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1,868 results for “Spatial Data”
Type 2 Diabetes Specific Spatial Differential Gene Expression in Pancreas Visium Data
GEO Series GSE264331. Homo sapiens. 16 samples. Type: Other.
Spatial transcriptomics (Visium, 10x Genomics) data of Duchenne mouse models
GEO Series GSE199659. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Spatial transcriptomics data of GAN-KP tumor treated with regorafenib
GEO Series GSE214363. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing; Other.
Histopathological-based analysis of human kidney spatial transcriptomics data: toward precision pathology
GEO Series GSE261545. Homo sapiens. 1 samples. Type: Other.
Data for manuscript: Sediment Routing and Floodplain Exchange (SeRFE): A spatially explicit model of sediment balance and connectivity through river networks
<p>Data used to calibrate and run the SeRFE model in the applications presented in the manuscript "Sediment Routing and Floodplain Exchange (SeRFE): A spatially explicit model of sediment balance and connectivity through river networks."</p>
DATA: A thalamic reticular circuit for head direction cell tuning and spatial navigation
<p>As we navigate in space, external landmarks and internal information guide our movement. Circuit and synaptic mechanisms that integrate these cues with head-direction (HD) signals remain, however, unclear. We identify an excitatory synaptic projection from the presubiculum (PreS) and the multisensory-associative retrosplenial cortex (RSC) to the anterodorsal thalamic reticular nucleus (TRN), so far classically implied in gating sensory information flow. <em>In vitro</em>, projections to TRN involve AMPA/NMDA-type glutamate receptors that initiate TRN cell burst discharge and feedforward inhibition of anterior thalamic nuclei. <em>In vivo</em>, chemogenetic anterodorsal TRN inhibition modulates PreS/RSC-induced anterior thalamic firing dynamics, broadens the tuning of thalamic HD cells, and lead to preferential use of allo- over egocentric search strategies in the Morris water maze. TRN-dependent thalamic inhibition is thus an integral part of limbic navigational circuits wherein it coordinates external sensory and internal HD signals to regulate the choice of search strategies during spatial navigation.</p>
Data and results from Spage2vec: Unsupervised representation of localized spatial gene expression signatures
<p>This repository contains spatial gene expression data for reproducing analysis results of spage2vec manuscript [1].</p> <p>[1] Partel G, Wählby C. Spage2vec: Unsupervised representation of localized spatial gene expression signatures. The FEBS Journal. 2020.</p> <p>Acknowledgement:</p> <p>We thank Xiaoyan Qian, Simone Codeluppi, Jeffrey Moffitt, Kok Hao Chen, Alistair N. Boettiger and Dhananjay Bambah-Mukku for generating and sharing in situ sequencing [2], osmFISH [3] and MERFISH [4-5] datasets. And Jeongbin Park, Wonyl Choi for uploading osmFISH [3] and MERFISH [4] data to public repository.</p> <p> </p> <p>[2] Qian, Xiaoyan, et al. "Probabilistic cell typing enables fine mapping of closely related cell types in situ." Nature methods 17.1 (2020): 101-106.</p> <p>[3] Codeluppi, Simone, et al. "Spatial organization of the somatosensory cortex revealed by osmFISH." Nature methods 15.11 (2018): 932-935.</p> <p>[4] Moffitt, Jeffrey R., et al. "Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region." Science 362.6416 (2018): eaau5324.</p> <p>[5] Chen, Kok Hao, et al. "Spatially resolved, highly multiplexed RNA profiling in single cells." <em>Science</em> 348.6233 (2015): aaa6090.</p>
Data from: Limited evidence for spatial resource partitioning across temperate grassland biodiversity experiments
Locally, plant species richness supports many ecosystem functions. Yet, the mechanisms driving these often-positive biodiversity–ecosystem functioning relationships are not well understood. Spatial resource partitioning across vertical resource gradients is one of the main hypothesized causes for enhanced ecosystem functioning in more biodiverse grasslands. Spatial resource partitioning occurs if species differ in where they acquire resources and can happen both above- and belowground. However, studies investigating spatial resource partitioning in grasslands provide inconsistent evidence. We present the results of a meta-analysis of 21 datasets from experimental species-richness gradients in grasslands. We test the hypothesis that increasing spatial resource partitioning along vertical resource gradients enhances ecosystem functioning in diverse grassland plant communities above- and belowground. To test this hypothesis, we asked three questions: 1. Does species richness enhance biomass production or community resource uptake across sites? 2. Is there evidence of spatial resource partitioning as indicated by resource tracer uptake and biomass allocation above- and belowground? 3. Is evidence of spatial resource partitioning correlated with increased biomass production or community resource uptake? Although plant species richness enhanced community nitrogen and potassium uptake and biomass production above- and belowground, we found that plant communities did not meet our criteria for spatial resource partitioning, though they did invest in significantly more aboveground biomass in higher canopy layers in mixture relative to monoculture. Furthermore, the extent of spatial resource partitioning across studies was not positively correlated with either biomass production or community resource uptake. Our results suggest that spatial resource partitioning across vertical resource gradients alone does not offer a general explanation for enhanced ecosystem functioning in more diverse temperate grasslands.
Data from: Visuo-spatial cueing in children with differential reading and spelling profiles
Dyslexia has been claimed to be causally related to deficits in visuo-spatial attention. In particular, inefficient shifting of visual attention during spatial cueing paradigms is assumed to be associated with problems in graphemic parsing during sublexical reading. The current study investigated visuo-spatial attention performance in an exogenous cueing paradigm in a large sample (N = 191) of third and fourth graders with different reading and spelling profiles (controls, isolated reading deficit, isolated spelling deficit, combined deficit in reading and spelling). Once individual variability in reaction times was taken into account by means of z-transformation, a cueing deficit (i.e. no significant difference between valid and invalid trials) was found for children with combined deficits in reading and spelling. However, poor readers without spelling problems showed a cueing effect comparable to controls, but exhibited a particularly strong right-over-left advantage (position effect). Isolated poor spellers showed a significant cueing effect, but no position effect. While we replicated earlier findings of a reduced cueing effect among poor nonword readers (indicating deficits in sublexical processing), we also found a reduced cueing effect among children with particularly poor orthographic spelling (indicating deficits in lexical processing). Thus, earlier claims of a specific association with nonword reading could not be confirmed. Controlling for ADHD-symptoms reported in a parental questionnaire did not impact on the statistical analysis, indicating that cueing deficits are not caused by more general attentional limitations. Between 31 and 48 % of participants in the three reading and/or spelling deficit groups as well as 32 % of the control group showed reduced spatial cueing. These findings indicate a significant, but moderate association between certain aspects of visuo-spatial attention and subcomponents of written language processing, the causal status of which is yet unclear.
Data from: Evolutionary processes driving spatial patterns of intra-specific genetic diversity in river ecosystems
Describing, understanding and predicting the spatial distribution of genetic diversity is a central issue in biological sciences. In river landscapes, it is generally predicted that neutral genetic diversity should increase downstream, but there have been few attempts to test and validate this assumption across taxonomic groups. Moreover, it is still unclear what are the evolutionary processes that may generate this apparent spatial pattern of diversity. Here, we quantitatively synthesized published results from diverse taxa living in river ecosystems, and we performed a meta-analysis to show that a downstream increase in intraspecific genetic diversity (DIGD) actually constitutes a general spatial pattern of biodiversity that is repeatable across taxa. We further demonstrated that DIGD was stronger for strictly waterborne dispersing than for overland dispersing species. However, for a restricted data set focusing on fishes, there was no evidence that DIGD was related to particular species traits. We then searched for general processes underlying DIGD by simulating genetic data in dendritic-like river systems. Simulations revealed that the three processes we considered (downstream-biased dispersal, increase in habitat availability downstream and upstream-directed colonization) might generate DIGD. Using random forest models, we identified from simulations a set of highly informative summary statistics allowing discriminating among the processes causing DIGD. Finally, combining these discriminant statistics and approximate Bayesian computations on a set of twelve empirical case studies, we hypothesized that DIGD were most likely due to the interaction of two of these three processes and that contrary to expectation, they were not solely caused by downstream-biased dispersal.
Data from: The genetics of phenotypic plasticity. XII. Temporal and spatial heterogeneity
In order to understand empirical patterns of phenotypic plasticity, we need to explore the complexities of environmental heterogeneity and how it interacts with cue reliability. I consider both temporal and spatial variation separately and in combination, the timing of temporal variation relative to development , the timing of movement relative to selection, and two different patterns of movement: stepping-stone and island. Among-generation temporal heterogeneity favors plasticity, while within-generation heterogeneity can result in cue unreliability. In general, spatial variation more strongly favors plasticity than temporal variation, and island migration more strongly favors plasticity than stepping-stone migration. Negative correlations among environments between the time of development and selection can result in seemingly maladaptive reaction norms. The effects of higher dispersal rates depends on the life history stage when dispersal occurs and the pattern of environmental heterogeneity. Thus, patterns of environmental heterogeneity can be complex and can interact in unforeseen ways to affect cue reliability. Proper interpretation of patterns of trait plasticity require consideration of the ecology and biology of the organism. More information on actual cue reliability and the ecological and developmental context of trait plasticity is needed.
Different intensity exercise and verbal spatial working memory Data
<p><span><b><span>Background:</span></b> The inconsistent results of the studies on whether acute exercise can improve working memory and the small effect sizes of meta-analysis indicate that there may be some moderating variables affecting the intensity of the relationship between acute exercise and working memory. This research examined the effects of different intensity acute exercise on the two types of working memory.</span></p> <p><span><b><span>Methods: </span></b>Seventy-eight low active college students aged 18 to 22 years were selected and randomly assigned to four groups. The low-intensity group (n=19), moderate-intensity group (n=19) and high-intensity group (n=19) completed 30-min cycle ergometer exercise bouts separately at the intensity of 40%, 60% and 80% of Vo2max, while the control group (n=21) read for 30-min. The delayed match-to-sample test was used to test verbal and spatial working memory after the intervention.</span></p> <p><span><b><span>Results: </span></b>On response time and accuracy, the main effects of acute exercise intensity and working memory type were significant (<i><span>p</span></i><0.05), and the interaction effect of acute exercise intensity and working memory type was significant (<i><span>p</span></i><0.05).</span></p> <p><span><b><span>Conclusions: </span></b>Acute exercise can improve verbal and spatial working memory, while the moderate intensity of acute exercise has the best effect. Compared with verbal working memory, the effect of acute exercise on spatial working memory is greater.</span></p> <p> </p>
Data from: Sensory deficiencies affect resources selection and associational effects at two spatial scales
Many insect species have limited sensory abilities and may not be able to perceive the quality of different types of resources while approaching patchily distributed resources. These restrictions may lead to differences in selection rates between separate patches and between different resource types within a patch, which may have consequences for associational effects between resources. In this study, we used an oviposition assay containing different frequencies of apple and banana substrates divided over two patches to compare resource selection rates of wild type Drosophila melanogaster at the between and within patch scales. Next, we compared the wild type behavior with that of the olfactory deficient strain Orco2, and the gustatory deficient strain PoxnΔM22-B5 and found comparable responses to patch heterogeneity and similarly strong selection rates for apple at both scales for the wild type and olfactory deficient flies. Their oviposition behavior translated into associational susceptibility for apple and associational resistance for banana. The gustatory deficient flies, on the other hand, no longer had a strong selection rate for apple, strongly differed in between and within patch selection rates from the wild type flies, and caused no associational effects between the resources. Our study suggests that differences in sensory capabilities can affect resource selection at different search behavior scales in different ways, and in turn underlie associational effects between resources at different spatial scales.
Data from: Population closure and the bias-precision trade-off in Spatial Capture-Recapture
1. Spatial capture-recapture (SCR) is an increasingly popular method for estimating ecological parameters. This method often relies on data collected over relatively long sampling periods. While longer sampling periods can yield larger sample sizes and thus increase precision of estimates, they also increase the risk of violating the closure assumption, thereby potentially introducing bias. The sampling period characteristics are therefore likely to play an important role in this bias-precision tradeoff. Yet few studies have studied this tradeoff and none has done so for SCR models. 2. In this study, we explored the influence of the length and timing of the sampling period on the bias-precision tradeoff of SCR population size estimators. Using a continuous time-to-event approach, we simulated populations with a wide range of life histories and sampling periods before quantifying the bias and precision of population size estimates returned by SCR models. 3. While longer sampling periods benefit the study of slow-living species (increased precision and lower bias), they lead to pronounced over-estimation of population size for fast living species. In addition, we show that both bias and uncertainty increase when the sampling period overlaps the species' reproductive season. 4. Based on our findings, we encourage investigators to carefully consider the life history of their study species when contemplating the length and the timing of the sampling period. We argue that SCR (and non-spatial capture-recapture) studies can safely extend the sampling period to increase precision, as long as it is timed to avoid peak recruitment periods. The simulation framework we propose here can be used to guide decisions regarding the sampling period for a specific situation.
Data from: Modeling spatial patterns of soil respiration in maize fields from vegetation and soil property factors with the use of remote sensing and geographical information system
To examine the method for estimating the spatial patterns of soil respiration (Rs) in agricultural ecosystems using remote sensing and geographical information system (GIS), Rs rates were measured at 53 sites during the peak growing season of maize in three counties in North China. Through Pearson's correlation analysis, leaf area index (LAI), canopy chlorophyll content, aboveground biomass, soil organic carbon (SOC) content, and soil total nitrogen content were selected as the factors that affected spatial variability in Rs during the peak growing season of maize. The use of a structural equation modeling approach revealed that only LAI and SOC content directly affected Rs. Meanwhile, other factors indirectly affected Rs through LAI and SOC content. When three greenness vegetation indices were extracted from an optical image of an environmental and disaster mitigation satellite in China, enhanced vegetation index (EVI) showed the best correlation with LAI and was thus used as a proxy for LAI to estimate Rs at the regional scale. The spatial distribution of SOC content was obtained by extrapolating the SOC content at the plot scale based on the kriging interpolation method in GIS. When data were pooled for 38 plots, a first-order exponential analysis indicated that approximately 73% of the spatial variability in Rs during the peak growing season of maize can be explained by EVI and SOC content. Further test analysis based on independent data from 15 plots showed that the simple exponential model had acceptable accuracy in estimating the spatial patterns of Rs in maize fields on the basis of remotely sensed EVI and GIS-interpolated SOC content, with R2 of 0.69 and root-mean-square error of 0.51 µmol CO2 m−2 s−1. The conclusions from this study provide valuable information for estimates of Rs during the peak growing season of maize in three counties in North China.
Data from: Grizzly bear response to fine spatial and temporal scale spring snow cover in Western Alberta
Snow dynamics influence seasonal behaviors of wildlife, such as denning patterns and habitat selection related to the availability of food resources. Under a changing climate, characteristics of the temporal and spatial patterns of snow are predicted to change, and as a result, there is a need to better understand how species interact with snow dynamics. This study examines grizzly bear (Ursus arctos) spring habitat selection and use across western Alberta, Canada. Made possible by newly available fine-scale snow cover data, this research tests a hypothesis that grizzly bears select for locations with less snow cover and areas where snow melts sooner during spring (den emergence to May 31st). Using Integrated Step Selection Analysis, a series of models were built to examine whether snow cover information such as fractional snow covered area and date of snow melt improved models constructed based on previous knowledge of grizzly bear selection during the spring. Comparing four different models fit to 62 individual bear-years, we found that the inclusion of fractional snow covered area improved model fit 60% of the time based on Akaike Information Criterion tallies. Probability of use was then used to evaluate grizzly bear habitat use in response to snow and environmental attributes, including fractional snow covered area, date since snow melt, elevation, and distance to road. Results indicate grizzly bears select for lower elevation, snow-free locations during spring, which has important implications for management of threatened grizzly bear populations in consideration of changing climatic conditions. This study is an example of how fine spatial and temporal scale remote sensing data can be used to improve our understanding of wildlife habitat selection and use in relation to key environmental attributes.
Data from: Intra-specific relatedness, spatial clustering and reduced demographic performance in tropical rainforest trees
Intra-specific negative density dependence promotes species coexistence by regulating population sizes. Patterns consistent with such density dependence are frequently reported in diverse tropical tree communities. Empirical evidence demonstrating whether intra-specific variation is related to these patterns, however, is lacking. The present study addresses this important knowledge gap by genotyping all individuals of a tropical tree in a long-term forest dynamics plot in tropical China. We show that related individuals are often spatially clustered, but having closely related neighbors reduces the growth performance of focal trees. We infer from the evidence, that dispersal limitation and negative density dependence are operating simultaneously to impact the spatial distributions of genotypes in a natural population. Furthermore, dispersal limitation decreases local intra-specific genetic diversity and increases negative density dependence thereby promoting niche differences and species co-existence as predicted by theory.
Data from: Social spider webs harbor largely consistent bacterial communities across broad spatial scales
Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbor microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbors compositionally distinct microbes from the more ephemeral capture webs in the desert social spider Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harbored similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey, and web samples. These data suggest that social spider webs can harbor characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.
Data from: Spatially explicit assessment of estuarine fish after Deepwater Horizon oil spill: tradeoffs in complexity and parsimony
Evaluating long-term contaminant effects on wildlife populations depends on spatial information about habitat quality, heterogeneity in contaminant exposure, and sensitivities and distributions of species integrated into a systems modeling approach. Rarely is this information readily available, making it difficult to determine the applicability of realistic models to quantify population-level risks. To evaluate the trade-offs between data demands and increased specificity of spatially explicit models for population-level risk assessments, we developed a model for a standard toxicity test species, the sheepshead minnow (Cyprinodon variegatus) exposed to oil contamination following the Deepwater Horizon oil spill and compared the output with various levels of model complexity to a standard risk quotient approach. The model uses habitat and fish occupancy data collected over five sampling periods throughout 2008-2010 in Pensacola and Choctawhatchee Bays, Florida, to predict species distribution, field-collected and publically available data on oil distribution and concentration, and chronic toxicity data from laboratory assays applied to a matrix population model. The habitat suitability model established distribution of fish within Barataria Bay, Louisiana, and the population model projected the dynamics of the species in the study area over a five-year period (October 2009 – September 2014). Vital rates were modified according to estimated contaminant concentrations to simulate oil exposure effects. To evaluate the differences in levels of model complexity, simulations varied from temporally and spatially explicit, including seasonal variation and location-specific oiling, to simple interpretations of a risk quotient derived for the study area. The results of this study indicate that species distribution, as well as spatially and temporally variable contaminant concentrations, can provide a more ecologically relevant evaluation of species recovery from catastrophic environmental impacts but might not be cost-effective or efficient for rapid assessment needs.
Data from: Spatial and temporal unpredictability of colony size in cliff swallows across 30 years
Most colonially breeding animals occupy colonies that range in size from a few pairs to thousands of individuals, but the causes of colony size variation are largely unknown. Three general hypotheses are: (1) that variation in colony size is maintained by fluctuating selection via spatial and temporal changes in fitness associated with different colony sizes; (2) that colony formation reflects heterogeneity in habitat, with some sites having resources to support more individuals than others; and (3) that individuals assess the presence or annual reproductive success of current colony residents at each site and aggregate preferentially at high-quality sites. These hypotheses make predictions about how consistent colony size should be across sites and among years. We examined temporal and spatial variability of colony size for >200 Cliff Swallow (Petrochelidon pyrrhonota) colony sites in western Nebraska across a 30-year period. A colony's substrate type, annual population size in the study area, and whether the nesting season was relatively warm or cool, influenced average annual colony size. While some Cliff Swallow colony sites hosted perennially large colonies and others perennially small ones, between-year variability in colony size at most sites was high. Annual colony size distributions were relatively stable over 30 years and provided no evidence for long-term directional changes in colony size. The only ecological characteristic that was strongly associated with Cliff Swallow colony size at a site was the type of nesting substrate, with bridges tending to have larger colonies and being more frequently occupied than other substrates. Some sites showed annual changes in colony size consistent with the birds' basing their choice of colony on the presence or success of conspecifics, but many sites did not conform to a pattern expected if coloniality is a by-product of traditional aggregation. Colony size in Cliff Swallows was temporally and spatially unpredictable when viewed across the 30 years of this study. Each of the three hypotheses to explain size variation may have applied at certain sites, but the pattern of colony size variability leant the most support to the hypothesis that fluctuating selection on group size maintains colonies of widely different sizes.
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.