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75 results for “spatiotemporal model”
Data, scripts and model output to perform spatiotemporal analysis of plankton drivers in the Belgian part of the North Sea
<p>This archive contains the input data, R scripts and final results of a mechanistic model that uses near real-time data from the Belgian Part of the North Sea (2011-2017) to quantify the relative contributions of the bottom-up and top-down drivers in phytoplankton dynamics. Input data are zooplankton and phytoplankton abundances, nutrients, Sea Surface Temperature (SST), photosynthetically active radiation (PAR); from the LifeWatch data and infrastructure, funded by Research Foundation - Flanders (FWO). Water temperature data for one of the locations was obtained from Flemish Banks Monitoring Network at https://meetnetvlaamsebanken.be/. The R scripts are presented in a R Markdown file that can be executed in the Blue-Cloud Zoo and Phytoplankton EOV products Vlab at https://blue-cloud.d4science.org/web/zoo-phytoplankton_eov, operated by D4Science.org, www.d4science.org (Assante et al., 2019). </p>
High-resolution spatiotemporal modelling of sand fly abundance in Cyprus in 2015
<p>The expected population size of <em>P. papatasi</em> in Cyprus in 2015 was simulated using the stochastic climate-driven population dynamics model of the species presented in Erguler <em>et al.</em> (2019). The model was simulated with air temperature and relative humidity obtained from WRF-ARW. Two sets of parameters, one for Steni and one for Geri - each with 1000 alternative configurations - were used to simulate the average number of adult females per day per trap (a proxy to expected population size).</p>
Lake browning generates a spatiotemporal mismatch between DOC and limiting nutrients, 2018 spatial survey, modeled light limitation and whole-lake productivity changes in long-term Adirondack lake survey 1994-2012
This data set contains information on a spatial survey of dissolved organic matter (DOM) across lakes and wetlands in the Northeast and Midwest, USA and modeled long-term changes in light limitation and whole-lake productivity in a suite of lakes in the Adirondack State Park, New York, USA. Widespread long-term increases in DOM have been observed in many lakes in a process known as browning. This data set enables the assessment of potential changes in dissolved absorbance and dissolved organic nutrients associated with browning. This data set accompanies a manuscript in review at Limnology and Oceanography: Letters.
XIS: A daily spatiotemporal machine-learning model for environmental exposures in the contiguous United States
<p>These Parquet files contain the outputs used for many analyses and plots in the linked papers. For temperature and humidity, the full sets of observations for cross-validation aren't included because we used restricted-use MADIS data.</p>
Figure S4 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 S4. – Spatial-temporal correlation matrix at a 782 km2 (A) and 1043 km2 (B) scale displaying correlation from strongly negative (dark blue) to strongly positive (dark red).
Figure S2 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 S2. – Spatial hierarchical clustering at a 782 km2 (A) and 1043 km2 (B) scale. The rectangle outlines the communities that where find statistically significant by ASTEC given the approximately unbiased p-values expressed as proportion (red).
Figure 2 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 2. – Spatial correlation matrix at a 522 km2 scale displaying correlation from strongly negative (dark blue) to strongly positive (dark red).
Figure 11 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 11. – Scophthalmus rhombus from low (blue) to high (red) median densities of numbers/ km2 in log scale for 522 km2 for the Eastern English Channel.
Figure S5 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 S5. – Spatial-temporal hierarchical clustering at a 782 km2 (A) and 1043 km2 (B) scale. The rectangle outlines the communities that where find statistically significant by ASTEC given the approximately unbiased p-values expressed as proportion (red).
Spatiotemporal dysregulation of neuron-glia related genes and pro-/anti-inflammatory miRNAs in the 5xFAD mouse model of Alzheimer's disease - Supplementary data
<p><strong>Supplementary Table 1. </strong> Gene expression profile by RT-qPCR analysis revealed no significant differences when simultaneously considering the genotype (WT/5xFAD), age (6/9 months) and brain region (HPC, hippocampus/PFC, prefrontal cortex). </p> <p><strong>Supplementary Table 2.</strong> miRNA-target table for the Analyzed microRNAs and targets selected for this study. Obtained in the online platform https://www.mirnet.ca/</p> <p><strong>Supplementary Table 3. </strong> Node table for the analyzed microRNAs and targets selected for this study. We only considered miRNAs and/or targets with a node degree of at least 2. Obtained in the online platform https://www.mirnet.ca/</p> <p><strong>Supplementary Table 4.</strong> Bivariate Pearson’s correlation coefficients and respective p-values obtained between all miRNAs and genes.</p> <p><strong>Supplementary Table 5.</strong> List of microRNAs analyzed by RT-qPCR and their primer sequences.</p> <p><strong>Supplementary Table 6.</strong> List of genes and respective primer sequences used for mRNA analysis by RT-qPCR.</p> <p><strong>Supplementary Table 7.</strong> Raw data used for correlational analysis in hippocampus (HPC) and prefrontal cortex (PFC) using the cor function in RStudio software.</p>
Output from Linear Inverse Models (LIMs) emulating the observed spatiotemporal statistics of Australian precipitation and global sea surface temperatures
<p><strong>Data repository for <em>How unusual was Australia's 2017–2019 Tinderbox Drought?</em></strong></p> <p>This repository contains LIM data underpinning the paper <em>How unusual was Australia's 2017–2019 Tinderbox Drought?</em> [doi: 10.1016/j.wace.2024.100734 <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.wace.2024.100734" target="_blank" rel="noopener">available online in <em>Weather and Climate Extremes</em> 17 October 2024</a>]. All other datasets used in the paper are freely available online (see Data Availability statement in the paper for details). </p> <p>The repository contains 12 netcdf files, which together comprise the Linear Inverse Model (LIM) outputs described in the paper. <strong>In all cases, please see the paper for important details on the data and how they were produced.</strong> </p> <p><em>Global LIMs</em></p> <ul> <li>`LIM5000_COBE-globalSST_prec-anoms-aus_monthly.nc` <ul> <li>contains 5000 years of emulated Australian precipitation variability, modelled using Australian rainfall data from the Australian Gridded Climate Dataset v2 (AGCD) and global SST data from 'Centennial in situ Observation-Based Estimates of the Variability of SST and Marine Meteorological Variables version 2' (COBE)</li> </ul> </li> <li>`LIM5000_ERSST-globalSST_prec-anoms-aus_monthly.nc` <ul> <li>contains 5000 years of emulated Australian precipitation variability, modelled using Australian rainfall data from the AGCD and global SST data from US National Oceanic and Atmospheric Administration 'Extended Reconstruction SST version 5’ (ERSST)</li> </ul> </li> <li>`LIM5000_COBE-globalSST_SST-anoms-global_monthly.nc` <ul> <li>contains 5000 years of emulated global SST variability, modelled using global SST data from COBE</li> </ul> </li> <li>`LIM5000_ERSST-globalSST_SST-anoms-global_monthly.nc` <ul> <li>contains 5000 years of emulated global SST variability, modelled using global SST data from ERSST</li> </ul> </li> </ul> <p><em>Tropical Pacific Ocean LIMs</em></p> <ul> <li>`LIM5000_COBE-TropicalPacificSST_prec-anoms-aus_monthly.nc` <ul> <li>contains 5000 years of emulated Australian precipitation variability, modelled using Australian rainfall data from the AGCD and tropical Pacific Ocean SST data from COBE</li> </ul> </li> <li>`LIM5000_ERSST-TropicalPacificSST_prec-anoms-aus_monthly.nc` <ul> <li>contains 5000 years of emulated Australian precipitation variability, modelled using Australian rainfall data from the AGCD and tropical Pacific Ocean SST data from ERSST</li> </ul> </li> <li>`LIM5000_COBE-TropicalPacificSST_SST-anoms-TropicalPacific_monthly.nc` <ul> <li>contains 5000 years of emulated global SST variability, modelled using tropical Pacific Ocean SST data from COBE</li> </ul> </li> <li>`LIM5000_ERSST-TropicalPacificSST_SST-anoms-TropicalPacific_monthly.nc` <ul> <li>contains 5000 years of emulated global SST variability, modelled using tropical Pacific Ocean SST data from ERSST</li> </ul> </li> </ul> <p><em>Indian Ocean LIMs</em></p> <ul> <li>`LIM5000_COBE-IndianOceanSST_prec-anoms-aus_monthly.nc` <ul> <li>contains 5000 years of emulated Australian precipitation variability, modelled using Australian rainfall data from the AGCD and Indian Ocean SST data from COBE</li> </ul> </li> <li>`LIM5000_ERSST-IndianOceanSST_prec-anoms-aus_monthly.nc` <ul> <li>contains 5000 years of emulated Australian precipitation variability, modelled using Australian rainfall data from the AGCD and Indian Ocean SST data from ERSST</li> </ul> </li> <li>`LIM5000_COBE-IndianOceanSST_SST-anoms-TropicalPacific_monthly.nc` <ul> <li>contains 5000 years of emulated global SST variability, modelled using Indian Ocean SST data from COBE</li> </ul> </li> <li>`LIM5000_ERSST-IndianOceanSST_SST-anoms-TropicalPacific_monthly.nc` <ul> <li>contains 5000 years of emulated global SST variability, modelled using Indian Ocean SST data from ERSST</li> </ul> </li> </ul> <p><strong>How to cite this</strong> <strong>repository</strong></p> <p>If using this data, please cite the original publication, available from <a href="https://www.sciencedirect.com/science/article/pii/S2212094724000951" target="_blank" rel="noopener">https://www.sciencedirect.com/science/article/pii/S2212094724000951.</a> </p>
Spatiotemporal analysis of plankton drivers in the Belgian part of the North Sea. Data, scripts and model output
This archive contains the input data, R scripts and final results of a mechanistic model that uses near real-time data from the Belgian Part of the North Sea (2011-2017) to quantify the relative contributions of the bottom-up and top-down drivers in phytoplankton dynamics. Input data are zooplankton and phytoplankton abundances, nutrients, Sea Surface Temperature (SST), photosynthetically active radiation (PAR); from the LifeWatch data and infrastructure, funded by Research Foundation - Flanders (FWO). Water temperature data for one of the locations was obtained from Flemish Banks Monitoring Network at https://meetnetvlaamsebanken.be/. The R scripts are presented in a R Markdown file that can be executed in the Blue-Cloud Zoo and Phytoplankton EOV products Vlab at https://blue-cloud.d4science.org/web/zoo-phytoplankton_eov, operated by D4Science.org, www.d4science.org (Assante et al., 2019).
Data and codes for Landslide hazard spatiotemporal prediction based on data-driven models: Estimating where, when and how large landslide may be
<p>Data and codes for Landslide hazard spatiotemporal prediction based on data-driven models: Estimating where, when and how large landslide may be</p>
Data from: Spatiotemporal modeling reveals high-resolution invasion states in glioblastoma
<p>Diffuse invasion of glioblastoma cells through normal brain tissue is a key contributor to tumor aggressiveness, resistance to conventional therapies, and dismal prognosis in patients. A deeper understanding of how components of the tumor microenvironment (TME) contribute to overall tumor organization and to programs of invasion may reveal opportunities for improved therapeutic strategies. Towards this goal, we applied a novel computational workflow to a spatiotemporally profiled GBM xenograft cohort, leveraging the ability to distinguish human tumor from mouse TME to overcome previous limitations in analysis of diffuse invasion. Our analytic approach, based on unsupervised deconvolution, performs reference-free discovery of cell types and cell activities within the complete GBM ecosystem. We present a comprehensive catalogue of 15 tumor cell programs set within the spatiotemporal context of 90 mouse brain and TME cell types, cell activities, and anatomic structures. Distinct tumor programs related to invasion were aligned with routes of perivascular, white matter, and parenchymal invasion. Furthermore, sub-modules of genes serving as program hubs were highly prognostic in GBM patients. The compendium of programs presented here provides a basis for rational targeting of tumor and/or TME components. We anticipate that our approach will facilitate an ecosystem-level understanding of immediate and long-term consequences of such perturbations, including identification of compensatory programs that will inform improved combinatorial therapies.</p>
Data from:Modelling the spatiotemporal dynamics of soil nitrogen in croplands of Northeast China from 1980 to 2023 using multisource data and machine learning
<p>This dataset include the spatiotemporal distribution and uncertainty of cropland soil total nitrogen content at 0-30, 30-60, 60-100 cm depths in Northeast China from 1980 to 2023. The long-time series of TN were estimated by using an space-time automatic machine learning. The detail information on the products were given below:</p> <p>Period: 1980-2023</p> <p>Spatial resolution: 0.004166667 degree (~500 m)</p> <p>Temporal resolution: 1 year</p> <p>CRS: geographic latitude/longitude (EPSG:4326 - WGS 84 – Geographic)</p> <p>Data format: GeoTIFF</p>
S3GM: Learning spatiotemporal dynamics with a pretrained generative model
<h1>Datasets of Kuramoto-Sivashinsky equation (KSE) and Kolmogorov flow.</h1> <h2>Description of KSE data:</h2> <p>Each file for KSE datasets contains 4 dimensions in the following order: (B*V)*T*X*C. Details are listed in the following table:</p> <table> <tbody> <tr> <td>B</td> <td>number of varying initial conditions</td> </tr> <tr> <td>V</td> <td>number of varying parameters</td> </tr> <tr> <td>T</td> <td>number of temporal frames</td> </tr> <tr> <td>X</td> <td>spatial resolution</td> </tr> <tr> <td>C</td> <td>number of variables in solution (C = 1 for KSE)</td> </tr> <tr> <td>values of parameter used to generate <strong>training </strong>dataset</td> <td>1.0, 1.2, 1.4, 1.6, 1.8, 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, 3.6, 3.8, 4.0, 4.2, 4.4, 4.6, 4.8, 5.0</td> </tr> <tr> <td>values of parameter used to generate <strong>test </strong>dataset</td> <td>1.1, 2.5, 3.2</td> </tr> </tbody> </table> <h2>Description of Kolmogorov flow data:</h2> <p>Each file for Kolmogorov flow contains 5 dimensions inthe following order: (B*Re*K)*T*X*X*C. Details are listed in the following table:</p> <table> <tbody> <tr> <td>B</td> <td>number of varying initial conditions</td> </tr> <tr> <td>Re</td> <td>number of varying Reynolds numbers</td> </tr> <tr> <td>K</td> <td>number of varying source terms (controled by the value of k)</td> </tr> <tr> <td>T</td> <td>number of temporal frames</td> </tr> <tr> <td>X</td> <td>spatial resolution</td> </tr> <tr> <td>C</td> <td>number of variables in solution (C = 2 for Kolmogorov flow)</td> </tr> <tr> <td>values of Reynolds number used to generate <strong>training </strong>dataset</td> <td>100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050</td> </tr> <tr> <td>values of Reynolds number used to generate <strong>test </strong>dataset</td> <td> <div> <div>50, 125, 575, 1100, 1500</div> </div> </td> </tr> <tr> <td>values of k used to generate <strong>training </strong>dataset</td> <td>2, 3, 4, 5, 6, 7, 8</td> </tr> <tr> <td>values of k used to generate <strong>test </strong>dataset</td> <td> <div> <div>2, 4, 6, 8</div> </div> </td> </tr> </tbody> </table> <h2>Description of ERA5 data:</h2> <p>Training and testing dataset for ERA5 contains 5 dimensions inthe following order: 1*T*X*X*C, which is manually collected from <a href="https://cds.climate.copernicus.eu/datasets/reanalysis-era5-single-levels?tab=download">https://cds.climate.copernicus.eu/datasets/reanalysis-era5-single-levels?tab=download</a>. <strong>Note that the quantities in the datasets are already rescaled</strong> (the scale factors are saved in the scalar_era5.npy file, which is a 4x2 array recording the means and stds for the 4 quantities we used). Details are listed in the following table:</p> <table> <tbody> <tr> <td>T</td> <td>number of temporal frames</td> </tr> <tr> <td>X</td> <td>spatial resolution</td> </tr> <tr> <td>C</td> <td>number of variables in solution (C = 4 for ERA5)</td> </tr> <tr> <td>time span for <strong>training </strong>dataset</td> <td>1979-2022</td> </tr> <tr> <td>time span for <strong>test </strong>dataset</td> <td> <div> <div>2023</div> </div> </td> </tr> </tbody> </table> <h2>Pretrained checkpoints:</h2> <p>The .zip file contains the pretrained checkpoints for KSE, Kolmogorov flow and ERA5. Within the .zip file, the folder'kse_v0' is the checkpoint for KSE, 'kol_v0' is the checkpoint for Kolmogorov flow, and 'era5_v0' is the checkpoint for ERA5.</p> <h1><em>Source code:</em></h1> <p>The source code is upload as Github repository in <a href="https://github.com/lzy12301/S3GM">https://github.com/lzy12301/S3GM</a></p>
Data from: Modeling spatiotemporal abundance and movement dynamics using an integrated spatial capture-recapture movement model
<p>Animal movement is a fundamental ecological process affecting the survival and reproduction of individuals, the structure of populations, and the dynamics of communities. Methods to quantify animal movement and spatiotemporal abundances, however, are generally separate and thus omit linkages between individual-level and population-level processes. We describe an integrated spatial capture-recapture (SCR) movement model to jointly estimate (1) the number and distribution of individuals in a defined spatial region and (2) movement of those individuals through time. We applied our model to a study of polar bears (Ursus maritimus) in a 28,125 km<sup>2</sup> survey area of the eastern Chukchi Sea, USA in 2015 that incorporated capture-recapture and telemetry data. In simulation studies, the model provided unbiased estimates of movement, abundance, and detection parameters using a bivariate normal random walk and correlated random walk movement process. Our case study provided detailed evidence of directional movement persistence for both male and female bears, where individuals regularly traversed areas larger than the survey area during the 36-day study period. Scaling from individual- to population-level inferences, we found that densities varied from < 0.75 bears/625 km<sup>2</sup> grid cell/day in nearshore cells to 1.6–2.5 bears/grid cell/day for cells surrounded by sea ice. Daily abundance estimates ranged from 53–69 bears, with no trend across days. The cumulative number of unique bears that used the survey area increased through time due to movements into and out of the area, resulting in an estimated 171 individuals using the survey area during the study (95% credible interval 124–250). Abundance estimates were similar to a previous multi-year integrated population model using capture-recapture and telemetry data (2008–2016; Regehr et al. 2018). Overall, the SCR-movement model successfully quantified both individual- and population-level space use, including the effects of landscape characteristics on movement, abundance, and detection, while linking the movement and abundance processes to directly estimate density within a prescribed spatial region and temporal period. Integrated SCR-movement models provide a generalizable approach to incorporate greater movement realism into population dynamics and link movement to emergent properties including spatiotemporal densities and abundances.</p>
Spatiotemporal Modeling of Mitochondrial Network Architecture
<p>Mitochondrial fusion events and their classification into three categories (tip-tip, tip-side, side-side) acquired on widefield, confocal, instant structured illumination and structured illumination microscopes.</p> <p>This data was used as comparison to modelled, theoretical fusion rates and their contributions to the maintenance of mitochondrial network morphologies.</p>
Supporting data ocean model GMD submission: From Weather Data to River Runoff: Leveraging Spatiotemporal Convolutional Networks for Comprehensive Discharge Forecasting
<p>Ocean model salinity data used for the comparison of the ConvLSTM river runoff model and the original E-HYPE based model simulations.</p>
Conditional Neural Field Latent Diffusion Model for Generating Spatiotemporal Turbulence
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