek COPD prescribing patterns. It highlights the need for appropriate COPD classification in primary care illustrating the role of electronic prescribing in ensuring appropriate prescribing. Moreover, it indicates possible gender differences in treatment response or disease severity, and the impact of statutory co-payments on prescribing.
Data from: Using time series analysis to characterize evolutionary and plastic responses to environmental change: a case study of a shift toward earlier migration date in sockeye salmon
Environmental change can shift the phenotype of an organism through either evolutionary or nongenetic processes. Despite abundant evidence of phenotypic change in response to recent climate change, we typically lack sufficient genetic data to identify the role of evolution. We present a method of using phenotypic data to characterize the hypothesized role of natural selection and environmentally driven phenotypic shifts (plasticity). We modeled historical selection and environmental predictors of interannual variation in mean population phenotype using a multivariate state-space model framework. Through model comparisons, we assessed the extent to which an estimated selection differential explained observed variation better than environmental factors alone. We applied the method to a 60-year trend toward earlier migration in Columbia River sockeye salmon Oncorhynchus nerka, producing estimates of annual selection differentials, average realized heritability, and relative cumulative effects of selection and plasticity. We found that an evolutionary response to thermal selection was capable of explaining up to two-thirds of the phenotypic trend. Adaptive plastic responses to June river flow explain most of the remainder. This method is applicable to other populations with time series data if selection differentials are available or can be reconstructed. This method thus augments our toolbox for predicting responses to environmental change.
Data from: An environmental DNA-based method for monitoring spawning activity: a case study, using the endangered Macquarie perch (Macquaria australasica)
Determining the timing and location of reproductive events is critical for efficient management of species. However, methods currently used for aquatic species are costly, time intensive, biased and often require destructive or injurious sampling. Hence, developing a non-invasive sampling method to accurately determine the timing and location of reproduction for aquatic species would be extremely valuable. We conducted an experimental and field study to determine the influence of spawning, and the mass release of spermatozoa in particular, on environmental DNA (eDNA) concentrations. Using a quantitative PCR approach we monitored changes in nuclear and mitochondrial eDNA concentrations over time. The data from the experimental study and the field survey supported our hypothesis that spawning events are characterized by higher concentrations of nuclear relative to mitochondrial eDNA. Outside of the reproductive period, we find that nuclear and mitochondrial DNA fragments are equally abundant in environmental water samples. We have shown that changes in the relative abundance of nuclear and mitochondrial eDNA can be used to monitor spawning activity of the endangered Macquarie perch. Our method is likely to be transferrable to other aquatic species and can be particularly useful to increase our understanding of the spawning biology of cryptic, rare or threatened species as well as design and evaluate environmental management actions and determine species establishment.
Data from: Ten cases of divergence in the seedling ecology of Dudleya (Crassulaceae)
Dudleya is a genus of succulents consisting of 49 terminal taxa. Many are restricted to narrow geographic ranges with closely related forms living in differing climates. Previously, we found an intriguing set of correlations among nine more or less sympatric Dudleya: species with a smaller mature body size had a lower tolerance for an arid inland climate compared to larger bodied species. Thus, we were motivated to test for rules caused by convergent evolution. We sampled 20 populations from locations across much of the range of the genus. The 20 populations were placed into 10 pairs of close relatives. For each pair, one form was judged to be more mesophilic and the other to be more xerophilic, based on climate-of-origin. We measured germination rate, survival through the summer drought in a coastal garden, and survival through the summer in an inland garden. We hypothesized (among other things) that the xerophilic taxa would have larger mature body sizes and greater rates of survival than mesophilic relatives; however, this and other expected patterns were not repeated across the 10 pairs. Members of pairs have diverged both in various morphological traits and in seedling ecology, but evolution has seemingly not converged on rules. For nearly all taxa, habitat dependence was clear, i.e. plants survived significantly better through the summer at the coastal garden than at the inland garden. Quite possibly the correlations we previously found were caused by divergence between particular lineages coupled with phylogenetic conservatism. Considering the 10 pairs, Dudleya divergences appear to each evolve individualistically.
Data from: A case for considering individual variation in diel activity patterns
There is a growing recognition of the role of individual variation in patterns emerging at higher levels of biological organization. Despite the importance of the temporal configuration of ecological processes and patterns, intraspecific individual variation in diel activity patterns is almost never accounted for in behavioral studies at the population level. We used individual-based monitoring data from 98 GPS-collared brown bears in Scandinavia to estimate diel activity patterns before the fall hunting season. We extracted 7 activity measures related to timing and regularity of activity from individual activity profiles. We then used multivariate analysis to test for the existence of distinct activity tactics and their environmental determinants, followed by generalized linear regression to estimate the extent of within-individual repeatability of activity tactics. We detected 4 distinct activity tactics, with a high degree of individual fidelity to a given tactic. Demographic factors, availability of key foraging habitat, and human disturbance were important determinants of activity tactics. Younger individuals and those with higher bear and road densities within their home range were more nocturnal and more likely to rest during the day. Good foraging habitat and increasing age led to more diurnal activity patterns and nocturnal resting periods. We did not find evidence of diel activity tactics influencing survival during the subsequent hunting season. We conclude that individual variation in activity deserves greater attention than it currently receives, as it may help account for individual heterogeneity in fitness and could facilitate within-population niche partitioning that can have population- or community-level consequences.
Data from: Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species – a case study of Pacific oysters (Crassostrea gigas)
Human-mediated introduction of non-native species into coastal areas via aquaculture is one of the main pathways that can lead to biological invasions. To develop strategies to counteract invasions it is critical to determine whether populations establishing in the wild are self-sustaining or based on repeated introductions. Invasions by the Pacific oyster (Crassostrea gigas) have been associated with the growing oyster aquaculture industry worldwide. In this study, temporal genetic variability of farmed and wild oysters from the largest enclosed bay in Ireland was assessed to reconstruct the recent biological history of the feral populations using seven anonymous and seven microsatellites linked to expressed sequence tags (ESTs). There was no evidence of EST-linked markers showing footprints of selection. Allelic richness was higher in feral than in aquaculture samples (p=0.003, paired t-test). Significant deviations from Hardy-Weinberg equilibrium (HWE) due to heterozygote deficiencies were detected for almost all loci and samples, most likely explained by the presence of null-alleles. Relatively high genetic differentiation was found between aquaculture and feral oysters (largest pairwise multilocus FST 0.074, p < 0.01) and between year classes of oysters from aquaculture (largest pairwise multilocus FST 0.073, p < 0.01), which was also confirmed by the strong separation of aquaculture and wild samples using Bayesian clustering approaches. A ten-fold higher effective population size (Ne) – and a high number of private alleles – in wild oysters suggest an established self-sustaining feral population. The wild oyster population studied appears demographically independent from the current aquaculture activities in the estuary and alternative scenarios of introduction pathways are discussed.
Data from: Reframing the evidence base for policy-relevance to increase impact: a case study on forest fragmentation in the oil palm sector
It is necessary to improve knowledge exchange between scientists and decision-makers so that scientific evidence can be readily accessed to inform policy. To maximise impact of scientific evidence in policy development, the scientific community should engage more fully with decision-makers, building long-term working relationships in order to identify and respond to 'policy windows' with science that is reframed for policy-relevance. We illustrate the process and challenges using a case study in which we synthesised evidence from studies of habitat fragmentation to provide information for improved biodiversity conservation in the oil palm sector, resulting in the uptake of this research into new industry guidelines. Policy implications. The case study demonstrates how having an in-depth understanding of the 'policy arena' (the state of policy and the actors and influencing factors that affect policy) and responding with relevant and specific information, enabled effective uptake of science to inform the design of conservation set-asides in the oil palm industry.
Data from: Predicting the cover and richness of intertidal macroalgae in remote areas: a case study in the Antarctic Peninsula
1. Antarctica is an iconic region for scientific explorations as it is remote and a critical component of the global climate system. Recent climate change causes dramatic retreat of ice in Antarctica with associated impacts to its coastal ecosystem. These anthropogenic impacts have a potential to increase habitat availability for Antarctic intertidal assemblages. Assessing the extent and ecological consequences of these changes requires us to develop accurate biotic baselines and quantitative predictive tools. 2. In this study, we demonstrated that satellite based remote sensing, when used jointly with in-situ ground-truthing and machine learning algorithms, provides a powerful tool to predict the cover and richness of intertidal macroalgae. 3. The salient finding was that the Sentinel-based remote sensing described a significant proportion of variability in the cover and richness of Antarctic macroalgae. The highest performing models were for macroalgal richness and the cover of brown and green algae as opposed to the model of red algal cover. 4. When expanding the geographical range of the ground-truthing, even involving only a few sample points, it becomes possible to potentially map other Antarctic intertidal macroalgal habitats and monitor their dynamics. This is a significant milestone as logistical constraints are an integral part of the Antarctic expeditions. The method has also a potential in other remote coastal areas where extensive in-situ mapping is not feasible.
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.