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308 results for “Dynamic Network”
Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome
<p>This is the repository associated with the manuscript <strong>Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome</strong>. It contains all data files used for figures presented in the manuscript. The code to reproduce the files can be found on <a href="https://github.com/SushiLab/coralmicrobiome-hostbiodiversity)">GitHub</a>.</p> <p> </p> <h2>Files</h2> <p><br><code>raw_host-associated_1.asvs.tsv --> ASV table, host-associated samples</code><br><code>raw_host-associated_2.asvs.tsv --> ASV table, host-associated samples</code><br><code>raw_free-living_1.asvs.tsv --> ASV table, Sterivex samples</code><br><code>raw_free-living_2.asvs.tsv --> ASV table, Sterivex samples</code><br><code>metadata_host-associated.csv --> metadata, host-associated samples</code><br><code>metadata_free-living.csv --> ASV table, Sterivex samples</code><br><code>asv_dat_taxinfo.tsv --> taxonomy annotated using SILVA v138.1</code><br><code>asv_bctab.tsv --> square-root transformed Bray-Curtis dissimilarities </code><br><code>asv_richtab.tsv --> Hill number diversity indices</code><br><code>asv_shared.tsv --> number of shared ASVs</code><br><code>pathway_list_cat.csv --> KEGG pathway list with hand-annotated categories</code><br><code>KEGG_path_to_ko.tsv --> KEGG file mapping pathways to KOs</code></p> <p> </p>
Patch size distribution affects species invasion dynamics in dendritic networks
<div class="page"> <div class="section"> <div class="layoutArea"> <div class="column"> <p>Biological invasions are globally affecting ecosystems, causing local species loss and altering ecosystem functioning. Understanding how such biological invasions occur and succeed is thus of high priority. Both local properties and the spatial network structure have been shown to be determinants of invasion success, and the identification of spatial invasion hubs directly promoting invasion dynamics is gaining attention. Spatial dynamics, however, could also indirectly alter invasion success by shaping pre- invasion local community structure: in many ecosystems, such as riverine networks, regional properties such as patch size distribution are known drivers of local community structures, which themselves may affect the establishment success of invading species. Using microcosm experiments in dendritic networks, we disentangled how inherent patch size distribution and dispersal along specific network topologies shaped local resident communities, and, subsequently, affected the establishment success of invading species. After controlling for regional-scale effects of connectivity on pre-invasion diversity, we find that patch size distributions independently shaped pre-invasion community diversity and invasion success, with no direct effect of pre-invasion diversity on invasion success. Our results suggest that 1) landscape configuration plays an underestimated role in invasion success and that 2) invasion success should follow predictable landscape-scale patterns in riverine networks given non-random patch-size distribution.</p> </div> </div> </div> </div>
The appendix for dynamic model of respiratory infectious disease transmission by population mobility based on city network
<p>First, a scale-free city network was established, and the shortest path between any two nodes was determined. Second, the movement path of tourists was designed based on the shortest path. Subsequently, every infected person's information, such as the city, infection time, onset, and hospitalisation, was confirmed based on their movement path. Third, the features of the transmission path and time distribution of the epidemic were characterised after summarising the information. Finally, the reliability of the model was verified.</p>
Alien plants and flower visitors disrupt the seasonal dynamics of mutualistic networks - Dataset
<p>Dataset associated with the manuscript "Alien plants and flower visitors disrupt the seasonal dynamics of mutualistic networks" (Arroyo-Correa et al. 2019)</p>
Supplementary Data:Risk Analysis for Real-time Flood Control Operation of a Multi-reservoir System Using a Dynamic Bayesian Network
<p>The files in this record contain data for risk analysis for real-time flood control operation of a multi-reservoir system using a dynamic bayesian network considered for publication in Water Resources Research.</p> <p>The files consist of:</p> <ul> <li>Reservoir data and river flood routing parameters</li> <li>Flood data</li> <li>Code and results of the Monte Carlo simulations</li> <li>Code and results of the Bayesian network</li> </ul>
supplementary tables for 'The dynamic landscape of competing endogenous RNA (ceRNA) network in Early-Onset Preeclampsia under hypoxia condition '
Open the record for dataset details and reuse information.
Data for the "Systems NMR: simultaneous quantification of RNA, protein, and metabolite reaction dynamics for biomolecular network analysis."
<p>This dataset contains raw NMR data used in the publication.</p> <p>Detailed protocol for the presented NMR setup and analysis is included in the publication, and at https://github.com/systemsnmr/ivtnmr.</p> <p>v0.2 includes the integr_results_31P_pure_PO4.txt files - phosphate-spectra integration files which were missing in v0.1 submission.</p>
Fig. 2 Mitochondrial haplotype network using the 590 in Differentiation of North African foxes and population genetic dynamics in the desert-insights into the evolutionary history of two sister taxa, Vulpes rueppellii and Vulpes vulpes
Fig. 2 Mitochondrial haplotype network using the 590-bp concatenated sequences from Cyt-b and D-loop and a total of 46 sequences (same as in Fig. 1, except for C. lupus not being used as an outgroup in the TCS network). a Neighbour-Net network based on uncorrected patristic distances as implemented in SPLITSTREE. Canis lupus (DQ480504) was used as an outgroup. Numbers indicate bootstrap values. Scale bar represents 0.01 sequence divergence. Highlighoed are the four species, the three V. vulpes clades and the location within the network of the V. vulpes sample from Egypt. Colour patterns are concordant with Fig. 1 and b. b Statistical parsimony network assuming a 95 % parsimony threshold, as constructed by TCS. Symbol size and branch lengths are proportional to the number of shared individuals per haplotype and the number of mutational steps amongst haplotypes, respectively. Numbers in black background also refer to the number of mutation steps between species and V. vulpes clades. Symbols and colours are concordant with Fig. 1 and a. Haplotype codes, sample origin and corresponding accession numbers are available in Online Resource Table S1
Multi-omics with dynamic network biomarker algorithm prefigures organ-specific metastasis of lung adenocarcinoma
<p><span>Efficacious strategies for early detection of lung cancer metastasis are of significance for improving the survival of lung cancer patients. Utilizing two clinical cohorts of four major types of lung cancer distant metastases, with single-cell RNA sequencing (scRNA-seq) of primary lesions and liquid chromatography mass spectrometry data of sera, we identified the marker genes and serum secretome foreshadowing the lung cancer site-specific metastasis through dynamic network biomarker (DNB)</span> <span>algorithm. Also, we located the intermediate status of cancer cells, along with its gene signatures, in each metastatic state trajectory that cancer cells at this stage still had no specific organotropism. Furthermore, an integrated neural network model based on the filtered scRNA-seq data was successfully constructed and validated to predict the metastatic state trajectory of cancer cells. Overall, our study provided a new insight to locate the pre-metastasis status of lung cancer and primarily examined its clinical application value, contributing to the early detection of lung cancer metastasis in a more feasible and efficacious way.</span></p>
Graph neural network emulator for modeling of ice dynamics and calving in the Pine Island Glacier, Antarctica
<p>These files include the following codes and datasets for developing graph neural network (GNN) emulators for the Ice-sheet and Sea-level System Model (ISSM) for modeling ice sheet dynamics and calving in the Pine Island Glacier, Antarctica</p> <ul> <li>ISSM_DGL_PIG2.py: Python file for training GNN models (*single.py: code for single GPU environment)</li> <li>ISSM_CNN_PIG.py: Python file for training convolutional neural network (CNN) models</li> <li>*.mat: Datasets of the ISSM transient simulation results (graphs for GNNs)</li> <li>*.pkl: Datasets of the ISSM transient simulation results (grids for CNNs)</li> </ul>
Data for "Learning Collective Cell Migratory Dynamics from a Static Snapshot with Graph Neural Networks"
<p>This dataset contains snapshots of cell monolayers, represented as graphs, along with their corresponding average displacement measurements.</p>
Information diffusion assumptions can distort our understanding of social network dynamics (code and data)
<p>This repository contains the data (<code>cascade_reconstruction.tar.gz</code>) and code (<code>code_repository.tar.gz</code>) for a paper titled "Information diffusion assumptions can distort our understanding of social network dynamics" by <a href="https://www.matthewdeverna.com/">Matthew R. DeVerna</a>, <a href="https://pierri.faculty.polimi.it/">Francesco Pierri</a>, <a href="https://rachithaiyappa.github.io/">Rachith Aiyappa</a>, <a href="https://diogofpacheco.github.io/">Diogo Pachecho</a>, <a href="https://jbryden.co.uk/home/">John Bryden</a>, and <a href="https://cnets.indiana.edu/fil">Filippo Menczer</a> .</p> <p>Please see the README.md file for important details! If you would like to report issues with the code, you can do so through an associated GitHub repository that houses the project's code, which can be found <a href="https://github.com/osome-iu/cascade_reconstruction">here</a>.</p>
Data from: Disentangling invasion processes in a dynamic shipping - boating network
The relative importance of multiple vectors to the initial establishment, spread, and population dynamics of invasive species remains poorly understood. This study used molecular methods to clarify the roles of commercial shipping and recreational boating in the invasion by the cosmopolitan tunicate, Botryllus schlosseri. We evaluated i) single vs. multiple introduction scenarios, ii) the relative importance of shipping and boating to primary introductions, iii) the interaction between these vectors for spread (i.e., the presence of a shipping-boating network), and iv) the role of boating in determining population similarity. Tunicates were sampled from 26 populations along the Nova Scotia, Canada, coast that were exposed to either shipping (i.e., ports), or boating (i.e., marinas) activities. A total of 874 individuals (~30 per population) from 5 ports and 21 marinas was collected and analyzed using both mitochondrial cytochrome c oxidase subunit I gene (COI) and 10 nuclear microsatellite markers. The geographical location of multiple hotspot populations indicates that multiple invasions have occurred in Nova Scotia. A loss of genetic diversity from port to marina populations suggests a stronger influence of ships than recreational boats on primary coastal introductions. Population similarity analysis reveals a clear dependence of marina populations on those that had been previously established in ports and connectivity due to a boating network better explains patterns in population similarities than does natural spread. We conclude that frequent primary introductions arise by ships and that secondary spread occurs gradually thereafter around individual ports, facilitated by recreational boating.
Data from: Recurrent circuit dynamics underlie persistent activity in the macaque frontoparietal network
<p>During delayed oculomotor response tasks, neurons in the lateral intraparietal area (LIP) and the frontal eye fields (FEF) exhibit persistent activity that reflects the active maintenance of behaviorally relevant information. Despite many computational models of the mechanisms of persistent activity, there is a lack of circuit-level data from the primate to inform the theories. To fill this gap, we simultaneously recorded ensembles of neurons in both LIP and FEF while macaques performed a memory-guided saccade task. A population encoding model revealed strong and symmetric long-timescale recurrent excitation between LIP and FEF. Unexpectedly, LIP exhibited stronger local functional connectivity than FEF, and many neurons in LIP had longer network and intrinsic timescales. The differences in connectivity could be explained by the strength of recurrent dynamics in attractor networks. These findings reveal reciprocal multi-area circuit dynamics in the frontoparietal network during persistent activity and lay the groundwork for quantitative comparisons to theoretical models.</p>
Additional data "Client binding shifts the populations of dynamic Hsp90 conformations through an allosteric network"
<p>Additional data containing chemical shift perturbations and intensity changes of Hsp90 upon client binding, intermolecular PREs, and raw scattering data of Hsp90-client complexes.</p>
Single-cell RNA sequencing of Sox17-expressing lineages reveals distinct gene regulatory networks and dynamic developmental trajectories
<p>Two seurat objects contains single-cell RNA sequencing data that captures <em>Sox17</em>-expressing lineages during embryogenesis.</p> <p>sox17_integrated_Figure2B.rds :</p> <p>This is a seurat object that contains single-cell RNA sequencing data from integration of GFP+ cells produced from <em>Sox17<sup>GFPCre</sup></em> allele marking cells that currently express <em>Sox17</em> or short-term progeny of <em>Sox17­-</em>expressing progenitors and TdTomato+ cells produced from <em>R26<sup>LSL.TdTomato</sup></em> reporter allele in the presence of <em>Sox17<sup>GFPCre</sup></em> marking long-term progeny of <em>Sox17</em>-expressing progenitors. Inferred cell types in this seurat object reflects Figure 2B in the article.</p> <p>sox17_Prox1_endoderm_Figure5A.rds :</p> <p>This is a seurat object that contain single-cell RNA sequencing data from integration of <em>Sox17</em>- and <em>Prox1</em>-expressing endoderm dataset. Prox-1 expressing endoderm data is from the Willnow et al. <em>Nature</em>(2021). Inferred cell types in this seurat object reflects Figure 5A in the article.</p>
Data set for Dynamic Service Restoration of Distribution Networks with Volt-Var Devices, Distributed Energy Resources, and Energy Storage Systems
<p>Data for three power distribution systems are presented in this document. The first system consists of 53 nodes and 61 branches. The second is composed of 217 nodes and 219 branches. Finally, the third system consists of 404 nodes and 430 branches. Both distribution systems offer extensive applications in problems related to multi-time service restoration, Volt/Var devices, and distributed energy resource operation.</p>
Cell-Penetrating Dynamic-Covalent Benzopolysulfane Networks - Raw data
<p>Raw data</p>
Multimodal Investigation of Cortico-Basal Ganglia-Thalamo-Cortical Network Dynamics in Dystonic Patients with Deep Brain Stimulation
ClinicalTrials.gov study NCT06716983. IPD Sharing: Not stated. Countries: 1. Publications: 13.
Mindful Network Dynamics Regulation Under Stress
ClinicalTrials.gov study NCT05541263. IPD Sharing: YES. Countries: 1. Publications: 6.
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.