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208
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ShareScore release 0.9.0
Dataset results
208 results for “spatial association”
Distinct oral-associated gastric microbiota and Helicobacter pylori communities for spatial microbial heterogeneity in gastric cancer
<p><span>STROBE Statement—Checklist of items that should be included in reports of <strong><em>case-control studies</em></strong> </span></p>
Dataset associated with A. Hallou, R. He, et al. A computational pipeline for spatial mechano-transcriptomics. bioRxiv 2023.08.03.551894
<p>Dataset associated with:</p> <p>Adrien Hallou, Ruiyang He, Benjamin David Simons and Bianca Dumitrascu. A computational pipeline for spatial mechano-transcriptomics. bioRxiv 2023.08.03.551894; doi: <a href="https://doi.org/10.1101/2023.08.03.551894">https://doi.org/10.1101/2023.08.03.551894</a></p> <p>Licence</p> <p>This dataset is licensed under the <a href="https://creativecommons.org/licenses/by-nc/4.0/">Creative Commons Attribution-NonCommercial 4.0 International License</a>.</p>
Social dominance status is associated with differences in spatial cognitive flexibility in wild mountain chickadees
Social dominance has long been used as a model to investigate social stress. However, many studies using such comparisons have been performed in captive environments. These environments may produce unnaturally high antagonistic interactions, exaggerating the stress of social subordination and any associated adverse consequences. One such adverse effect concerns impaired cognitive ability, often thought to be associated with social subordination. Here, we tested whether social dominance rank is associated with differences in spatial learning and memory and in reversal spatial learning (flexibility) abilities in wild food-caching mountain chickadees at different montane elevations. Higher dominance rank was associated with higher spatial cognitive flexibility in harsh environments at higher elevations, but not at lower, milder elevations. In contrast, there were no consistent differences in spatial learning and memory ability associated with dominance rank. Our results suggest that spatial learning and memory ability in specialized food-caching species is a stable trait resilient to social influences. Spatial cognitive flexibility, on the other hand, appears to be more sensitive to environmental influences including social dominance. These findings contradict those from laboratory studies and suggest that it is critical to investigate the biological consequences of social dominance under natural conditions.
Data and code for: Functional traits mediate individualistic species-environment distributions at broad spatial scales while fine-scale species' associations remain unpredictable
<p>Ecological communities are structured by a diverse set of processes acting at different spatial scales. In plant communities, assembly processes like ecological sorting, limiting similarity, and stochastic events are all expected to influence plant distributions and co-occurrence patterns. We assembled a data set describing the distribution of 139 herbaceous plant species within and among 257 forest stands in Wisconsin (USA) to elucidate the spatial scales at which these assembly processes operate. Analyses of these data in conjunction with detailed information about environmental conditions, plant functional traits, and phylogenetic relationships provided new insights into the scale-dependent drivers of plant community assembly in temperate forest understories. Traits like leaf height, specific leaf area, and seed mass all influenced individualistic plant distributions along landscape-scale gradients in soil texture, soil fertility, light availability, and climate while phylogenetic relationships did not predict species-environment relationships. These findings point to the importance of trait-mediated ecological sorting in shaping individualistic plant distributions at broad spatial scales. Contrary to our expectations about the importance of limiting similarity at local scales, neither functionally similar nor phylogenetically related herbs segregated among microsites within forest stands. We hypothesize strong ecological sorting among forest stands coupled with stochastic fine-scale interactions among species appear deterministic, niche-based assembly processes at local scales.</p>
Cancer-Associated Fibroblast Classification in Single-Cell and Spatial Proteomics Data
<p>ometiff: Imaging Data</p> <p>Cell Masks: Masks generated with cellprofiler from ilastik segmentation training</p> <p>cp-output_config: All relevant cellprofiler output and additional configuration files (for example clinical data) necessary to generate the single cell experiments.</p> <p>IMC Data Objects: Single cell experiment RDS files.</p> <p> </p> <p>scRNA-seq_dataobjects: .Rds files containing the clustered breast cancer, colon cancer, HNSCC, NSCLC and PDAC datasets as well as the integrated validation dataset.</p>
Code and Output data associated with M.E. Orive, M, Barfield, R.D. Holt. Partial clonality expands the opportunity for spatial adaptation. Submitted to The American Naturalist.
<p>This contains the source code, all output files and sample input files used to create the graphs in the manuscript " M.E. Orive, M, Barfield, R.D. Holt. Partial clonality expands the opportunity for spatial adaptation," submitted to The American Naturalist. The readme.rtf file summarizes the manuscript, lists all code files and output files, and explains the output file format and which output data was used, organized by figure number.</p>
Fine-scale environmentally associated spatial structure of Lumpfish ( Cyclopterus lumpus) across the Northwest Atlantic
<p><span>Lumpfish, <em>Cyclopterus lumpus</em>, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms – a process which involves both the domestication and the transfer of lumpfish between geographic regions. Here, we have 70K SNP array data and whole genome re-sequencing data (WGS) for a variety of sample sites across the Northwest Atlantic. </span></p>
Effect of egocentric and allocentric reference frames on spatial numerical associations
<p>From an embodied view of cognition, sensorimotor mechanisms are strongly involved in abstract processing, such as Arabic number meanings. For example, spatial cognition can influence number processing. These spatial-numerical associations (SNAs) have been deeply explored since the seminal spatial-numerical associations of response code (SNARC) effect (i.e., faster left/right sided responses to small/large magnitude numbers, respectively). While these SNAs along the transverse plane (left-to-right axis) have been extensively studied in cognitive sciences, no systematic assessment of other planes of the tridimensional space has been afforded. Moreover, there is no evidence of how SNAs organize themselves throughout the changes in spatial body-reference frames (egocentric and allocentric). Hence, this study aimed to explore how SNAs organize themselves along the transverse and sagittal planes when egocentric and allocentric changes are processed during body displacements in the environment. In the first experiment, the results revealed that when the participants used an egocentric reference, SNAs were observed only along the sagittal plane. In a second experiment that used an allocentric reference, the reversed pattern of results was observed: SNAs were present only along the transverse plane of the body. Overall, these findings suggest that depending on the spatial reference frames of the body, SNAs are strongly flexible.</p>
Single-cell spatial transcriptomics of an inducible destabilized-domain Cre mouse line to target disease associated microglia
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Data from: Spatial transitions in tree cover are associated with soil hydrology, but not with grass biomass, fire frequency, or herbivore biomass in Serengeti savannahs
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Data from: Soil biotic quality lacks spatial structure and is positively associated with fertility in a northern grassland
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High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal
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Data and code for: Functional traits mediate individualistic species-environment distributions at broad spatial scales while fine-scale species’ associations remain unpredictable
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Spatial variation in avian bill size is associated with temperature extremes in a major radiation of Australian passerines
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Specialized spatial cognition is associated with reduced cognitive senescence in a food-caching bird
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Data from: A heritable symbiont and host-associated factors shape fungal endophyte communities across spatial scales
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Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition
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Social dominance status is associated with differences in spatial cognitive flexibility in wild mountain chickadees
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Fine-scale environmentally associated spatial structure of Lumpfish ( Cyclopterus lumpus) across the Northwest Atlantic
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Spatial variation in landlocked Atlantic Salmon smolt survival associated with dam passage, avian predation, and stocking location
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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.