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54 results for “network heterogeneity”
Data belonging to: Teurlincx, S., Verhofstad, M. J., Bakker, E. S., & Declerck, S. A. (2018). Managing successional stage heterogeneity to maximize landscape-wide biodiversity of aquatic vegetation in ditch networks. Frontiers in plant science, 9, 1013.
<p>Data belonging to the paper Teurlincx, S., Verhofstad, M. J., Bakker, E. S., & Declerck, S. A. (2018). Managing successional stage heterogeneity to maximize landscape-wide biodiversity of aquatic vegetation in ditch networks. Frontiers in plant science, 9, 1013.</p> <p>Data includes analysis scripts (R Language) and all used data files. Data is composed of location information of the different sites, environmental conditions on site and vegetation composition.</p>
Spectral decompositions dataset for the paper "Random walk informed heterogeneities detection reveals how the lymph node conduits network influences T-cells collective exploration behavior"
<p>This file contains the left and right approximated eigenvectors, as well as the approximated eigenvalues of the networks analyzed in the paper : Random walk informed heterogeneities detection reveals how<br> the lymph node conduits network influences T-cells collective<br> exploration behavior</p>
Dataset from: Spatially heterogeneous shifts in vegetation phenology induced by climate change threaten the integrity of the avian migration network
<p>Original data and code for the study:</p> <p>Wei, J., Xu, F., Cole, E. F., Sheldon, B. C., de Boer, W. F., Wielstra, B., Fu, H., Gong, P., & Si, Y. (2024, Accepted). Spatially heterogeneous shifts in vegetation phenology induced by climate change threaten the integrity of the avian migration network. Global Change Biology.</p> <p>The dataset mainly contains data showing the climate change-induced heterogeneous shifts in vegetation phenology and the migration integrity change from 2000 to 2020 for 16 Asian herbivorous waterfowl species. These data were derived from the following resources available in the public domain.</p> <p>The Global Lakes and Wetlands Database is available from “https://www.worldwildlife.org/pages/global-lakes-and-wetlands-database”. The global land cover datasets are available from European Space Agency (ESA) Climate Change Initiative (CCI) products, “https://maps.elie.ucl.ac.be/CCI/viewer/download.php”. The Global Multi-resolution Terrain Elevation Data are available from “https://www.usgs.gov/centers/eros/science/terrain-monitoring-and-modeling”. The Moderate Resolution Imaging Spectroradiometer (MODIS) Terra surface reflectance product is available from “https://modis.gsfc.nasa.gov/data/dataprod/mod09.php”. The bird distribution maps are available from Birdlife International, “https://www.birdlife.org/”. The bird foraging attribute data are available from EltonTraits 1.0, “https://figshare.com”. The bird occurrence data are available from eBird Basic Dataset (EBD), “https://science.ebird.org/en/use-ebird-data/download-ebird-data-products”. The Hackett backbone phylogenetic trees are available from “https://birdtree.org/”.</p> <p>The code contains the R scripts and MATLAB scripts that we used for this study.</p> <p>For details please see the file “Readme.txt”, and the research paper.</p>
Data Set for the Journal Article "Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis"
<p>This dataset includes the XYZ structures of the centroids of all compounds found. Charge and multiplicity are given in the comment line of each XYZ file.</p>
PGB: A PubMed Graph Benchmark for Heterogeneous Network Representation Learning
<p>PubMed Graph Benchmark (PGB) aggregates the metadata associated with the biomedical articles from PubMed into a unified source. The benchmark contains metadata including title, abstract, authors, in/out citations, MeSH terms, MeSH hierarchy, venue, publication type, and chemicals.</p>
Code from: Spatial resource heterogeneity stabilizes local and regional predator-prey dynamics in ecologically-realistic networks
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Dataset for publication "Spectral graph theory efficiently characterises ventilation heterogeneity in airway networks".
<p>This directory contains files for the tree networks used in the manuscript "Spectral graph theory efficiently characterises ventilation heterogeneity in airway networks" by C Whitfield et al. Publication details to follow.</p> <p>Each folder contains the network as labelled in the paper in two formats:<br> - .vtk format<br> - plain text format where it is split into 3 files with suffixes .branches .nodes and .termnodes<br> - The .nodes file has 4 columns, the first is the node index and the other 3 are the (x,y,z) node coordinates in mm<br> - The .branches file has 4 columns (ignoring extra info in following columns), which are the edge index, node in index, node out index and radius (mm)<br> - The .termnodes file contains a list of node indices corresponding to terminal nodes of the tree.</p> <p>Each folder also contains the CT centerline data (identified by the suffix _CT) in .vtk format.</p>
Computational modeling of hemoglobin saturation heterogeneity in capillary networks
<p>This repository contains the C++ code based on OpenFOAM used for simulating oxygen transport with moving red blood cells. The OpenFOAM cases used to generate all results in the research article "The heterogeneity of hemoglobin saturation in capillaries and its relation to red blood cell transit time" are included.</p> <p>The archive 'code-axisymmetric.tgz' contains the code for the simulations in axisymmetric domains. This code works with OpenFOAM 2.1.1.</p> <p>The archive 'code-parallel_capillaries.tgz' contains the code for the simulations with parallel capillaries. This code is based on OpenFOAM 2.3.0.</p> <p>The archive 'code-graph.tgz' contains the simulation code for the simulations in reconstructed capillary networks. The postprocessing and plotting script are also in this archive. This code is based on OpenFOAM 2.3.0.</p> <p>The archive 'code-flow_reconstruction.tgz' contains the code for the flow reconstruction algorithm.</p> <p>The remaining archives contain the OpenFOAM cases that were used to run the oxygen transport simulations reported in the research article "The Heterogeneity of Hemoglobin Saturation in Capillary Networks and its Relation to Red Blood Cell Transit Time".</p>
Forest structure and heterogeneity increase diversity and alter the composition of host-parasitoid networks
<p>Antagonistic host-parasitoid interactions can be quantified using bipartite and meta networks, which have the potential to reveal how habitat structural elements relate to this important ecosystem function. Here, we analysed the host-parasitoid interactions of cavity-nesting bees and wasps, as well as their abundance, diversity, and species richness with forest structural elements from 127 forest research plots in southwestern Germany. We found that parasitoid abundance, diversity, and species richness all increase with host abundance, a potential mediator between parasitoids and forest structure. Both parasitoid abundance and diversity increased with stand structural complexity, possibly mediated by the abundance of hosts. Additionally, parasitoid abundance increased with increasing standing deadwood and herb cover. The bipartite networks of host-parasitoid interactions showed higher connectance with increasing standing deadwood, herb cover, and host abundance. Analyses of interactions within the host-parasitoid metanetwork revealed that increasing host abundance and decreasing canopy cover diversify the suites of interactions present at the plot level. These results demonstrate that forest structural elements can improve the stability and resilience of host-parasitoid networks by promoting parasitoids and diversifying interactions in ecological networks.</p>
Appendix for the paper "Assessment of Aging and Rejuvenation for Resiliency in Heterogeneous Network Clusters"
<p><strong>Appendix for the paper "Alberto Avritzer, Andrea Janes, Andrea Marin, Andre van Hoorn, Matteo Camilli, Catia Trubiani, Daniel S. Menasché: Assessment of Aging and Rejuvenation for Resiliency in Heterogeneous Network Clusters"</strong></p> <p>This repository contains the complete set of charts for all core machines (in the paper, figures 3-8 contain only the results of one machine) and the collected data for each strategy.</p> <p><strong>Contents</strong></p> <p>The files contained in this appendix are:</p> <ul> <li>18 files of the format "experiment(strategy)(granularity).pdf, where "strategy" goes from -1 to 4 and granularity is one of i, dc, or dp (see table I in the paper).</li> <li>18 files of the format "output-(strategy)(granularity).csv, with the same format as the files above, containing the raw data.</li> </ul>
A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods
<p>This repository contains all the datasets used for benchmarking drug repositioning methods based on heterogeneous networks, including drug-drug similarity, disease-disease similarity, and drug-disease associations.</p> <p>The repository consists of:</p> <ol> <li>Name or keyword information for drugs and diseases information contained in the dataset</li> <li>Inputs needed for different drug repositioning methods: multiple drug similarity matrices,multiple disease similarity matrices, and drug-disease associations matrices.</li> </ol> <p> </p> <p> </p> <blockquote> <p><strong>Please cite us :</strong><br>Yinghong Li, Yinqi Yang, Zhuohao Tong, Yu Wang, Qin Mi, Mingze Bai, Guizhao Liang, Bo Li, Kunxian Shu, A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods, <em>Briefings in Bioinformatics</em>, Volume 25, Issue 3, May 2024, bbae172, <a href="https://doi.org/10.1093/bib/bbae172">https://doi.org/10.1093/bib/bbae172</a></p> </blockquote>
Forest structure and heterogeneity increase diversity and alter the composition of host-parasitoid networks
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Data from: Within-reach temperature heterogeneity is limited in a southern Appalachian stream network, southeastern USA
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Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction
<p>We include samples of various data types used in the work "Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction"</p> <p>More information about the software package and instructions are provided in <a href="https://github.com/hallamlab/pathway2vec">hallamlab/pathway2vec</a></p>
Data of A recurrent neural network-accelerated multi-scale model for elasto-plastic heterogeneous materials subjected to random cyclic and non-proportional loading paths
<pre>Data related to the publication (we would be grateful if you could cite the paper in the case in which you are using the data) title = "A recurrent neural network-accelerated multi-scale model for elasto-plastic heterogeneous materials subjected to random cyclic and non-proportional loading paths", journal = "Computer Methods in Applied Mechanics and Engineering", pages = " 113234", year = "2020", issn = "0045-7825", doi = "https://doi.org/10.1016/j.cma.2020.113234", author = "Wu, Ling and Nguyen, Van Dung and Kilingar, Nanda Gopala and Noels, Ludovic"</pre>
Data for "CryoDRGN: Reconstruction of heterogeneous cryo-EM structures using neural networks"
<p>Trained models and reconstructed density maps for:</p> <ul> <li>EMPIAR-10028: "Cryo-EM structure of a <em>Plasmodium falciparum</em> 80S ribosome bound to the anti-protozoan drug emetine" from Wong et al. (2014)</li> <li>EMPIAR-10049: "Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures" from Ru et al. (2015)</li> <li>EMPIAR-10076: "Modular assembly of the large bacterial ribosome" from Davis et al. (2016)</li> <li>EMPIAR-10180: "Structure of a pre-catalytic spliceosome" from Plaschka et al. (2017)</li> </ul> <p>Synthetic datasets with simulated heterogeneity and their ground truth density maps, poses, and labels:</p> <ul> <li>Uniform: 50k particle images (128x128, 6A/pix) uniformly sampled from 50 models along a 1-dimensional reaction coordinate</li> <li>Cooperative: 50k particle images (128x128, 6A/pix) sampled along the above reaction coordinate according to a 3-component Gaussian mixture model with overlapping components </li> <li>Noncontiguous: 50k particle images (128x128, 6A/pix) sampled along the above reaction coordinate according to a 3-component Gaussian mixture model without overlapping components</li> <li>Ribosomes: 50k particle images (128x128, 3A/pix) containing a mixture of 30S, 50S, 70S ribosomes simulating compositional heterogeneity</li> </ul>
Dataset of the paper "Modeling the Flow and Geomorphic Heterogeneity Induced by Salt Marsh Vegetation Patches Based on Convolutional Neural Network UNet-Flow"
<p>Modeling the Flow and Geomorphic Heterogeneity Induced by Salt Marsh Vegetation Patches Based on Convolutional Neural Network UNet-Flow</p>
Pan-cancer networks for TREE, including six homogeneous and two heterogeneous networks
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DMGAT: Predicting ncRNA-Drug resistance associations based on diffusion map and heterogeneous graph attention network
<p>Dataset for the paper: DMGAT: Predicting ncRNA-Drug resistance associations based on diffusion map and heterogeneous graph attention network</p>
Exploring functional flow heterogeneity in regulated flow regime: fish species turnover along hydraulic gradients in an artificial waterway network
<p><span>Humans have altered river flows and lateral aquatic habitats. The expansion of agriculture in floodplains has resulted in landscapes dominated by irrigated farmland. A key challenge in water management is to conserve existing ecological communities and habitat heterogeneity, while simultaneously maintaining engineered infrastructure for agriculture. In this study, we focused on an artificial channel network for irrigation with a regulated flow regime and its function as habitat for various fish species. Differences of hydraulic conditions among channels and compositional changes in fish species were examined to clarify functional flow heterogeneity. Species turnover was analyzed using pairwise Simpson dissimilarity among sampling reaches. Species turnover was positively associated with Froude number (flow intensity) differences at intermediate discharges, and with differences in cross-sectional areas (flow magnitude) at low discharges. Drastic changes in inflows should be considered for the effective conservation of flow heterogeneity, even under a regulated flow regime. Improved engineering design to manage the hydraulic environment is one option for maintaining the ecological value of lateral waterbodies in human-dominated landscapes. Our findings provide insights into the importance of functional flow heterogeneity to conserve fish species diversity.</span></p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.