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63 results for “directed network”
Algebraic invariants for inferring 4-leaf semi-directed phylogenetic networks
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Optimal mechanical interactions direct multicellular network formation on elastic substrates
<p>Cells self-organize into functional, ordered structures during tissue morphogenesis, a process that is evocative of colloidal self-assembly into engineered soft materials. Understanding how intercellular mechanical interactions may drive the formation of ordered and functional multicellular structures is important in developmental biology and tissue engineering. Here, by combining an agent-based model for contractile cells on elastic substrates with endothelial cell culture experiments, we show that substrate deformation–mediated mechanical interactions between cells can cluster and align them into branched networks. Motivated by the structure and function of vasculogenic networks, we predict how measures of network connectivity like percolation probability and fractal dimension as well as local morphological features including junctions, branches, and rings depend on cell contractility and density and on substrate elastic properties including stiffness and compressibility. We predict and confirm with experiments that cell network formation is substrate stiffness dependent, being optimal at intermediate stiffness. We also show the agreement between experimental data and predicted cell cluster types by mapping a combined phase diagram in cell density substrate stiffness. Overall, we show that long-range, mechanical interactions provide an optimal and general strategy for multicellular self-organization, leading to more robust and efficient realizations of space-spanning networks than through just local intercellular interactions.</p>
Trophic rewilding benefits a tropical community through direct and indirect network effects
Species reintroductions can be used as a conservation strategy to restore ecological interactions and the functionality of impoverished ecosystems. The ecological effects of reintroductions go beyond restoring pairwise interactions, because reintroductions can change how extant species are indirectly linked to each other in an ecological community. These indirect pathways, in turn, may shape a myriad of ecological and evolutionary processes operating in ecological systems. Here, we investigated how reintroductions may affect the direct and indirect pathways connecting species in ecological networks. We modeled the potential effects of the reintroduction of four frugivore species (channel-billed toucans, red-humped agoutis, brown howler monkeys and yellow-footed tortoises) to the local seed dispersal network in an Atlantic Forest site, the Tijuca National Park (Tijuca, Brazil). We used a seed dispersal interaction dataset together with data on species occurrences in Tijuca to build network models. Then, we calculated how network structure and the total amount of indirect effects varied across simulated networks with and without the reintroduced species. Using random reintroduction simulations, we tested if the observed network changes were expected merely from the increase in species richness. The reintroduction of the frugivore species increased network connectance, nestedness, robustness, number of pathways and total amount of indirect effects in all simulated networks. The increase in number of pathways with the addition of the four reintroduced species was greater than the sum of isolated effects for each species, as some interaction pathways contained several reintroduced species. These changes in network metrics were significantly greater than if a randomly chosen set of four species were reintroduced. Furthermore, our results indicate that multiple reintroductions in the same area, known as refaunation, may have an even greater restoration effect than single species reintroductions through increased indirect connections in the network.
Direct observation of a dynamical glass transition in a nanomagnetic artificial Hopfield network
<p>Source files used to produce the publication "Direct observation of a dynamical glass transition in a nanomagnetic artificial Hopfield network."</p>
Different functional networks underlying human walking with pulling force fields acting in forward or backward directions
<p><span>Walking with pulling force fields acting at the body center of mass (in </span><span>the </span><span>forward or backward directions) is compatible with inclined walking and is used in clinical practice for gait training. From the perspective of known differences in the motor strategies that underlie walking with the respective force fields, the present study elucidated whether the adaptation acquired by walking on a split-belt treadmill with either one of the force fields affects subsequent walking in other directions. Walking with the force field induced an adaptive and de-adaptive behavior of the subjects</span><span>, with the aspect evident </span><span>in the anterior breaking and posterior propulsive impulses of the ground reaction force as parameters. In the parameters, </span><span>the </span><span>adaptation acquired during walking with </span><span>a force field </span><span>acting in one direction was transferred to that in </span><span>the opposite direction only partially. </span><span>Furthermore, </span><span>the adaptation that occurred </span><span>while walking in </span><span>a force field </span><span>in one direction was rarely washed out by subsequent walking in </span><span>a force field </span><span>in </span><span>the opposite direction</span> <span>and thus was maintained independently of the other</span><span>. These results demonstrated possible independence in the neural functional networks capable of controlling walking in each movement task with </span><span>an opposing force field</span><span>.</span></p>
Supplementary data from: Bimodal retrograde signaling disrupts a suppressor network and activates a key transcriptional activator to direct stress responses
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Optimal mechanical interactions direct multicellular network formation on elastic substrates
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Different functional networks underlying human walking with pulling force fields acting in forward or backward directions
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Trophic rewilding benefits a tropical community through direct and indirect network effects
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Data from: Social network analysis shows direct evidence for social transmission of tool use in wild chimpanzees.
Claims of culture in animals have been stimulated by studies on a wide range of taxa revealing group-specific behavior patterns that remain stable through generations, consistent with different behavioral innovations spreading within groups by social transmission in a manner similar to human culture. In chimpanzees, 39 behaviors have been identified as 'cultural', because alternative genetic and environmental explanations for the observed regional variation appear less plausible. This interpretation is supported by experimental data from captive chimpanzee groups. However, there is no experimental evidence for social learning in the wild, nor has there been direct observation of social diffusion of spontaneously occurring behavioral innovations. Here, we document the spread of two novel tool-use variants, 'moss-sponging' and 'leaf-sponge re-use', in the Sonso chimpanzee community of Budongo Forest, Uganda. We use traditional network-based diffusion analysis (NBDA) to test whether these novel behaviors spread by social learning, as well as a newly developed dynamic version of NBDA, capable of capturing temporal aspects of acquisition, i.e. how each successive personal observations impact the subsequent acquisition of behavior. Both models provide strong evidence that diffusion patterns of moss-sponging, but not leaf-sponge re-use, are significantly better explained by social than asocial learning, therefore showing that wild chimpanzees socially learned moss-sponging from each other. The most conservative estimate of social transmission accounts for 85% of observed events with an estimated 11-fold increase in learning rate for each time a novice observed an informed individual performing moss-sponging. We conclude that group-specific behavioral variants in chimpanzees can be socially learned, suggesting this prerequisite for culture originated in a common ancestor of great apes and humans, long before the advent of modern humans.
Metadata - Direct C−H Arylation of Dithiophene-Tetrathiafulvalene: Tuneable Electronic Properties and 2D Self-Assembled Molecular Networks at the Solid/Liquid Interface
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FoS Co-occurrence networks related to 103 FoS, and Direct ancestors to emerging topics between 2001~2010
<p>FoS Co-occurrence networks related to 311 Level 0 and 1 FoS, and Direct ancestors to emerging topics between 2000~2010.</p> <p> </p> <p>graphs.7z contains python graph binary files, and Golden dataset.7z contains python list binary files.</p>
Dataset and results for paper: Predicting missing links in directed networks: An investment-profit index
<p>Dataset and raw results for paper: Predicting missing links in directed networks: An investment-profit index. File "All_indices_12_dataset.mat" contains results of all 9 indices in 12 datasets. File "IP_sigma_12_dataset.mat" contains AUC and precision values when parameter sigma changes in IP index.</p>
Tables of direct, indirect and networks estimates and Forests plots of pairwise comparisons for all secondary outcomes
<p>Supplementary File #12 for Cochrane review entitled: "Non-invasive respiratory support in preterm infants as primary mode: a network meta-analysis"</p>
The Study on Effect and Neural Network Mechanism of Transcranial Direct Current Stimulation for Sudden Deafness With Tinnitus
ClinicalTrials.gov study NCT05964725. IPD Sharing: Not stated. Countries: 1. Publications: 19.
Targeting Language-specific and Executive-control Networks With Transcranial Direct Current Stimulation in Logopenic Variant PPA
ClinicalTrials.gov study NCT03887481. IPD Sharing: Not stated. Countries: 1. Publications: 8.
Directed network analysis of 2-year-old and 4-year-old children
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Data from: Temporal dynamics of direct reciprocal and indirect effects in a host-parasite network
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Data from: Social network analysis shows direct evidence for social transmission of tool use in wild chimpanzees.
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Supplementary File 12: Tables of direct, indirect and networks estimates and Forests plots of pairwise comparisons for all secondary outcomes
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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.