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208 results for “spatial association”
Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna
<p>Data related to the "Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna" paper by Salo, Nieminen, Salovius-Laurén and Rinne published in Estuarine, Coastal and Shelf Science in 2024. <a href="https://doi.org/10.1016/j.ecss.2024.108822">https://doi.org/10.1016/j.ecss.2024.108822</a></p> <p>The data describes the community data collected with the community science method described in the paper. </p>
Data and code associated with "Spatial wavefront shaping with a nanostructured metasurface for structured illumination microscopy"
<p>Data and code associated with the manuscript "Spatial wavefront shaping with a nanostructured metasurface for structured illumination microscopy"</p>
Human lung cancer harbors spatially-organized stem-immunity hubs that associate with response to immunotherapy
<p>Data associated with Chen, Nieman, Spurrell et al "Human lung cancer harbors spatially-organized stem-immunity hubs that associate with response to immunotherapy" Nature Immunology, 2024. </p> <p>(1) Multiplex RNA scope. Processed cell-level data from 3 datasets, separated into manually selected "Stem Immunity" regions and "Tumor" regions, in separate files. </p> <p>(2) GeoMx. Unprocessed GeoMex data, with standard fields provided by Nanostring software. </p> <p>(3) MERFISH. Transcript-level information, including CellPose and Baysor segmentation. </p> <p>(4) Co-registered multispectral RNA and protein images. Processed cell-level data from 46 patients. Patient-level meta data information is available in supplementary table 1, tab B_Patient_Metadata. Fluorophore channel information is Figure 1a. </p> <p>Paper: <a title="https://secure-web.cisco.com/1OQRHTBMPf1SngM0FLdNuKQOPPx7fLOR87kGiirhnF_e0M74duym9zratwJMs0WJXqHJPAlkZoWXBoHafhJ72n9s0edU76bj8nCUblNWpOnoK6c8KGEQgcNuk8OuBqXAooW9yoh6etJ0bq6VGDmoFd95MrgMob6is1GxcOWx-XK996d_j8QDVu1rptbeyI8n08UfqmHA3n0A0P37k_-DYUWMh7VFNSmbLGzVqGG2n-czoFN3vL5JrMDPRvo0LDGJs96rzB6zYiaLdk6UgYXXc6eUV6FI64MTxmuXCbEmVRqONrjLdyG6HJULOrJLmKURM/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41590-024-01792-2" href="https://secure-web.cisco.com/1OQRHTBMPf1SngM0FLdNuKQOPPx7fLOR87kGiirhnF_e0M74duym9zratwJMs0WJXqHJPAlkZoWXBoHafhJ72n9s0edU76bj8nCUblNWpOnoK6c8KGEQgcNuk8OuBqXAooW9yoh6etJ0bq6VGDmoFd95MrgMob6is1GxcOWx-XK996d_j8QDVu1rptbeyI8n08UfqmHA3n0A0P37k_-DYUWMh7VFNSmbLGzVqGG2n-czoFN3vL5JrMDPRvo0LDGJs96rzB6zYiaLdk6UgYXXc6eUV6FI64MTxmuXCbEmVRqONrjLdyG6HJULOrJLmKURM/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41590-024-01792-2">https://www.nature.com/articles/s41590-024-01792-2</a></p>
Fig. 2 in Spatial variation of dung beetle assemblages associated with forest structure in remnants of southern Brazilian Atlantic Forest
Fig. 2. Principal coordinates analysis (PCoA) of dung beetle species based on Bray–Curtis similarity and environmental variables based on Euclidean distance. The analysis was performed using presence–absence (a), abundance (b) and biomass (c) data of dung beetles, and 15 environmental variables (d). ANH: Anhatomirim Environmental Protection Area; ITA: Permanent Protection Areas of Itapema; PER: Peri Lagoon Municipal Park; RAT: Permanent Protection Areas of Ratones.
Linked collectors and determiners for: First records of Leucania rawlinsi Adams and L. senescens M ̂ schler (Lepidoptera: Noctuidae) in Brazil: redescription, potential association with Bt maize, larval parasitoids, and spatial and temporal distribution.
Natural history specimen data linked to collectors and determiners held within, "First records of Leucania rawlinsi Adams and L. senescens M ̂ schler (Lepidoptera: Noctuidae) in Brazil: redescription, potential association with Bt maize, larval parasitoids, and spatial and temporal distribution". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/4c9c5163-7fce-43f3-be05-c64780788e96">https://bionomia.net/dataset/4c9c5163-7fce-43f3-be05-c64780788e96</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/4c9c5163-7fce-43f3-be05-c64780788e96">https://gbif.org/dataset/4c9c5163-7fce-43f3-be05-c64780788e96</a>. Formatted as a Frictionless Data package.
Clusters of cause specific neonatal mortality and its association with per capita gross domestic product: a structured spatial analytical approach
<p>Database used for the analysis of the manuscript entitled: Clusters of cause specific neonatal mortality and its association with per capita gross domestic product: a structured spatial analytical approach. The aim of the study was to investigate the cluster areas of asphyxia-associated neonatal mortality and to explore the per capita gross domestic product (GDP) as an associated risk factor in São Paulo State (SP), Brazil.</p>
Data for: The interactive effects of soil fertility and tree mycorrhizal association explain spatial variation of diversity-biomass relationships in a subtropical forest
<p><span>Observed biodiversity-ecosystem function (BEF) relationships are highly variable, particularly in natural forests. However, our understanding of the factors that generate these often contradictory patterns, especially the role of different mycorrhizal associations, is still limited. By relating tree species richness and aboveground biomass (AGB) in a fully-mapped 24-ha subtropical forest dynamics plot, we evaluated the impacts of soil fertility and tree mycorrhizal type in mediating BEF relationships at multiple spatial scales. Our results demonstrate a highly positive total richness effect on AGB for arbuscular mycorrhizal (AM) trees but a negative effect on AGB for ectomycorrhizal (EcM) trees, and their relationships were highly spatial scale dependent. However, the observed BEF relationships turned into positive at small spatial scales (i.e., 10 m and 20 m) after controlling for other confounding factors (i.e., topography, soil fertility, and AM proportion). In addition, we found significant interactions between soil fertility and species richness on AGB. Specifically, the positive effect of total species richness on AGB for major mycorrhizal types gradually weakened with increasing soil fertility, while the positive effect of EcM species richness on AM AGB gradually enhanced at small spatial scales, suggesting the observed diversity effects can be largely attributed to resource niche complementarity and the role of EcM fungi.</span></p> <p><span>Synthesis. We conclude that the variable BEF relationships among forest communities could be explained by spatial variation in abiotic environments and community mycorrhizal composition because different types of symbionts perform different nutrient uptake strategies and ability in protection from antagonists. Our findings provide novel insights into the understanding of the variation in the shape of BEF relationships in natural forests, which is critical for forest management, conservation, and restoration in a changing world.</span></p>
Spatial datasets associated with decontamination and remediation operations following the Fukushima nuclear accident, Japan (2011–2023)
<p>At the onset of the full reopening in Spring 2023 of the Difficult-to-Return Zone of Northeastern Japan following the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident that took place in March 2011, several spatial layers were regrouped and compiled to facilitate environmental studies dealing with the redistribution of radiocesium fallout across landscapes.</p> <p><strong>The current dataset is composed of 23 shapefiles including those of the delineations of different spatial zones (Intensive Contamination Survey Areas – ICAs, Special Decontamination Zones – SDZ, Difficult-to-Return Zone –</strong> <strong>DTRZ, and FNDPP location) (Evrard et al. 2019), municipalities where mushroom consumption restrictions were enforced (restricted and partially lifted restrictions), river hydrographic networks and their respective drainage areas (Mano, Niida, Ota, Takase, and Ukedo), dam reservoirs and drainage areas (Mano, Ogaki, Takanokura, and Yokokawa), multiple administrative delineations in Japan (whole Japan administrative boundaries, Prefectures, and municipalities) (GIS, 2016), and one raster file of the reconstruction of initial <sup>137</sup>Cs fallout across eastern Japan (from Kato et al., 2019).</strong></p> <p><strong>The current dataset provides a support to a publication submitted to the SOIL journal:<br></strong></p> <div> <div><strong>Evrard, O., Chalaux-Clergue, T., Chaboche, P.-A., Wakiyama, Y., and Thiry Y. (2023). Research and Management Challenges Following Soil and Landscape Decontamination at the Onset of the Reopening of the Difficult-To-Return Zone, Fukushima (Japan)’. <em>SOIL</em> 9: 479–97. <a href="https://doi.org/10.5194/soil-9-479-2023">https://doi.org/10.5194/soil-9-479-2023</a>. </strong></div> <div> </div> </div> <p>All map processing was carried out using QGIS 3.26.0 (QGIS, 2022) and under the EPSG:WGS 84 projection system.</p> <p>The <sup>137</sup>Cs fallout raster (in Bq m<sup>-2</sup>, decay-corrected to July 2011) was generated from the point grid of Kato et al. (2019). A total of 126 tiles (0.25 x 0.25 degree) were generated by Inverse Distance Weighted (IDW) interpolation using the '<em>IDW interpolation'</em> tool with the following settings: distance coefficient P = 1.0 and pixel size (x and y) = 0.0015 degree. Tiles were then merged into a single tile using the raster<em> 'Merge'</em> tool. The initial point grid footprint was manually delineated to define the spatial applicability zone of the airborne survey. A buffer zone corresponding to half plus 10% of the longest distance between two airborne points (x = 0.002, y = 0.003), i.e. 0.0017 degree, was generated using the '<em>buffer'</em> tool. The single tile was then cut according to the footprint of the buffer zone using the <em>'clip a raster by a mask layer'</em> tool. A <em>single-band pseudo-colour </em>scale is provided and displays pixels with a value above 1000 Bq m<sup>-2</sup> (eq. global background).</p>
Associated Dataset for Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes
<p>The dataset contains the final methylation call set (n=14,627,533), variant calling file for population genomics analyses, analysis codes/scripts, and other associated files related to the research (Constitutive and variable patterns of genome-wide DNA methylation in populations from spatial-environmental range extremes of the bumble bee <em>Bombus vosnesenskii)</em>. Raw WGBS reads generated in this study have been deposited and are currently available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under NCBI BioProject PRJNA956115.</p>
Atlantic cod individual spatial behaviour and stable isotope associations in a no-take marine reserve
<ol> <li>Foraging is a behavioural process and, therefore, individual behaviour and diet are theorized to covary. However, few comparisons of individual behaviour type and diet exist in the wild.</li> <li>We tested whether behaviour type and diet covary in a protected population of Atlantic cod, <em>Gadus</em> <em>morhua</em>. </li> <li>Working in a no-take marine reserve, we could collect data on natural behavioural variation and diet choice with minimal anthropogenic disturbance. We inferred behaviour using acoustic telemetry and diet from stable isotope compositions (expressed as δ<sup>13</sup>C and δ<sup>15</sup>N values). We further investigated whether behaviour and diet could have survival costs.</li> <li>We found cod with shorter diel vertical migration distances fed at higher trophic levels. Cod δ<sup>13</sup>C and δ<sup>15</sup>N values scaled positively with body size. Neither behaviour nor diet predicted survival, indicating phenotypic diversity is maintained without survival costs for cod in a protected ecosystem.</li> <li>The links between diet and diel vertical migration highlight that future work is needed to understand whether the shifts in this behaviour during environmental change (e.g. fishing or climate), could lead to trophic cascades. </li> </ol>
Data for: The interactive effects of soil fertility and tree mycorrhizal association explain spatial variation of diversity-biomass relationships in a subtropical forest
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Data from: Mother of all bonds: influences on spatial association across the lifespan in capuchins
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Atlantic cod individual spatial behaviour and stable isotope associations in a no-take marine reserve
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Mycorrhizal types regulate tree spatial associations in temperate forests: ectomycorrhizal trees might favor species coexistence
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Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition
<ol> <li>Microbial communities are increasingly recognised as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free-living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison to other factors such as host characteristics or spatial proximity of hosts.</li> </ol> <p> </p> <ol> <li>Here we ask how gut microbial communities are structured in a population of North American moose (<i>Alces alces</i>). We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition.</li> </ol> <p> </p> <ol> <li>We sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information.</li> </ol> <p> </p> <ol> <li>We found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure, or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with ~90% accuracy.</li> </ol> <p> </p> <ol> <li>Collectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping gut microbial communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non-model hosts.</li> </ol>
Data from: A heritable symbiont and host-associated factors shape fungal endophyte communities across spatial scales
1. Although microbial ecologists are intensely interested in the processes governing microbial community assembly, progress has been limited by a lack of studies that span multiple geographical scales and levels of biological organization. 2. We used high throughput sequencing to characterize foliar fungal endophyte communities and host plant genetic structure both within, and among, 24 populations of spotted locoweed (Astragalus lentiginosus) across the Great Basin Desert. 3. Across the Great Basin, both within, and among populations of the host plant, fungal endophyte richness was predicted by plant size and variation in the seed-borne, heritable fungus, Alternaria fulva, which produces the bioactive alkaloid swainsonine. 4. The degree of between-plant turnover in the endophyte community was inversely related to host plant inbreeding and average plant size, and positively related to the relative abundance of A. fulva. Plant size was inversely related to endophyte community richness, both among, and within populations. The genetic and physical distance between host populations was not predictive of differences in fungal community structure. 5. Synthesis: Through pairing intensive local- and regional sampling, we uncovered a primacy of deterministic forces imposed by a heritable symbiont on the community structure of locoweed endophytes.
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
1. Although there is a well-known association between tree cover and soil texture in savannahs, the hydrological drivers of tree cover variation have not been systematically explored, particularly in parallel with factors such as fire, herbivory, and tree-grass interactions. The relationship between hydrological factors and tree cover is important for resolving the relative contribution of bottom-up vs. top-down factors in structuring savannah vegetation. 2. We quantified soil moisture dynamics across eight 1-km transects spanning tree cover gradients from open to woody savannah in Serengeti National Park in Tanzania using soil moisture sensors coupled with dataloggers. We mapped tree cover at two spatial scales through supervised classification of high-resolution satellite imagery. We simultaneously produced water retention curves in open and woody habitats within each transect to compare soil hydrological properties and to convert volumetric water content (θ) from dataloggers to plant-available water over the course of an annual cycle. We also quantified grass biomass at 100 locations per transect, estimated fire frequency from MODIS satellite data, and quantified herbivore occupancy with paired camera traps situated in open and woody habitats within each transect. 3. We found a positive relationship between tree cover and soil moisture drainage rate, and found that open habitats had more negative water potentials than woody habitats for a given value of θ. In contrast, we found no evidence for a consistent relationship between grass biomass or fire frequency and tree cover. We found evidence for higher browser occupancy in woody than open habitats, but no habitat effects on herbivores as a group (browsers plus grazers), suggesting that herbivory is unlikely to be the dominant factor explaining variation in tree cover. 4. Our results suggest that variation in tree cover is partly driven by hydrological (edaphic) factors unrelated to fire, herbivory, tree-grass interactions or mean annual precipitation at these spatial scales in Serengeti. We contrast our findings with previous work attributing tree cover shifts in Serengeti to precipitation gradients.
Spatial variation in avian bill size is associated with temperature extremes in a major radiation of Australian passerines
<p>Morphology is integral to body temperature regulation. Recent advances in understanding of thermal physiology suggest a role of the avian bill in thermoregulation. To explore the adaptive significance of bill size for thermoregulation we characterized relationships between bill size and climate extremes. Most previous studies have focussed on climate means, ignoring extremes, and do not reflect thermoregulatory costs experienced over shorter time scales. Using 79 species (9,847 museum specimens), we explore how bill size variation is associated with temperature extremes in a large and diverse radiation of Australasian birds, Meliphagides. Overall, across the continent, bill size variation was associated with both climate extremes and means and was most strongly associated with winter temperatures; associations at the level of climate zones differed from continent-wide associations, were complex and non-linear, yet consistent with physiology and a thermoregulatory role for avian bills. We provide strong evidence that climate extremes have contributed to the evolution of bill morphology in relation to thermoregulation and demonstrate the importance of including extremes to understand fine-scale trait variation across space. Increasing frequency and intensity of climate extremes, a signature of climate change, may lead to changes in bill size, but this is yet to be tested.</p>
Regulatory T cell therapy is associated with distinct immune regulatory lymphocytic infiltrates in kidney transplants: Spatial transcriptomic dataset and images
<p>The outputs of the NanoString GeoMx DSP platform were concatenated into three xlsx files, each illustrating a separate experiment along with their sample annotations. This technique analyzes protein or RNA abundance within regions of interest (ROIs) or specific cell segments selected based on histological features and immunofluorescence. In this repository, the concatenated GeoMx output files are presented, along with PowerPoint presentations for each biopsy that show immunofluorescence images of the selected ROIs and/or cell segments.</p> <ul> <li><strong>Protein_Full ROI:</strong> This experiment measured the abundance of 41 proteins in discrete regions of interest (ROIs) within transplant kidney biopsies.</li> <li><strong>Protein_Rare cell:</strong> This experiment measured the abundance of 40 proteins in specific cell segments, such as CD4+FoxP3- cells vs. CD4+FoxP3+ cells, within transplant kidney biopsies.</li> <li><strong>RNA:</strong> This experiment measured the abundance of 90 genes in discrete ROIs within transplant kidney biopsies.</li> </ul>
High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal
<p>Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (<em>Echinophthirius horridus</em>) infesting the Saimaa ringed seal (<em>Phoca hispida saimensis</em>), which is endemic to Lake Saimaa in Finland and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.</p>
ScienceDex guides
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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.