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1,868 results for “Spatial Data”
Data from: Spatial heterogeneity of plant-soil feedbacks increases per capita reproductive biomass of species at an establishment disadvantage
Plant–soil feedbacks have been widely implicated as a driver of plant community diversity, and the coexistence prediction generated by a negative plant–soil feedback can be tested using the mutual invasibility criterion: if two populations are able to invade one another, this result is consistent with stable coexistence. We previously showed that two co-occurring Rumex species exhibit negative pairwise plant–soil feedbacks, predicting that plant–soil feedbacks could lead to their coexistence. However, whether plants are able to reproduce when at an establishment disadvantage ("invasibility"), or what drivers in the soil might correlate with this pattern, are unknown. To address these questions, we created experimental plots with heterogeneous and homogeneous soils using field-collected conditioned soils from each of these Rumex species. We then allowed resident plants of each species to establish and added invader seeds of the congener to evaluate invasibility. Rumex congeners were mutually invasible, in that both species were able to establish and reproduce in the other's resident population. Invaders of both species had twice as much reproduction in heterogeneous compared to homogeneous soils; thus the spatial arrangement of plant–soil feedbacks may influence coexistence. Soil mixing had a non-additive effect on the soil bacterial and fungal communities, soil moisture, and phosphorous availability, suggesting that disturbance could dramatically alter soil legacy effects. Because the spatial arrangement of soil patches has coexistence implications, plant–soil feedback studies should move beyond studies of mean effects of single patch types, to consider how the spatial arrangement of patches in the field influences plant communities.
Data from: Spatial variation of the rain-snow temperature threshold across the Northern Hemisphere
We present the first continuous map of rain-snow air temperature thresholds over the Northern Hemisphere land surface, underlining the spatial variability of precipitation phase partitioning. Land surface models typically discriminate between rain and snow using a simple, spatially uniform air temperature threshold, but observations indicate the threshold is not static. Our analysis of a 29-year observational dataset (n = 17.8 million) shows the threshold varies significantly, averaging 1.0°C and ranging from -0.4°C to 2.4°C for 95% of Northern Hemisphere stations, with continental climates exhibiting the warmest thresholds and maritime the coolest. Relative humidity exerts the strongest control on phase partitioning, while surface pressure plays a secondary role. Simulations indicate the selection of a rain-snow threshold introduces significant uncertainty to snowfall frequency and that including relative humidity as a predictor variable provides the greatest improvement to precipitation phase prediction between 0.6°C and 3.4°C, the interval where phase partitioning is most uncertain.
Data from: Ultra-fine scale spatially-integrated mapping of habitat and occupancy using structure-from-motion
Organisms respond to and often simultaneously modify their environment. While these interactions are apparent at the landscape extent, the driving mechanisms often occur at very fine spatial scales. Structure-from-Motion (SfM), a computer vision technique, allows the simultaneous mapping of organisms and fine scale habitat, and will greatly improve our understanding of habitat suitability, ecophysiology, and the bi-directional relationship between geomorphology and habitat use. SfM can be used to create high-resolution (centimeter-scale) three-dimensional (3D) habitat models at low cost. These models can capture the abiotic conditions formed by terrain and simultaneously record the position of individual organisms within that terrain. While coloniality is common in seabird species, we have a poor understanding of the extent to which dense breeding aggregations are driven by fine-scale active aggregation or limited suitable habitat. We demonstrate the use of SfM for fine-scale habitat suitability by reconstructing the locations of nests in a gentoo penguin colony and fitting models that explicitly account for conspecific attraction. The resulting digital elevation models (DEMs) are used as covariates in an inhomogeneous hybrid point process model. We find that gentoo penguin nest site selection is a function of the topography of the landscape, but that nests are far more aggregated than would be expected based on terrain alone, suggesting a strong role of behavioral aggregation in driving coloniality in this species. This integrated mapping of organisms and fine scale habitat will greatly improve our understanding of fine-scale habitat suitability, ecophysiology, and the complex bi-directional relationship between geomorphology and habitat use.
Data from: Testing for human impacts in the mismatch of living and dead ostracode assemblages at nested spatial scales in subtropical lakes from the Bahamian archipelago
Naturally time-averaged accumulations of skeletal remains – death assemblages – provide reliable, albeit temporally coarse, information on the species composition and structure of communities in diverse settings, and their mismatch with local living communities usually signals recent human-driven ecological change. Here, we present the first test of live-dead mismatch as an indicator of human stress using ostracodes. On three islands along a gradient of human population density in the Bahamas, we compared the similarity of living and death assemblages in ten lakes with relatively low levels of human stress to live-dead similarity in eleven physically comparable lakes subject to industrial, agricultural, or other human activities currently or in the past. We find that live-dead agreement in pristine lakes is consistently excellent, boding well for using death assemblages in modern-day and paleolimnological biodiversity assessments. In most comparison of physically-similar paired lakes, sample-level live-dead mismatch in both taxonomic composition and species' rank-abundance is on average significantly greater in the stressed lake; live-dead agreement is not lower in all samples from stressed lakes, but is more variable. When samples are pooled for lake-level and island-level comparisons, stressed lakes still yield lower live-dead agreement but the significance of the difference with pristine lakes decreases – species that occur dead-only (or alive-only) in one sample are likely to occur alive (or dead) in other samples. Inter-island differences in live-dead agreement are congruent with, but not significantly correlated with, differences in human population density. This situation arises from heterogeneity in the timing and magnitudes of stresses and in the extent of post-stress recovery. Live-dead mismatch in ostracode assemblages thus may be a reliable indicator of human impact at the sample-level with the potential to be a widely-applicable tool for identifying impacted habitats, and perhaps, monitor the progress of their recovery.
Data from: Assessing spatial patterns of soil erosion in a high‐latitude rangeland
<p>High‐latitude areas are experiencing rapid change: we therefore need a better understanding of the processes controlling soil erosion in these environments. We used a spatiotemporal approach to investigate soil erosion in Svalbarðstunga, Iceland (66° N, 15° W), a degraded rangeland. We used three complementary datasets: 1) high‐resolution UAV imagery collected from 12 sites (total area ~0.75 km<sup>2</sup>); 2) historical imagery of the same sites; and 3) a simple, spatially‐explicit cellular automata model. Sites were located along a gradient of increasing altitude and distance from the sea, and varied in erosion severity (5–47% eroded). We found that there was no simple relationship between location along the environmental gradient and the spatial characteristics of erosion. Patch‐size frequency distributions lacked a characteristic scale of variation, but followed a power‐law distribution on five of the 12 sites. Present total eroded area is poorly related to current, site‐scale levels of environmental stress, but the number of small erosion patches did reflect site‐level stress. Small (< 25 m<sup>2</sup>) erosion patches clustered near large patches. The model results suggested that the large‐scale patterns observed likely arise from strong, local interactions, which mean that erosion spreads from degraded areas. Our findings suggest that contemporary erosion patterns reflect historical stresses, as well as current environmental conditions. The importance of abiotic processes to the growth of large erosion patches and their relative insensitivity to current environmental conditions makes it likely that the total eroded area will continue to increase, despite a warming climate and reducing levels of grazing pressure.</p>
Data for the paper "Addressing Uncertainties in Modelling Cumulative Impacts within Maritime Spatial Planning in the Adriatic and Ionian Region"
<p>Data for the paper "Addressing Uncertainties in Modelling Cumulative Impacts within Maritime Spatial Planning in the Adriatic and Ionian Region."</p>
Spatial Tournament Data for Complex Networks Non Deterministic Size - MSc Dissertation
<p>A data set that contains the results of various spatial tournaments, for the iterated prisoner's dilemma. Three different types of complex networks have been used as topology for the spatial tournaments. Small world, random and complete networks.</p>
COLOURATION IN 2.5D LOCAL WAVE FIELD SYNTHESIS USING SPATIAL BANDWIDTH-LIMITATION -- Data
<p>This data set contains stimuli and results from an experiment for human perception of colouration in Stereophonics, Wave Field Synthesis, Near-Field-Compensated Higher-Order Ambisonics and Local Wave Field Synthesis simulated via binaural synthesis using head related impulse responses (HRIRs). The corresponding binaural room scanning (BRS) files for the binaural simulation can be found in the directory `brs`. The employed stimuli is contained in `stimuli`. The Multiple Stimulus with Hidden Reference and Anchor (MUSHRA) ratings are stored in `results` together with a text file to describe the content in more detail. The `analysis` directory includes scripts for the statistical evaluation in the publication. The source code is licensed under GPL v3.</p> <p>Abstract of the Publication:</p> <p>Sound Field Synthesis techniques, such as Wave Field Synthesis aim at a physically accurate reproduction of a desired sound field inside an extended listening area. This area is surrounded by loudspeakers individually driven by their respective driving signals. Due to practical limitations, artefacts impair the synthesis accuracy resulting in a perceivable change in timbre compared to the desired sound field. Recently, an approach for so-called Local Wave Field Synthesis was published which enhances the reproduction accuracy in a limited region by applying a spatial bandwidth limitation in the circular/spherical harmonics domain to the desired sound field. This paper reports on a listening experiment comparing conventional Sound Field Synthesis techniques with the mentioned approach. Also the influence of the different parametrisations for Local Wave Field Synthesis is investigated. The results show that the enhanced reproduction accuracy in Local Wave Field Synthesis leads to an improvement with regard to the perceived colouration.</p>
Data from a flexible framework to assess patterns and drivers of beta diversity across spatial scales
<p><span>The patterns and underlying ecological (e.g., environmental filtering) and </span><span>historical</span><span> (e.g., priority effects) drivers of beta diversity are scale-dependent but generally difficult to distinguish</span> <span>and rarely explored with a sufficiently broad range of spatial scales. We propose a general scale-explicit framework to assess and contrast the patterns and drivers of beta diversity across hierarchical spatial scales ranging from within fine-scale ecoregion-scale to among broad-scale ecoregion-scale. By applying this framework to aquatic macroinvertebrate datasets, we show that beta diversity generally increases with spatial extent.</span> <span>With an increasing spatial extent, beta diversity shifts from being more influenced by environmental filtering to being more influenced by recent historical factors (i.e., past beta diversity). Such recent historical effects may result from past environmental variation rather than priority effects.</span><span> We also found that the small-scale and large-scale environmental drivers act differently on beta diversity across spatial extents. Our research reveals a complex spatial-scale dependence in beta diversity patterns and their drivers and provides a more holistic understanding of beta diversity dynamics. Our framework represents a flexible way to unravel the internal structure of beta diversity across scales by partitioning of entire beta diversity variation into scale-specific differences and may have broad application in community ecology, landscape planning and biodiversity conservation.</span></p>
Data from: Cortical reactivation of spatial and non-spatial features coordinates with hippocampus to form a memory dialogue
<p>Episodic memories comprise diverse attributes of experience distributed across neocortical areas. The hippocampus is integral to rapidly binding these diffuse representations, as they occur, to be later reinstated. However, the nature of the information exchanged during this hippocampal-cortical dialogue remains poorly understood. A recent study has shown that the secondary motor cortex carries two types of representations: place cell-like activity, which were impaired by hippocampal lesions, and responses tied to visuo-tactile cues, which became more pronounced following hippocampal lesions. Using two-photon Ca<sup>2+</sup> imaging to record neuronal activities in the secondary motor cortex of male Thy1-GCaMP6s mice, we assessed the cortical retrieval of spatial and non-spatial attributes from previous explorations in a virtual environment. We show that, following navigation, spontaneous resting state reactivations convey varying degrees of spatial (trajectory sequences) and non-spatial (visuo-tactile attributes) information, while reactivations of non-spatial attributes tend to precede reactivations of spatial representations surrounding hippocampal sharp-wave ripples.</p>
Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species
<p>Most Central African rainforest canopies consist of light-demanding tree species that hold high commercial value but also suffer locally from regeneration deficits, raising concerns about the sustainability of logging. Regeneration is influenced by factors such as past perturbations (including human activity), mating systems, and seed/pollen dispersal processes that impact demographic, spatial, and genetic structures within populations. To gain a better understanding of these interactions, we studied the spatial distribution and trunk diameter structure of <em><span>Cylicodiscus gabunensis</span></em> (Fabaceae) - a wind-dispersed, insect-pollinated, timber species - in three plots ranging from 400 to 839<span> </span>ha situated in various environmental contexts (e.g. forest types and elephant densities) across Central Africa. We also genotyped adults and juveniles using microsatellite markers to analyze the spatial genetic structure of each population and infer the selfing rate, seed and pollen dispersal capacities and selection gradients using the <span>'</span>neighborhood model<span>'</span>. The selfing rate was low (3 <span>–</span> 4<span> </span>%), and seed dispersal distances (<em><span>ds</span></em><span> </span>=<span> </span>184<span> </span>m) were much shorter than pollen dispersal distances (<em><span>dp</span></em><span> </span>><span> </span>2<span> </span>km). The three populations displayed contrasted spatial, demographic and genetic structures. One population showed no spatial aggregation or genetic structure, and a multimodal diameter structure indicating pulses of regeneration events. Two populations showed strong spatial aggregation and genetic structures. One exhibited a unimodal diameter structure indicating one ancient pulse of regeneration, while the other displayed a 'reverse J-shaped' diameter structure, typical of ongoing regeneration. In the latter, reproductive success appeared leptokurtic, three mother trees accounting for over 90<span> </span>% of the regeneration and no tree below the minimum cutting diameter implemented by logging companies had offspring. The idiosyncratic nature of population characteristics observed in <em><span>C. gabunensis</span></em> suggests that, for sustainable management, a nuanced approach is needed. This involves protecting productive seed trees in areas where natural regeneration is occurring and actively supporting regeneration in areas exhibiting deficits, especially in contexts with low elephant densities.</p>
Data from "FICTURE: Scalable segmentation-free analysis of sub-micron resolution spatial transcriptomics"
Open the record for dataset details and reuse information.
Data from: Spatial scale matters for predicting plant invasions along roads
<p>Biological invasions threaten global biodiversity and can have severe economic and social impacts. The complexity of this problem challenges effective management of invasive alien species as the contribution of many factors involved in the invasion processes across different spatial scales is not well understood.</p> <p>Here, we identify the most important determinants associated with the occurrence of two invasive alien plants, the North American goldenrods (<em>Solidago canadensis</em> and <em>S. gigantea</em>), commonly found in agricultural landscapes of Europe. We used Google Street View images to perform a remote, large-scale inventory of goldenrods along 1,347 roadside transects across Poland. Using open access geospatial data and machine learning techniques, we investigated the relative role of nearly 50 variables potentially affecting the distribution of studied species at five spatial scales (from within 0.25 km to 5 km of the studied locations).</p> <p>We found that the occurrence of goldenrods along roadsides was simultaneously associated with multiple drivers among which those related to human impacts, climate, soil properties and landscape structure were the most important, while local characteristics, such as road parameters or the presence of other alien plants were less influential. However, the relative contribution of different variables in predicting goldenrod distribution changed across spatial scales.</p> <p><em>Synthesis</em>:<em> </em>Mechanisms underlying plant invasions are highly complex and a number of factors can jointly influence the outcomes of this process. However, since different invasion drivers operate at different spatial scales, some important associations may be overlooked when focusing on a single spatial context. Although associations were consistent in direction (positive or negative) across scales, their relative influence on goldenrod occurrence often changed. Socio-economic factors were largely important at local scales, while the effect of landscape factors broadly increased with increasing spatial scale. We highlight that using multi-scale approaches involving a wide range of variables may enable setting priorities for the management of invasive alien plants.</p>
STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer
<p>Scripts generating figures of the paper titled "STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer".</p>
Spatial data for Chaplin-Kramer et al. "Spatial heterogeneity in forest carbon storage affects priorities for reforestation"
<p>Spatial data generated for the forest carbon edge effects analysis and optimization performed in Chaplin-Kramer et al. "Spatial heterogeneity in forest carbon storage affects priorities for reforestation". The files included are described below.</p><p>fc_stack_hansen_forest_cover2014_compressed_std_forest_edge_result.tif - Carbon (Mg/ha) predicted by the regression model for Hansen forest cover 2014 (this is the LULC map that produced the model with the best fit and was used in the model validation)</p><p>fig1_edge_effect_hansen_compressed_nr_md5_63366a.tif – Figure 1 in the manuscript</p><p>fig2_ipcc1_regression2_overlap3_md5_43e130.tif – Figure 2 in the manuscript</p><p>figS5_ipcc1_regression2_overlap3_avgov_md5_fe8b72.tif – Alternate styling of manuscript Fig. 2 (resampling with "average" instead of "near"), shown in Supplemental Fig. S5</p><p>ipcc_carbon_restoration_limited_md5_cd012d.tif - Carbon (Mg/ha) in restoration LULC calculated with the IPCC Tier 1 approach</p><p>ipcc_tier1_carbon_data.zip - Data needed to run the IPCC approach are contained within two files in the zip folder: the carbon table (carbon zones are rows and ESA LULC codes are columns) IPCC_carbon_table_md5_a91f7ade46871575861005764d85cfa7.csv; and the carbon zones map: carbon_zones_md5_aa16830f64d1ef66ebdf2552fb8a9c0d.gpkg</p><p>ipcc_carbon_esa_compressed_md5_5b4803.tif - Carbon (Mg/ha) in ESA 2014 LULC calculated with the IPCC Tier 1 approach (shown in Fig. S1)</p><p>PNV_jsmith_060420_md5_8dd464e0e23fefaaabe52e44aa296330.tif – Potential Natural Vegetation (PNV) created by Jeff Smith (unpublished) through a cross-walk of ESA to Dinerstein biomes</p><p>regression_carbon_esa_compressed_md5_c867a0.tif - Carbon (Mg/ha) in ESA 2014 LULC calculated with the regression approach (shown in Fig. S1)</p><p>regression_carbon_restoration_md5_1f5ca8.tif - Carbon (Mg/ha) in restoration LULC calculated with the regression approach</p><p>restoration_limited_md5_372bdfd9ffaf810b5f68ddeb4704f48f.tif – the LULC scenario of reforestation (based on PNV, but excluding agriculture and urban areas) </p>
Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data: intermediate results
<p>This directory contains all intermediate results generated in the "Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data" for reproducibility purpose. Associated scripts are available at https://github.com/JiayuSuPKU/Smoother_paper. Raw and processed data can be downloaded at https://zenodo.org/records/10223862.</p><p>Note that some intermediate results and figures in the notebooks may not be exactly the same as those in the paper due to the randomness in some analysis steps, but should be very close.</p>
Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data: raw and processed data files
<p>This directory contains all spatial and single-cell omics datasets analyzed in the "Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data". Associated scripts are available at https://github.com/JiayuSuPKU/Smoother_paper. See https://github.com/JiayuSuPKU/Smoother_paper/blob/main/data/README.md for details on folder structure and data sources.</p>
Data for: The meta-analysis of the effects of spatial sampling bias correction on presence only species distribution models
<p>This dataset contains information extracted from 70 studies identified through a systematic review of the peer-reviewed literature (Web of Science and SCOPUS databases both searched on the 13/02/2023) to evaluate the effect of spatial sampling bias correction methods in presence-only species distribution models.</p>
Spatial data of Synthesis of the land carbon fluxes of the Amazon region between 2010 and 2020
<p>Spatial data used in the main figures of the manuscript Synthesis of the land carbon fluxes of the Amazon region between 2010 and 2020. </p> <p>To reproduce Figure 4b sum the maps of Figure 2c+2e and Figure 4c sum the maps of Figure 2d+2e. </p> <p>To reproduce Figure 5b sum the maps of Figure 3c+3d. </p> <p>The shapefiles with the Brazilian Amazon and biogeographical Amazon are also provided. </p>
Lagain et al., (2023) - Icarus - Recalibration of the lunar chronology due to spatial cratering-rate variability - Data and Code
<ul> <li>CR_moon.csv: Relative cratering rate shown in Fig.3. The<strong> </strong>data are provided over the full range of latitudes and longitudes, with a 1-degree bin.</li> <li>SI_convert_age.m: Matlab code converting model ages of Plutarch and Kirkwood craters from Neukum et al. (2001) chronology into the one presented in this study. </li> </ul>
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.