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1,956 results for “test data”
Data from: What caused over a century of decline in general intelligence? Testing predictions from the genetic selection and neurotoxin hypotheses
Several converging lines of evidence indicate that general intelligence (g) has declined in Western populations. The causes of these declines are debated. Here, two hypotheses are tested: (1) selection acting against genetic variants that promote g causes the decline and (2) the presence of neurotoxic pollution in the environment causes the decline. A linear mixed model was devised to test (1) and (2), in which the secular decline in a "heritable g" (g.h) chronometric factor (comprised of convergent indicators of simple reaction time, working memory, utilization frequencies of high difficulty and also social-intelligence-indicating vocabulary items and per capita macro-innovation rates) was predicted using a neurotoxin chronometric factor (comprised of convergent secular trends among measures of lead, mercury and dioxin + furan pollution, in addition to alcohol consumption) and a polygenic score chronometric factor (comprised of polygenic score means for genetic variants predictive of g, sourced from US and Icelandic age-stratified cohorts). Bivariate correlations revealed that (other than time) only the polygenic score factor was significantly associated with declining g.h (r = .393, p < .05 vs. .033, ns for the neurotoxin factor). Using a hierarchical linear mixed model approach incorporating 25 year lags between the predictors and g.h, time period, operationalized categorically as fifths of a century, accounted for the majority of the variance in the decline in g.h (partial η^2 = .584, p < .05). Net of time period and neurotoxins, changing levels of polygenic scores also significantly predicted variance in the decline in g.h (partial η^2 = .253, p < .05); however, changing levels of neurotoxins did not significantly predict variance in g.h net of time (partial η^2 = .027 ns). Within-period analysis indicates that the independent significant positive effect of the polygenic score factor on g.h was restricted to the third fifth of a century period (β = .202, p < .05).
Data from: An experimental test of whether pyrodiversity promotes mammal diversity in a northern Australian savanna
1. The increasing awareness that a fire regime that promotes biodiversity in one system can threaten biodiversity in another has resulted in a shift away from fire management based on vague notions of maximising pyrodiversity, towards determining the optimal fire regime based on the demonstrated requirements of target species. 2. We utilised a long-running, replicated fire experiment on Melville Island, the largest island off the northern Australian coast, to test the importance of pyrodiversity for native mammals in a northern Australian savanna landscape. We first developed statistical models to determine how native mammal abundance has responded to nine years of experimentally-manipulated fire frequency. Next, given each species' modelled response to fire frequency, we identified the level of pyrodiversity and optimal mix of fire frequencies that would be expected to maximise mammal diversity and abundance, and minimise extinction risk. This was done for both the entire mammal assemblage and for the mammal species currently declining on Melville Island. 3. Fire frequency was a significant predictor of abundance of the northern brown bandicoot (Isoodon macrourus), black-footed tree-rat (Mesembriomys gouldii), brush-tailed rabbit-rat (Conilurus penicillatus), grassland melomys (Melomys burtoni), pale field-rat (Rattus tunneyi), and mice/dunnarts but not for the common brushtail possum (Trichosurus vulpecula). 4. The geometric mean abundance (GMA) of the entire mammal assemblage was positively associated with pyrodiversity, but peaked at an intermediate value. Hence, maximising pyrodiversity would reduce native mammal assemblage GMA below its potential maximum. The fire history for an area that maximised the entire native mammal assemblage GMA consisted of 57% long-unburnt, 43% triennially burnt and <1% annually burnt. Pyrodiversity did not reduce the extinction risk, nor increase the GMA of declining mammals above that predicted in areas entirely annually or triennially burnt. 5. Synthesis and applications: We demonstrate a useful approach with which to develop fire management strategies based on the demonstrated requirements of target species. By comparing the optimal fire regime identified for the conservation of threatened species and that identified for the entire mammal assemblage, we demonstrate the flexibility of this approach to tailor fire management to address specific management priorities in other fire-prone environments.
Data from: Does increased heat resistance result in higher susceptibility to predation? A test using (Drosophila melanogaster) selection and hardening
Heat resistance of ectotherms can be increased both by plasticity and evolution, but these effects may have trade-offs resulting from biotic interactions. Here we test for predation costs in <i>Drosophila melanogaster</i> populations with altered heat resistance produced by adult hardening and directional selection for increased heat resistance. In addition, we also tested for genetic trade-offs by testing heat resistance in lines that have evolved under increased predation risk. We show that while 35/37°C hardening increases heat resistance as expected, it does not increase predation risk from jumping spiders or mantids; in fact there was an indication that survival may have increased under predation following a triple 37°C compared to a single 35°C hardening treatment. Flies that survived a 39°C selection cycle showed lower survival under predation, suggesting a predation cost of exposure to a more severe heat stress. There was however no correlated response to selection because survival did not differ between control and selected lines after selection was relaxed for one or two generations. In addition, lines selected for increased predation risk did not differ in heat resistance. Our findings suggest independent evolutionary responses to predation and heat as measured in laboratory assays, and no costs of heat hardening on susceptibility to predation.
Data from: Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling
Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth–death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18–0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48–1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89–3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36–1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for "replicate adaptive radiations" in the sense of convergent morphological and ecological trajectories among species in different clades, these results are consistent with the hypothesis that iteroparity functioned as an adaptive key innovation, providing a mechanism for range expansion and rapid divergence in upper elevation regions across much of the New World.
Data from: Testing the applicability of a benthic foraminiferal-based transfer function for the reconstruction of paleowater depth changes in Rhodes (Greece) during the early Pleistocene
We present paleo-water depth reconstructions for the Pefka E section deposited on the island of Rhodes (Greece) during the early Pleistocene. For these reconstructions, a transfer function (TF) using modern benthic foraminifera surface samples from the Adriatic and Western Mediterranean Seas has been developed. The TF model gives an overall predictive accuracy of ~50 m over a water depth range of ~1200 m. Two separate TF models for shallower and deeper water depth ranges indicate a good predictive accuracy of 9 m for shallower water depths (0-200 m) but far less accuracy of 130 m for deeper water depths (200-1200 m) due to uneven sampling along the water depth gradient. To test the robustness of the TF, we randomly selected modern samples to develop random TFs, showing that the model is robust for water depths between 20 and 850 m while greater water depths are underestimated. We applied the TF to the Pefka E fossil data set. The goodness-of-fit statistics showed that most fossil samples have a poor to extremely poor fit to water depth. We interpret this as a consequence of a lack of modern analogues for the fossil samples and removed all samples with extremely poor fit. To test the robustness and significance of the reconstructions, we compared them to reconstructions from an alternative TF model based on the modern analogue technique and applied the randomization TF test. We found our estimates to be robust and significant at the 95% confidence level, but we also observed that our estimates are strongly overprinted by orbital, precession-driven changes in paleo-productivity and corrected our estimates by filtering out the precession-related component. We compared our corrected record to reconstructions based on a modified plankton/benthos (P/B) ratio, excluding infaunal species, and to stable oxygen isotope data from the same section, as well as to paleo-water depth estimates for the Lindos Bay Formation of other sediment sections of Rhodes. These comparisons indicate that our orbital-corrected reconstructions are reasonable and reflect major tectonic movements of Rhodes during the early Pleistocene.
Data from: Testing for reproductive interference in the population dynamics of two congeneric species of herbivorous mites
When phylogenetically close, two competing species may reproductively interfere, and thereby affect their population dynamics. We tested for reproductive interference (RI) between two congeneric haplo-diploid spider mites, Tetranychus evansi and Tetranychus urticae, by investigating their interspecific mating and their population dynamics when they competed on the same plants. They are both pests of tomato, but differ in the host plant defences that they suppress or induce. To reduce the effect of plant-mediated interaction, we used a mutant tomato plant lacking jasmonate-mediated anti-herbivore defences in the competition experiment. In addition, to manipulate the effect of RI, we introduced founder females already mated with conspecific males in mild RI treatments or founder, virgin females in strong RI treatments (in either case together with heterospecific and conspecific males). As females show first-male sperm precedence, RI should occur especially in the founder generation under strong RI treatments. We found that T. urticae outcompeted T. evansi in mild, but not in strong RI treatments. Thus, T. evansi interfered reproductively with T. urticae. This result was supported by crossing experiments showing frequent interspecific copulations, strong postmating reproductive isolation and a preference of T. evansi males to mate with T. urticae (instead of conspecific) females, whereas T. urticae males preferred conspecific females. We conclude that interspecific mating comes at a cost due to asymmetric mate preferences of males. Because RI by T. evansi can improve its competitiveness to T. urticae, we propose that RI partly explains why T. evansi became invasive in Europe where T. urticae is endemic.
Data from: What explains rare and conspicuous colours in a snail? A test of time-series data against models of drift, migration or selection
It is intriguing that conspicuous colour morphs of a prey species may be maintained at low frequencies alongside cryptic morphs. Negative frequency-dependent selection by predators using search images ('apostatic selection') is often suggested without rejecting alternative explanations. Using a maximum likelihood approach we fitted predictions from models of genetic drift, migration, constant selection, heterozygote advantage or negative frequency-dependent selection to time-series data of colour frequencies in isolated populations of a marine snail (Littorina saxatilis), re-established with perturbed colour morph frequencies and followed for >20 generations. Snails of conspicuous colours (white, red, banded) are naturally rare in the study area (usually <10%) but frequencies were manipulated to levels of ~50% (one colour per population) in 8 populations at the start of the experiment in 1992. In 2013, frequencies had declined to ~15–45%. Drift alone could not explain these changes. Migration could not be rejected in any population, but required rates much higher than those recorded. Directional selection was rejected in three populations in favour of balancing selection. Heterozygote advantage and negative frequency-dependent selection could not be distinguished statistically, although overall the results favoured the latter. Populations varied idiosyncratically as mild or variable colour selection (3–11%) interacted with demographic stochasticity, and the overall conclusion was that multiple mechanisms may contribute to maintaining the polymorphisms.
Data from: Is biasing offspring sex ratio adaptive? a test of Fisher's principle across multiple generations of a wild mammal in a fluctuating environment
Fisher's principle explains that population sex ratio in sexually reproducing organisms is maintained at 1:1 due to negative frequency-dependent selection, such that individuals of the rare sex realize greater reproductive opportunity than individuals of the more common sex until equilibrium is reached. If biasing offspring sex ratio towards the rare sex is adaptive, individuals that do so should have a higher number of grandoffspring. In a wild population of North American red squirrels (Tamiasciurus hudsonicus) that experiences fluctuations in resource abundance and population density, we show that overall across 26 years, the secondary sex ratio was 1:1; however, stretches of years during which adult sex ratio was biased did not yield offspring sex ratios biased towards the rare sex. Females that had litters biased towards the rare sex did not have more grandoffspring. Critically, adult sex ratio was not temporally autocorrelated across years, thus the population sex ratio experienced by parents was independent of the population sex ratio experienced by their offspring by the time of their primiparity. Expected fitness benefits of biasing offspring sex ratio may be masked or negated by fluctuating environments across years, which limit the predictive value of the current sex ratio.
Data from: A test of the umbrella species approach in restored floodplain ponds.
1.The umbrella species approach, where conservation actions targeted for one or a group of species should benefit the broader community, may provide an effective framework to guide habitat restoration. This requires congruence in the response of umbrella and co-occurring species to environmental stress and recovery, and the identification of potential mechanisms by which co-occurring species benefit from conservation of an umbrella species. 2.Past evaluations of this approach have considered only the presence/absence of umbrella species. In addition to presence/absence, we quantified abundance and biomass of both umbrella and co-occurring species to support a more quantitative evaluation of species co-occurrence. Floodplain ponds are restored in British Columbia and the Pacific Northwest to benefit coho salmon Oncorhynchus kisutch, a presumptive umbrella species. To test its effectiveness as an umbrella species, we assessed the relationships between species richness, abundance and biomass of aquatic vertebrates, including vertebrates of conservation concern ("listed"), and benthic invertebrates and the abundance and biomass of juvenile coho. We used ordination to evaluate relationships between species' abundance and biomass and environmental attributes. 3.Positive relationships were identified between coho abundance and biomass and species richness, abundance and biomass of fish and listed species. These relationships were negative for benthic invertebrates. Listed species were located close to coho in ordinations, suggesting they respond to similar environmental features while benthic invertebrates clustered away from coho. 4.Synthesis and applications. We found that where our umbrella species coho is most productive, so are other listed species and fish in general, a relationship that would not have been evident had we evaluated species richness alone. We also reported strong relationships between some environmental features manipulated in the habitat restoration and the presence and productivity of coho and co-occurring species. Our study demonstrates the umbrella species approach has potential to guide habitat restoration when there is congruence in the response of umbrella and co-occurring species to environmental attributes that can be manipulated in the restoration. Where this is possible, one can use restoration designed for one or several umbrella species and successfully restore habitats that are viable for other species, including listed species.
Data from: Feed or fight: testing the impact of food availability and intraspecific aggression on the functional ecology of an island lizard
Body size often varies among insular populations relative to continental conspecifics – the 'island rule' – and functional, context-dependent morphological differences tend to track this body size variation on islands. Two hypotheses are often proposed as potential drivers of insular population differences in morphology: one relating to diet and the other involving intraspecific competition and aggression. We directly tested whether differences in morphology and maximum bite capacity were explained by interisland changes in hardness of both available and consumed prey, and levels of lizard-to-lizard aggression among small-island populations. Our study included 11 islands in the Greek Cyclades and made use of a gradient in island area spanning five orders of magnitude. We focused on the widespread lizard Podarcis erhardii. We found that on smaller islands, P. erhardii body size was larger, head height was larger relative to body size, and maximum bite capacity became proportionally stronger. This pattern in morphology and performance was not related to differences in diet, but was highly correlated with proxies of intraspecific aggression – bite scars and missing toes. Our findings suggest that critical functional traits such as body size and bite force in P. erhardii follow the predictions of the island rule and are changing in response to changes in the competitive landscape across islands of different sizes.
Data from: A quantitative test of the predicted relationship between countershading and lighting environment.
Countershading, a vertical luminance gradient from a dark back to a light belly, is perhaps the most common coloration phenotype in the animal kingdom. Why? We investigated whether countershading functions as self-shadow concealment (SSC) in ruminants. We calculated "optimal" countershading for SSC by measuring illumination falling onto a model ruminant as a function of time of day and lighting environment. Calibrated images of 114 species of ruminant were compared to the countershading model, and phylogenetic analyses were used to find the best predictors of coats' countershading characteristics. In many species, countershading was close to the model's prediction of "optimal" countershading for SSC. Stronger countershading was associated with increased use of open lighting environments, living closer to the equator, and small body size. Abrupt transitions from dark to light tones were more common in open lighting environments but unassociated with group size or antipredator behavior. Though the SSC hypothesis prediction for stronger countershading in diurnal species was not supported and noncountershaded or reverse-countershaded species were unexpectedly common, this basic pattern of associations is explained only by the SSC hypothesis. Despite extreme variation in lighting conditions, many terrestrial animals still find protection from predation by compensating for their own shadows.
Data from: Testing scale-dependent effects of semi-natural habitats on farmland biodiversity
The effectiveness of conservation interventions for maximizing biodiversity benefits from agri-environment schemes (AESs) is expected to depend on the quantity of seminatural habitats in the surrounding landscape. To verify this hypothesis, we developed a hierarchical sampling design to assess the effects of field boundary type and cover of seminatural habitats in the landscape at two nested spatial scales. We sampled three types of field boundaries with increasing structural complexity (grass margin, simple hedgerow, complex hedgerow) in paired landscapes with the presence or absence of seminatural habitats (radius 0.5 km), that in turn, were nested within 15 areas with different proportions of seminatural habitats at a larger spatial scale (10 × 10 km). Overall, 90 field boundaries were sampled across a Mediterranean region (northeastern Italy). We considered species richness response across three different taxonomic groups: vascular plants, butterflies, and tachinid flies. No interactions between type of field boundary and surrounding landscape were found at either 0.5 and 10 km, indicating that the quality of field boundary had the same effect irrespective of the cover of seminatural habitats. At the local scale, extended-width grass margins yielded higher plant species richness, while hedgerows yielded higher species richness of butterflies and tachinids. At the 0.5-km landscape scale, the effect of the proportion of seminatural habitats was neutral for plants and tachinids, while butterflies were positively related to the proportion of forest. At the 10-km landscape scale, only butterflies responded positively to the proportion of seminatural habitats. Our study confirmed the importance of testing multiple scales when considering species from different taxa and with different mobility. We showed that the quality of field boundaries at the local scale was an important factor in enhancing farmland biodiversity. For butterflies, AESs should focus particular attention on preservation of forest patches in agricultural landscapes within 0.5 km, as well as the conservation of seminatural habitats at a wider landscape scale.
Data from: Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika
We obtained 398 cytochrome c oxidase subunit I barcodes of 96 morphospecies of Lake Tanganyika (LT) cichlids from the littoral zone. The potential of DNA barcoding in these fishes was tested using both species identification and species delineation methods. The best match (BM) and best close match (BCM) methods were used to evaluate the overall identification success. For this, three libraries were analysed in which the specimens were categorized into Operational Taxonomic Units (OTU) in three alternative ways: (A) morphologically distinct, including undescribed, species, (B) valid species and (C) complexes of morphologically similar or closely related species. For libraries A, B and C, 73, 73 and 96% (BM) and 72, 70 and 94% (BCM) of the specimens were correctly identified. Additionally, the potential of two species delineation methods was tested. The General Mixed Yule Coalescent (GMYC) analysis suggested 70 hypothetical species, while the Automatic Barcode Gap Discovery (ABGD) method revealed 115 putative species. Although the ABGD method had a tendency to oversplit, it outperformed the GMYC analysis in retrieving the species. In most cases where ABGD suggested oversplitting, this was due to intraspecific geographical variation. The failure of the GMYC method to retrieve many species could be attributed to discrepancies between mitochondrial gene trees and the evolutionary histories of LT cichlid species. Littoral LT cichlids have complex evolutionary histories that include instances of hybridization, introgression and rapid speciation. Nevertheless, although the utility of DNA barcoding in identification is restricted to the level of complexes, it has potential for species discovery in cichlid radiations.
Data from: Oxygen and carbon isoscapes for the Baltic Sea: testing their applicability in fish migration studies
Conventional tags applied to individuals have been used to investigate animal movement, but these methods require tagged individuals be recaptured. Maps of regional isotopic variability known as "isoscapes" offer potential for various applications in migration research without tagging wherein isotope values of tissues are compared to environmental isotope values. In this study, we present the spatial variability in oxygen (math formula) and dissolved inorganic carbon (δ13CDIC) isotope values of Baltic Sea water. We also provide an example of how these isoscapes can reveal locations of individual animal via spatial probability surface maps, using the high-resolution salmon otolith isotope data from salmon during their sea-feeding phase in the Baltic Sea. A clear latitudinal and vertical gradient was found for both math formula and δ13CDIC values. The difference between summer and winter in the Baltic Sea math formula values was only slight, whereas δ13CDIC values exhibited substantial seasonal variability related to algal productivity. Salmon otolith δ18Ooto and δ13Coto values showed clear differences between feeding areas and seasons. Our example demonstrates that dual isotope approach offers great potential for estimating probable fish habitats once issues in model parameterization have been resolved.
Data from: Molecular phylogeny of the marmots (Rodentia: Sciuridae): tests of evolutionary and biogeographic hypotheses
There are 14 species of marmots distributed across the Holarctic, and despite extensive systematic study, their phylogenetic relationships remain largely unresolved. In particular, comprehensive studies have been lacking. A well-supported phylogeny is needed to place the numerous ecological and behavioral studies on marmots in an evolutionary context. To address this situation, we obtained complete cytochrome (cyt) b sequences for 13 of the species and partial sequence for the 14th. We employed a statistical approach to both phylogeny estimation and hypothesis testing using parsimony and maximum likelihood based methods. We conducted statistical tests on a suite of previously proposed hypotheses of phylogenetic relationships and biogeographic histories. The cyt b data strongly support the monophyly of Marmota and a western montane clade in the Nearctic. The results are consistent with an initial diversification in North America followed by an invasion and subsequent rapid diversification in the Palearctic. These analyses reject the two major competing hypotheses of M. broweri's phylogenetic relationships: namely, that it is the sister species to camtschatica of eastern Siberia and that it is related closely to caligata of the Nearctic. The Alaskan distribution of M. broweri is best explained as a reinvasion from the Palearctic but a Nearctic origin can not be rejected. Several other conventionally recognized species groups can also be rejected. Social evolution has been homoplastic, with large colonial systems evolving in two groups convergently. The cyt b data do not provide unambiguous resolution of several basal nodes in the Palearctic radiation, leaving some aspects of pelage and karyotypic evolution equivocal.
Data from: Resist globally, infect locally: a transcontinental test of adaptation by stickleback and their tapeworm parasite
Parasite infections are a product of both ecological processes affecting host-parasite encounter rates and evolutionary dynamics affecting host susceptibility. However, few studies examine natural infection variation from both ecological and evolutionary perspectives. Here, we describe the ecological and evolutionary factors generating variation in infection rates by a tapeworm (Schistocephalus solidus) in a vertebrate host, the threespine stickleback (Gasterosteus aculeatus). To explore ecological aspects of infection, we measured tapeworm prevalence in Canadian stickleback inhabiting two distinct environments: marine and freshwater. Consistent with ecological control of infection, the tapeworm is very rare in marine environments, even though marine fish are highly susceptible. Conversely, commonly infected freshwater stickleback exhibit substantial resistance in controlled laboratory trials, suggesting that high exposure risk overwhelms their recently evolved resistance. We also tested for parasite adaptation to its host by performing transcontinental reciprocal infections, using stickleback and tapeworm populations from Europe and western Canada. More infections occurred in same-continent host-parasite combinations, indicating parasite "local" adaptation, at least on the scale of continents. However, the recently evolved immunity of freshwater hosts applies to both local and foreign parasites. The pattern of adaptation described here is not wholly compatible with either of the common models of host-parasite coevolution (i.e., matching infection or targeted recognition). Instead, we propose a hybrid, eco-evolutionary model to explain the remarkable pattern of global host resistance and local parasite infectivity.
LCTSC PyDicer Test Data
<p>Subset of TCIA LCTSC data which has been converted using PyDicer for use in testing and examples.</p><p><strong>Warning:</strong> This data has been manipulated (downsampled) to reduce size to make it more appropriate for testing.</p><p>Citations & Data Usage Policy </p><p>Users of this data must abide by the <a href="https://wiki.cancerimagingarchive.net/x/c4hF">TCIA Data Usage Policy</a> and the <a href="https://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution 3.0 Unported License</a> under which it has been published. Attribution should include references to the following citations:</p><p>Data Citation</p><p>Yang, J., Sharp, G., Veeraraghavan, H., Van Elmpt, W., Dekker, A., Lustberg, T., & Gooding, M. (2017). <strong>Data from Lung CT Segmentation Challenge (LCTSC) (Version 3) [Data set]</strong>. The Cancer Imaging Archive. <a href="https://doi.org/10.7937/K9/TCIA.2017.3R3FVZ08">https://doi.org/10.7937/K9/TCIA.2017.3R3FVZ08</a></p><p>Publication Citation</p><p>Yang, J. , Veeraraghavan, H. , Armato, S. G., Farahani, K. , Kirby, J. S., Kalpathy‐Kramer, J. , van Elmpt, W. , Dekker, A. , Han, X. , Feng, X. , Aljabar, P. , Oliveira, B. , van der Heyden, B. , Zamdborg, L. , Lam, D. , Gooding, M. and Sharp, G. C. (2018), <strong>Autosegmentation for thoracic radiation treatment planning: A grand challenge at AAPM 2017</strong>. Med. Phys. <a href="https://doi.org/10.1002/mp.13141">https://doi.org/10.1002/mp.13141</a> </p><p>TCIA Citation</p><p>Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). <strong>The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository.</strong> In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045–1057). Springer Science and Business Media LLC. <a href="https://doi.org/10.1007/s10278-013-9622-7">https://doi.org/10.1007/s10278-013-9622-7</a></p>
Data for model analysis in "Beyond the growth rate of cosmic structure: Testing modified gravity models with an extra degree of freedom", arXiv:1502.03710
<p>SQLite databases containing theoretical predictions for the model comparison in arXiv:1502:03710.</p>
SCARlink test data (PBMC)
<p>Seurat and ArchR test files for running SCARlink <a href="https://github.com/snehamitra/SCARlink/blob/main/notebooks/tutorial.ipynb">tutorial notebook</a>. Related manuscript: <a href="https://www.nature.com/articles/s41588-024-01689-8">https://www.nature.com/articles/s41588-024-01689-8</a></p>
Supplementary Data for "Exploring the Integration of Large Language Models in Industrial Test Maintenance Processes"
<p>This package contains supplementary data not directly included in the paper, including per-commit results for each prototype and the prompts used in the proof-of-concept implementations.</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.