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1,868 results for “Spatial Data”
Upscaling Tower-Based Net Ecosystem Productivity to global 250m using the Data Augmentation Method by Considering their Spatial Distribution
<p>Terrestrial ecosystems have emerged as critical carbon sinks, holding a crucial role in the carbon cycle. Net ecosystem productivity (NEP) is a highly significant parameter in terrestrial ecosystems, representing the net ecosystem exchange (NEE) between ecosystems and the atmosphere, without considering other carbon fluxes from disturbances. In this NEP product, we harmonized various sets of tower-based NEP from flux sites as target variable, remote sensing product and meteorological data as traning variables. We further optimizied these smaple sets to address the problems in spatial distribution, culminating in a global NEP product spanning the years 2001-2022, achieved through the application of the random forest method. This dataset contains NEP data for global terrestrial ecosystems for the period 2001-2022 in MgC with a temporal resolution of 1 year. The spatial resolution of the product is 250m and the data format is TIFF.</p> <p><strong>For detailed instructions on how to use the dataset, see User Guides.doc!</strong></p>
Test dataset for "Spatial Integration of Multi-Omics Data from Serial Sections using the novel Multi-Omics Imaging Integration Toolset"
<p>The uploaded tar file contains anonymized and reduced test data for the paper "Spatial Integration of Multi-Omics Data from Serial Sections using the novel Multi-Omics Imaging Integration Toolset". (doi: https://doi.org/10.1101/2024.06.11.598306; https://github.com/mwess/miit)</p> <p>Dataset description:<br>- 9 serial histology sections with the following stains: (HES, HE, HES, HES, HES, MTS, IHC, IHC, HES)<br>- Sections are indexed in the following way (due to some sections not being part of this project): 1,2,3,6,7,8,9,10,11<br>- Each serial section contains: <br> - landmarks with matching labels across all sections.<br> - semi-manually generated tissue masks <br>- Section 2 contain spatial transcriptomics data and one annotation file in geojson format.<br>- Sections 6 and 7 contain imzml data that were generated with MALDI-MSI in positive ion mode (section 6) and negative ion mode (section 7) and additional histology annotations.<br>- MALDI-MSI is reduced. The positive ion data contains only intensities and spectra for spermine. The negative ion mode data contains only intensities and spectra for citrate and zinc.<br>- ST data contains only locations of spots and scalefactors. (I.e. no count data is included.). Barcode ids are randomly generated. <br>- In addition, for each ST spot histopathological annotations and GSEA scores for the Citrate-Spermine Secretion gene signature are provided.</p> <p>Abbreviations:</p> <p>- HES = Hematoxylin-Erythrosine-Saffron<br>- HE = Hematoxylin-Eosin<br>- MTS = Masson's Trichrome Staining<br>- IHC = Immunohistochemistry<br>- ST = Spatial Transcriptomics, here refers to Visium10X arrays.<br>- MALDI-MSI = Matrix-Assisted Laser Desorption Ionization - Mass Spectrometry Imaging.</p> <p> </p>
Data from: Urbanization affects oak–pathogen interactions across spatial scales
<p>The world is rapidly urbanizing, thereby transforming natural landscapes and changing the abundance and distribution of organisms. However, insights into the effects of urbanization on species interactions, and plant-pathogen interactions in particular, are lacking. We investigated the effects of urbanization on powdery mildew infection on <i>Quercus robur</i> at continental and within-city scales. At the continental scale, we compared infection levels between urban and rural areas of different-sized cities in Europe, and investigated whether plant traits, climatic variables and CO<sub>2 </sub>emissions mediated the effect of urbanization on infection levels. Within one large city (Stockholm, Sweden), we further explored whether local habitat features and spatial connectivity influenced infection levels during multiple years. At the continental scale, infection severity was consistently higher on trees in urban than rural areas, with some indication that temperature mediated this effect. Within Stockholm city, temperature had no effect, while local accumulation of leaf litter negatively affected powdery mildew incidence in one out of three years, and more connected trees had lower infection levels. This study is the first to describe the effects of urbanization on plant-pathogen interactions both within and among cities, and to uncover the potential mechanisms behind the observed patterns at each scale.</p>
The value of increased spatial resolution of pesticide usage data for assessing risk to endangered species: Data, notebooks, and results
<p>Decision makers often cite data quality as a limitation in environmental management. Value of information approaches evaluates the benefit of new data collection for management outcomes. Pesticide exposure risk assessment for endangered species is one context where data limitations may affect decisions and a value of information type approach could be useful for identifying optimal data <span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>quality and resolution. Under the U.S. Federal Insecticide, Fungicide and Rodenticide Act, the U.S. Environmental Protection Agency (EPA) is responsible for registering pesticides before they can be sold and regularly reviewing pesticides. Section 7 of the Endangered Species Act requires that the EPA consider potential impacts of pesticides to listed endangered species and critical habitats in this process, and for the Services—U.S. Fish and Wildlife Service and National Marine Fisheries Service—to complete a formal Section 7 consultation if the EPA deems it necessary. The current process is time‐intensive, lacks transparency and confidence among stakeholders, and leaves hundreds of unreviewed pesticides on the market. Increasing the resolution of pesticide usage data could address these concerns by improving estimated overlaps between species ranges and pesticide usage. Thus, we evaluated the relative importance of different resolutions of pesticide usage data for assessing expected carbaryl exposure to endangered plant species endemic to California. We found that spatially explicit, township resolution usage data (~36</span></span></span></span></span></span></span></span></span></span></span></span></span></span></span> <span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>mile</span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><sup>2</sup><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>) excluded 33% of terrestrial plants (55/168) and 51% their critical habitats (27/53) from requiring a Section 7 consultation, while coarser resolution data excluded none. In contrast, the EPA's biological evaluation for carbaryl only excludes 4% of terrestrial plants (nationally) from requiring formal Section 7 consultation. This suggests high‐resolution data could increase pesticide review efficiency and decrease the amount of time pesticides remain on the market without a formal evaluation.</span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></p>
Data from: The ecology of spider sociality – A spatial model
<p>The emergence of animal societies offers unsolved problems for both evolutionary and ecological studies. Social spiders are specially well suited to address this problem given their multiple independent origins and distinct geographical distribution. Based on long term research on the spider genus <em>Anelosimus</em>, we developed a spatial model that recreates observed macroecological patterns in the distribution of social and subsocial spiders. We show that parallel gradients of increasing insect size and disturbance (rain, predation) with proximity to the lowland tropical rainforest would explain why social species are concentrated in the lowland wet tropics, but absent from higher elevations and latitudes. The model further shows that disturbance, which disproportionately affects small colonies, not only creates conditions that require group living, but also tempers the dynamics of large social groups. Similarly simple underlying processes, albeit with different players on a somewhat different stage, may explain the diversity of other social systems.</p> <p> </p>
Data for 'Membrane marker selection for segmenting single cell spatial proteomics data'
<p>Additional data for 'Membrane marker selection for segmenting single cell spatial proteomics data'</p>
Data from: Spatial variation in the biotic and abiotic filters of oyster recruitment: Implications for restoration
<p>Attempts to restore marine ecosystems are increasing, but the success of projects remains variable. For marine invertebrates, the establishment of self-sustaining populations requires a larval supply as well as conditions that permit recruitment.</p> <p>Abiotic and biotic conditions that determine recruitment can vary across environmental gradients and have opposing or reinforcing effects. We assessed how predation and tidal inundation influence recruitment of the reef-forming oyster, Saccostrea glomerata, at 15 sites, 5 estuaries and 8 degrees of latitude in eastern Australia.</p> <p>Oysters recruited to all 15 sites, but their density displayed spatially variable effects of tidal inundation and caging. Effects of tidal inundation and caging were weakest at the two lower-latitude estuaries where recruitment was low overall, average temperature and turbidity were high and dissolved oxygen low.</p> <p>At higher-latitude estuaries, where abiotic conditions were more favourable for recruitment, recruit density displayed tidal elevation gradients that were dependent on caging and time. Initially, recruit density decreased with tidal inundation (and exposure to finfish predators), in the uncaged but not the caged treatment. However, over time the elevation gradient disappeared, and recruitment and survival of oysters was greater in caged than uncaged treatments irrespective of elevation.</p> <p>Synthesis and applications: Our results suggest that both abiotic (i.e. temperature, turbidity and dissolved oxygen) and biotic (i.e. predation) factors can negatively influence oyster recruitment and, hence, restoration success. Consequently, oyster reef restoration projects should be planned to prioritise sites with low turbidity, high dissolved oxygen and low predation unless these stressors can be mitigated. Restoration projects that are designed with knowledge of local stressors are more likely to be successful.</p>
Supplementary material for "Spatio-temporal modelling of abundance from multiple data sources in an integrated spatial distribution model"
<p><strong>Abstract</strong></p> <p><strong>Aim:</strong> In biodiversity monitoring, observational data are often collected in multiple, disparate schemes with greatly varying degrees of standardization and possibly at different spatial and temporal scales. Technical advances also change the type of data over time. The resulting heterogeneous data sets are often deemed to be incompatible. Consequently, many available data sets may be ignored in practical analyses. Here, we propose a more efficient use of disparate biodiversity data to assess species distributions and population trends.<br> <br> <strong>Location:</strong> Switzerland (Europe)<br> <br> <strong>Taxon:</strong> Birds</p> <p><strong>Methods: </strong>We developed an integrated, hierarchical species distribution model with a joint likelihood for all data sets using a shared state process (e.g., latent species abundance or occurrence), but distinct observation process for each data set. We show how the abundance submodel of a binomial N-mixture model can fuse four different data types (count, detection/non-detection, presence-only, and absence-only data) and enable improved inferences about spatio-temporal patterns in abundance. As case studies, we use data from multiple avian biodiversity monitoring schemes. In the first, the goal is estimating abundance-based species distribution maps. In the second, we infer trends in population abundance across time.</p> <p><strong>Results: </strong>Accuracy and precision of abundance estimates increased when combining data from different sources compared to using a single data source alone. This is particularly valuable when data from each single data source is too sparse for reliable parameter estimation.<br> Main conclusions: We show that exploiting the complementary nature of "cheap", but abundant, citizen-science data and less abundant, but more information-rich, data from structured monitoring programs might be ideal to estimate distribution and population trends more accurately, especially for rare species. Joint likelihoods allow to include a wide variety of different data sets to (1) combine all the available information and to (2) mitigate weaknesses of one by the strength of another.</p> <p> </p> <p> </p>
Raw data repository for the article: "Spatially resolved fluorescence of caesium lead halide perovskite supercrystals reveals quasi-atomic behavior of nanocrystals"
<p>Raw data depository for the article in Nature Communications journal: <a href="https://doi.org/10.1038/s41467-022-28486-3">DOI: 10.1038/s41467-022-28486-3</a>. Details and the file description are given in the file "Lapkin_Dataset_Info.pdf"</p>
Data for "Changing spatial distribution of water flow charts major change in Mars' greenhouse effect"
<p>Data for "Changing spatial distribution of water flow charts major change in Mars’ greenhouse effect". The script "summaryplot_v2.m" generates the summary figures used in the paper. The script "GCM_data_comparison_v5.m" generates additional figures used in the paper. The full underlying temperature output from the GCM runs listed in Table S1 is given in the allTsurf.txt file within the corresponding numbered subdirectory.</p>
Data from: Prairie dogs, cattle subsidies, and alternative prey: Seasonal and spatial variation in coyote diet in a temperate grassland
<p class="MsoNormal"><span>As the dominant predator on North America's grasslands, coyotes (<em>Canis latrans</em>) have a large influence on biodiversity, both on working ranches and in protected parks. Ground squirrel (sciurid) species and livestock carrion are often abundant on grasslands worldwide and have the potential to influence a predator's consumption of alternative prey. We collected 1321 scats in four seasons over two years in and adjacent to Grasslands National Park, Saskatchewan, to test the hypothesis that seasonal and spatial variation in consumption of sciurid prey and cattle (<em>Bos taurus</em>) carrion influenced coyote consumption of alternative prey.<strong> </strong>Sciurid (black-tailed prairie dog <em>Cynomy</em>s<em> ludovicianus</em> and Richardson's ground squirrel </span><em>Urocitellus richardsonii</em><span>) remains were common from spring to fall and had a strong inverse relationship with deer (mule deer <em>Odocoileus hemionus</em> and white-tailed deer <em>O. virginianus</em>), which were most common in winter scats. Cattle remains were most common during spring, fall and winter, occurring in 10.6% of scats annually. Biomass estimates indicated that cattle was the highest ranked food on cattle grazing land year-round, and the 2<sup>nd</sup> ranked food, after deer, during winter on the portion of the park from which cattle were excluded. Closer proximity of scats to a prairie dog colony increased the likelihood of prairie dog remains throughout the year and reduced the likelihood of cattle remains in scats from spring to fall, but not during winter. Individual differences in foraging and ranging behavior may explain the spatial distribution of prairie dog versus cattle in scats. </span><span>Further work is needed to determine whether </span><span>sciurid prey, deer, or livestock carrion </span><span>support large predator populations on grassland habitats to a level that may negatively affect coexisting prey species, including species at risk.</span></p>
Data from: A new approach for investigating spatial relationships of ichnofossils: a case study of Ediacaran–Cambrian animal traces
<p class="MsoNormal"><span class="Heading1Char"><em>Abstract — </em></span>Trace fossils record foraging behaviours, the search for resources in patchy environments, of animals in the rock record. Quantification of the strength, density and nature of foraging behaviours enables the investigation of how these may have changed through time. Here, we present a novel approach to explore such patterns using spatial point process analyses to quantify the scale and strength of ichnofossil spatial distributions on horizontal bedding planes. To demonstrate the utility of this approach we use two samples from the terminal Ediacaran Shibantan Member in South China (between 551 and 543 Ma) and the early Cambrian Nagaur Sandstone in northwestern India (between 539 and 509 Ma). We find that ichnotaxa on both surfaces exhibited significant non-homogeneous lateral patterns, with distinct levels of heterogeneity exhibited by different types of trace fossils. In the Shibantan, two ichnotaxa show evidence for mutual positive aggregation over a shared resource, suggesting the ability to focus on optimal resource areas. Trace fossils from the Nagaur Sandstone exhibit more sophisticated foraging behaviour, with greater niche differentiation. Critically, mark correlation functions highlight significant spatial autocorrelation of trace fossil orientations, demonstrating the greater ability of these Cambrian tracemakers to focus on optimal patches. Despite potential limitations, these analyses hint at changes in the development and optimisation of foraging at the Ediacaran–Cambrian transition and highlight the potential of spatial point process analysis to tease apart subtle differences in behaviour in the trace fossil record.</p>
data&result of Time Series Surface Water Reconstruction Method (TSWR) based on Spatial Relationship of Multi-stage Water Boundaries
<p>It is a dataset for a paper of Time Series Surface Water Reconstruction Method (TSWR) based on Spatial Relationship of Multi-stage Water Boundaries.</p>
Processed data for "SpotClean adjusts for spot swapping in spatial transcriptomics data"
<p>This repo contains processed data to reproduce results in the paper "SpotClean adjusts for spot swapping in spatial transcriptomics data".</p>
Data from: Balanced spatial distribution of green areas creates healthier urban landscapes
<div> <span>The benefits of green infrastructure on human well-being in urban areas are already well established, with strong evidence of the positive effects of the amount and proximity to green areas. However, the understanding of how the spatial distribution and type of green areas affect health is still an open question. <br>Here, we explore how different spatial configurations of green and built-up areas, through a land sharing and sparing framework, and how different types of green areas affect cardiovascular and respiratory hospitalizations in São Paulo city, Brazil. <br>Sharing/sparing indicators were selected as the main explanatory factors in the control of all groups of diseases. Land sharing appeared as a favourable spatial condition to prevent cardiovascular hospitalization, while land sparing and arboreal vegetation were relevant to reduce hospitalization by lower respiratory diseases. <br>For upper respiratory diseases, forests seem to provide a disservice, once they were associated with increased rates of hospitalization by respiratory allergies causes.<br>Considering that hospitalization rates and severity of cardiovascular diseases are substantially higher than those of upper respiratory ones, dense vegetation tends to provide more services than disservices. The land sharing configuration, which is characterized by green areas spread throughout the urban network (in streets, gardens, small squares, or parks), should lead to higher exposure and use of the benefits of green areas, which may then explain the greater prevention of cardiovascular diseases. <br>These novel results indicate that a more balanced distribution of green areas across built-up areas creates healthier urban spaces, and thus can be used as an urban planning strategy to leverage the health benefits provided by green infrastructure. <br>Policy implications: </span><span><span>Aiming to reduce hospitalizations by cardiovascular and pulmonary causes, urban planning should promote the spreading of green areas across the cities, in order to increase daily contact with natural attributes, giving preference to distribution over total quantity of green in urban landscape.</span></span> </div>
Source data and codes for the paper "Inviting atomic mechanics to macro-continua: A study on monocrystalline Si using a spatial multilevel coarsening model"
<p>Source data and codes for the paper "Inviting atomic mechanics to macro-continua: A study on monocrystalline Si using a spatial multilevel coarsening model"</p> <p>This file includes </p> <p>- Source data for Figs 1-5 and Supplementary Materials</p> <p>- LAMMPS codes and raw log files used to produce the results of this study</p> <p> </p>
Processed Data 1 : Spatial multi-omic map of human myocardial infarction
<p>We provide here the processed snRNA-seq, snATAC-seq, and visium data for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022</p>
Video Data: Optic flow in the natural habitats of zebrafish supports spatial biases in visual self-motion estimation
<p>Video dataset accompanying "Spatial Biases in Optic-Flow Sampling for Self-Motion Estimation in Natural Environments." See accompanying <a href="https://github.com/eacooper/AlexanderOpticFlow">Github repository</a> for more documentation and analysis code.</p>
Data from: Temporal and spatial comparisons of angiosperm diversity between eastern Asia and North America
<p>Eastern Asia (EA) and North America north of Mexico (NA) have comparable latitude, land area, and climate, but the overall plant diversity is much higher in EA than in NA. Despite intensive studies on disjunct taxa of the two regions, the temporal and spatial diversity patterns between the two floras remain unclear. Here we explore the floristic differences between EA and NA using the well-studied floras of China and the United States of America (USA) as exemplars, while also employing a newly generated dated phylogeny covering ~90% of the angiosperm genera of the two countries and comprehensive spatial distribution data. We find that China possesses both higher richness and phylogenetic diversity (PD) for angiosperm genera than the USA. Notably, most lineages contribute to the PD anomaly between the two floras, with 46 of 58 lineages having higher PD in China. Temporally, China has a higher proportion of genera that originated before the Miocene than are found in the USA (29.9% vs 23.2%). The eastern USA has more genera that originated during the Paleogene than does the western USA, but the reverse pattern is observed after the middle Miocene, with more genera originating in the west. Spatially, China shows a more distinct east-west deviation in diversity than the USA with eastern China possessing much higher generic richness and PD and more ancient lineages than western China. However, the eastern USA possesses lower generic richness, but higher PD and more ancient lineages than the western USA. Both the floras in China and the USA share a signature of an older east and a younger west, and this pattern may be largely driven by regional orogenic activities and climatic changes in the west of the two regions. Finally, our study indicates that more efforts are needed to enhance biodiversity conservation in southern China and the eastern USA by identifying and protecting phylogenetic diversity hotspots.</p>
Data from: Evaluating otter reintroduction outcomes using genetic spatial capture-recapture modified for dendritic networks
<p>River otters (Lontra canadensis) were extirpated from New Mexico by the 1950s. A limited reintroduction occurred during 2008–2010 in which 33 otters sourced from Washington (WA) were translocated to the Upper Rio Grande Basin (URG) of New Mexico. We conducted a noninvasive genetic capture-recapture survey during the winter of 2018 by collecting fecal DNA samples from river otter scats found at latrines in the URG dendritic network of perennial waterways. Our objectives were to: 1) estimate genetic diversity and effective population size; 2) genetic divergence from the WA source population and potential connectivity with regionally proximal populations; 3) spatially explicit population density and size; and 4) population growth rate since the founder event. Between February and April 2018, we collected 1,184 fecal DNA samples from 622 individual scats at 20 latrines; genotyping was attempted at 10 otter-specific microsatellite loci for a subsample of 543 samples. A bottlenecking founder effect was strongly supported, which, combined with genetic drift, reduced genetic diversity and effective population size by 20–26% and 106–170%, respectively, compared with the WA source population. Estimated population density from spatial capture-recapture models was 0.23–0.28 otter/km of waterway, or 1 otter/3.57–4.35 km of waterway, corresponding to a total population size of 83–100 otters across 359 km of the perennial dendritic network from La Mesilla, New Mexico to Alamosa National Wildlife Refuge, Colorado. Estimated average annual population growth rate since the founder event was 1.12–1.15/year. Despite successful population establishment, the URG river otter population remains small, is genetically degraded, and does not yet meet the criteria for long-term reintroduction success. Projections suggested that the population could reach the recommended minimum viable population size of ≥400 otters by the years 2030–2033, though sufficient habitat may not exist in the URG Basin to support that many otters. </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.