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365 results for “Spatial modeling”
Data from: Spatially explicit models of divergence and genome hitchhiking
Strong barriers to genetic exchange can exist at divergently selected loci, whereas alleles at neutral loci flow more readily between populations, thus impeding divergence and speciation in the face of gene flow. However, 'divergence hitchhiking' theory posits that divergent selection can generate large regions of differentiation around selected loci. 'Genome hitchhiking' theory suggests that selection can also cause reductions in average genome-wide rates of gene flow, resulting in widespread genomic divergence (rather than divergence only around specific selected loci). Spatial heterogeneity is ubiquitous in nature, yet previous models of genetic barriers to gene flow have explored limited combinations of spatial and selective scenarios. Using simulations of secondary contact of populations, we explore barriers to gene flow in various selective and spatial contexts in continuous, two-dimensional, spatially explicit environments. In general, effects of hitchhiking are strongest in environments with regular spatial patterning of starkly divergent habitat types. When divergent selection is very strong, the absence of intermediate habitat types increases the effects of hitchhiking. However, when selection is moderate or weak, regular (versus random) spatial arrangement of habitat types becomes more important than the presence of intermediate habitats per se. We also document counterintuitive processes arising from the stochastic interplay of selection, gene flow, and drift. Our results indicate that generalization of results from two-deme models requires caution and increase understanding of the genomic and geographic basis of population divergence.
04/04 - Spatial and Amplitude Dynamics of Neurostimulation: Insights from the Acute Intrahippocampal Kainate Seizure Mouse Model
<p>Dataset #4 of 4</p>
02/04 - Spatial and Amplitude Dynamics of Neurostimulation: Insights from the Acute Intrahippocampal Kainate Seizure Mouse Model
<p>Dataset #2 of 4</p>
Modelling the Global Distribution of Chorus Wave Induced Relativistic Microburst Spatial Scale Size
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Dataset for Analysis of Various Spatial Resolutions for Modelling Sector-Coupled Energy Systems
<p>Dataset for preprocessing Balmorel data in this Danish case study.</p>
U-Surf: a global 1km spatially continuous urban surface property dataset for kilometer-scale urban-resolving Earth system modeling
<p>High-resolution urban climate modeling has faced substantial challenges due to the absence of a globally consistent, spatially continuous, and accurate dataset to represent the spatial heterogeneity of urban surfaces and their biophysical properties. This deficiency has long obstructed the development of urban-resolving Earth System Models (ESMs) and ultra-high-resolution urban climate modeling, particularly at large scales. Here, we present a first-of-its-kind 1km-resolution present-day (circa-2020) global continuous urban surface parameter dataset – U-Surf. Using the urban canopy model (UCM) in the Community Earth System Model as a base model for developing dataset requirements, U-Surf leverages the latest advances in remote sensing, machine learning, and cloud computing to provide the most relevant urban surface biophysical parameters, including radiative, morphological, and thermal properties, for UCMs at the facet- and canopy-level. Our high-resolution U-Surf dataset significantly improves the representation of the urban land heterogeneity both within and across cities globally. U-Surf provides essential, high-fidelity surface biophysical constraints to urban-resolving ESMs, enables detailed city-to-city comparisons across the globe, and supports the next-generation kilometer-resolution Earth system modeling across scales. U-Surf parameters can be easily converted or adapted to various types of UCMs, such as those embedded in weather and regional climate models, as well as air quality models. The fundamental urban surface constraints provided by U-Surf are also relevant as features for machine learning models and can have other broad-scale applications for socioeconomic, public health, and urban planning contexts. We expect U-Surf to promote the research frontier on urban systems science, climate-sensitive urban design, and coupled human-Earth systems in the future.</p> <p>The complete list of parameters is presented in the table below.</p> <table> <tbody> <tr> <td>Category</td> <td>Parameter</td> <td>Notes</td> </tr> <tr> <td>Radiative</td> <td>Roof | Impervious | Pervious canyon floor | Wall emissivity</td> <td> </td> </tr> <tr> <td> </td> <td>Roof | Impervious | Pervious canyon floor | Wall albedo</td> <td> </td> </tr> <tr> <td>Morphological</td> <td>Roof | Pervious fraction</td> <td>Roof fraction is w.r.t. urban horizontal surface, and pervious fraction is w.r.t. canyon floor (i.e. pervious and impervious canyon floor).</td> </tr> <tr> <td> </td> <td>Building height</td> <td>Unit: m; Height of wind in the canyon is simply set as half of the building height in CLMU.</td> </tr> <tr> <td> </td> <td>Canyon height-to-width ratio</td> <td> </td> </tr> <tr> <td> </td> <td>Urban percentage</td> <td> </td> </tr> <tr> <td>Thermal</td> <td>Roof | Wall thickness</td> <td>Unit: m</td> </tr> <tr> <td> </td> <td>Roof | Impervious canyon floor | Wall thermal conductivity</td> <td>Unit: W/m*K</td> </tr> <tr> <td> </td> <td>Roof | Impervious canyon floor | Wall volumetric heat capacity</td> <td>Unit: J/m^3*K</td> </tr> <tr> <td> </td> <td>Number of impervious canyon floor layer</td> <td> </td> </tr> <tr> <td> </td> <td>Minimum | Maximum interior building temperature</td> <td>Unit: K</td> </tr> <tr> <td> </td> <td>Air conditioning adoption rate</td> <td> </td> </tr> </tbody> </table> <p> </p> <p>Radiative and morphological parameters are presented in the format of both .tif and .nc to accommodate different needs for the urban climate modeling community. Thermal parameters adapted from CLMU are available in a single .nc file. A CESM-compatiable surface dataset and a time-variant urban dataset (including P_AC and T_BUILDING_MAX; Li et al., 2024) at standard resolution (0.9375°x1.25°) are included for direct simulation use. Note that the urban percentage used to create the surface dataset comes from the PCT_URBAN parameter calculated in U-Surf, but users can input their own urban extent data to generate a customized surface dataset. The raw 1-km data can be easily aggregated/regridded to other resolution as needed.</p> <p> </p> <p><strong>Version 1.1 updates:</strong></p> <p>1. Fill part of the data gaps in Asia. </p> <p>2. Change the aggregation method of some parameters to be facet-area weighted in the 1deg surfdata.</p>
Data and results of opscr demographic and spatial projection models
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Imaging spatial transcriptomics in a transgenic mouse model of α-synucleinopathy
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Geographic range estimates and environmental requirements for the harpy eagle derived from spatial models of current and past distribution
<p>Understanding species-environment relationships is key to defining the spatial structure of species distributions and develop effective conservation plans. However, for many species this baseline information does not exist. With reliable presence data, spatial models that predict geographical ranges and identify environmental processes regulating distribution are a cost-effective and rapid method to achieve this. Yet these spatial models are lacking for many rare and threatened species, particularly in tropical regions. The harpy eagle (<i>Harpia harpyja</i>) is a Neotropical forest raptor of conservation concern with a continental distribution across lowland tropical forests in Central and South America.Currently the harpy eagle faces threats from habitat loss and persecution and is categorised as Near-Threatened by the International Union for the Conservation of Nature (IUCN). Within a point process modelling (PPM) framework, we use presence-only occurrences with climatic and topographical predictors to estimate current and past distributions and define environmental requirements using Ecological Niche Factor Analysis. The current PPM prediction had high calibration accuracy (Continuous Boyce Index = 0.838) and was robust to null expectations (pROC ratio = 1.407). Three predictors contributed 96 % to the PPM prediction, with Climatic Moisture Index the most important (72.1 %), followed by minimum temperature of the warmest month (15.6 %) and Terrain Roughness Index (8.3 %). Assessing distribution in environmental space confirmed the same predictors explaining distribution, along with precipitation in the wettest month. Our reclassified binary model estimated a current range size 11 % smaller than the current IUCN range polygon. Paleoclimatic projections combined with the current model predicted stable climatic refugia in the central Amazon, Guyana, eastern Colombia, and Panama. We propose a data-driven geographical range to complement the current IUCN range estimate, and that despite its continental distribution this tropical forest raptor is highly specialized to specific environmental requirements.</p> <p> </p>
Improving accuracy of breeding values by incorporating genomic information in spatial-competition mixed models
<p>Supplementary information of a <em>Eucalyptus grandis</em> population, genomic and pedigree data including identity information of trees, family, and provenance of the paper entitled: <strong>Improving accuracy of breeding values by incorporating genomic information in spatial-competition mixed models</strong>.</p> <p> </p>
Figure 1. – Eastern English Channel spatial grid using a in Spatiotemporal patterns in marine fish and cephalopods communities across scales: using an autoregressive spatiotemporal clustering model. A study of fish and cephalopods of the Eastern English Channel
Figure 1. – Eastern English Channel spatial grid using a triangular mesh at a 522 km2 (A), 782 km2 (B) and 1043 km2 (C) average scale with the geographic coordinates in WGS84 of all the English Channel groundfish hauls survey from 1995 to 2014 (blue). The red points are the vertices used to define the mesh.
Spatially explicit re-harmonized terrestrial carbon densities for calibrating Integrated human-Earth System Models
<p>Soil and vegetation carbon densities play a critical role in global and regional human-Earth system models. These densities affect variables such as land use change emissions and also influence land use change pathways under climate mitigation scenarios where terrestrial carbon is assigned a carbon price. Recently, more spatially explicit, fine resolution data have become available for both soil and vegetation carbon. However, for models to effectively use these data the fine resolution data need to be reharmonized to initial land use and land cover conditions represented by these models. Without such reharmonization the carbon values may be very inaccurate for particular land types and places where the source data and the model disagree on the land use/cover type. Here we present reharmonized soil and vegetation carbon densities both at the grid cell level at 5 arcmin resolution and also aggregated to 235 water sheds for 4 different land use and 15 land cover types. These data are particularly useful as initial land carbon conditions for global Multisectoral Dynamic Models (MSD). Moreover, these data include six different statistical states calculated using distinct resampling methods for each of the land use, land cover types. These statistical states are used to define a range of possible carbon values for each land classification, and any state can be used for defining initial conditions of soil and vegetation carbon in MSD models. We make use of these statistical states to calculate spatially distinct uncertainties in the carbon densities by land type. We have implemented these data in a state-of-the-art multi sector dynamics model, namely the Global Change Analysis Model (GCAM), and show that these new data improve several land use responses in the model, especially when terrestrial carbon is assigned a carbon price. The statistical states in our data are validated against similar estimates in the literature both at a grid cell level and at a regional level. </p> <p>This is a data record which corresponds to the paper "Spatially explicit re-harmonized terrestrial carbon densities for calibrating Integrated Multisectoral Models" (Narayan et al. 2023, under review)</p> <p>We have now also added a tabular version of the dataset aggregated to GTAP's AEZ definitions as opposed to GCAM's GLUs</p> <p> </p>
Dendritic prioritization through spatial stream network modeling informs targeted management of Himalayan riverscapes under brown trout invasion
<p>With the concept of 'riverscapes' long pending to be acknowledged in the 'landscape-centric' legislative framework of Himalayan nations, conservation of native riverine species stays practically unheeded. This necessitates urgent prioritization of stream networks to conserve the lotic taxa under invasion pressures. Himalayan riverscapes are pervaded with the invasive-exotic brown trout <i>Salmo trutta</i>,<i> </i>posing serious threats to the co-occurring native, the snow trout <i>Schizothorax richardsonii</i>. Using intensive surveys (218.7km) and geostatistical stream network models (n=537), we contrasted snow trout in two stream networks with and without invasives, for assessing differences in their spatial distribution. Our models indicate invasion-induced relegations of natives from the river mainstem into headwaters, with large sections of mainstem occupied by invasives. Furthermore, a concerningly small percentage of potential habitat left for natives to occupy in the mainstem is threatened, where a 100% overlap of native and invasive trout distributions is predicted. With a higher presence probability for the natives in headwaters of invaded watershed as compared to the non-invaded watershed, we highlight the headwater streams as<b> </b>potential refugia for the natives under invasion.</p> <p><i>Synthesis and Applications: </i>Our approach of basin-scale dendritic prioritization provides immediate management solutions to tackle brown trout invasion threats in Himalaya. We inform decisions on delineation of headwaters as invasion refugia for native fish, with assisted recovery of their fragmented populations in the river mainstems through targeted management of invasives</p>
Fig. 4 in Using a spatial mark-resight model to estimate the parameters of a wild pig (Sus scrofa) population in Singapore
Fig. 4. Frequency of Sus scrofa group sizes observed in 167 unique camera trap observations from May 2016 to August 2016.
Computational modeling of human multisensory spatial representation by a neural architecture
<p>Architecture and processed dataset used to train it, referring to the manuscript:</p> <p>Computational modeling of human multisensory spatial representation by a neural architecture</p>
Supplementary material 5 from: Neill AM, O`Donoghue C, Stout JC (2023) Spatial analysis of cultural ecosystem services using data from social media: A guide to model selection for research and practice. One Ecosystem 8: e95685. https://doi.org/10.3897/oneeco.8.e95685
MaxEnt Supplementary Info
Supplementary material 4 from: Neill AM, O`Donoghue C, Stout JC (2023) Spatial analysis of cultural ecosystem services using data from social media: A guide to model selection for research and practice. One Ecosystem 8: e95685. https://doi.org/10.3897/oneeco.8.e95685
Moran's I Correlograms
Supplementary material 3 from: Neill AM, O`Donoghue C, Stout JC (2023) Spatial analysis of cultural ecosystem services using data from social media: A guide to model selection for research and practice. One Ecosystem 8: e95685. https://doi.org/10.3897/oneeco.8.e95685
Sampled PUD occurrence
Supplementary material 2 from: Neill AM, O`Donoghue C, Stout JC (2023) Spatial analysis of cultural ecosystem services using data from social media: A guide to model selection for research and practice. One Ecosystem 8: e95685. https://doi.org/10.3897/oneeco.8.e95685
InVEST model configuration
Supplementary material 1 from: Neill AM, O`Donoghue C, Stout JC (2023) Spatial analysis of cultural ecosystem services using data from social media: A guide to model selection for research and practice. One Ecosystem 8: e95685. https://doi.org/10.3897/oneeco.8.e95685
Sites used for validation
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.