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92 results for “network analyses”
Fig. 3. Haplotype network for E in Prevalence, molecular characterisation and phylogenetic analyses of hydatid cysts and cysticercus tenuicollis isolates and first report of E. canadensis (G6/G7) in wild boars in Bingol province, Türkiye
Fig. 3. Haplotype network for E. canadensis (G6/G7) using cox1 gene (616 bp) sequences of different countries. The E. canadensis (G6/G7) isolate obtained in this investigation (Hap_01) and the sequences identified as G7 in the Genbank database were utilized. Circle size relative to haplotype data set frequency. Each hatch mark is representative of one nucleotide change. Haplotypes formed by the isolates obtained in this study are marked with an asterisk.
Fig. 2. Haplotype network constructed using cox1 in Prevalence, molecular characterisation and phylogenetic analyses of hydatid cysts and cysticercus tenuicollis isolates and first report of E. canadensis (G6/G7) in wild boars in Bingol province, Türkiye
Fig. 2. Haplotype network constructed using cox1 (744 bp) gene sequences of T. hydatigena. Seven haplotypes formed by the T. hydatigena isolates obtained in this study: (Hap 1-Hap 7). Circle size relative to haplotype data set frequency. Each hatch mark is representative of one nucleotide change. Haplotypes formed by the isolates obtained in this study are marked with an asterisk.
Data from: Species-habitat networks reveal conservation implications that other community analyses do not detect
<p><span>Grassland restoration is an important conservation intervention supporting declining insect pollinators, particularly in threatened calcareous grassland landscapes. While restoration is often assessed using simple diversity or the similarity to a target community metrics, this can fail to represent key aspects of community reconstruction. Here, we compare a new method, species-habitat networks, with techniques previously relied upon to understand the process of pollinator community restoration. The species-habitat network approach reveals details relevant to insect conservation that are not visible using standard measures of species richness, abundance, community similarity or network metrics. For instance, a shared set of butterflies and bumblebees found in ancient extensively managed grassland, the target community for restoration, were more likely to inhabit previously disturbed grassland than recently disturbed or reverting grasslands. We propose that species-habitat networks should be part of the standard analytical toolkit assessing the effectiveness of restoration, particularly for mobile species such as insects.</span></p>
Dataset for Validation of a Qualification Procedure Applied to the Verification of Partial Discharge Analysers Used for HVDC or HVAC Networks
<p>Data set for the publication named: "Validation of a Qualification Procedure Applied to the Verification of Partial Discharge Analysers Used for HVDC or HVAC Networks"</p>
Data from: Species-habitat networks reveal conservation implications that other community analyses do not detect
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Data from: The functional roles of species in metacommunities, as revealed by metanetwork analyses of bird-plant frugivory networks
<p>Understanding how biodiversity and interaction networks change across environmental gradients is a major challenge in ecology. We integrated metacommunity and metanetwork perspectives to test species' functional roles in bird-plant frugivory interactions in a fragmented forest landscape in Southwest China, with consequences for seed dispersal. Availability of fruit resources both on and under trees created vertical feeding stratification for frugivorous birds. Bird-plant interactions involving birds feeding only on the tree or both on and under the tree (shared) had a higher centrality and contributed more to metanetwork organization than interactions involving birds feeding only under the tree. Moreover, bird-plant interactions associated with large-seeded plants disproportionately contributed to metanetwork organization and centrality. Consequently, on-the-tree and shared birds contributed more to metanetwork organization whereas under-the-tree birds were more involved in local processes. We would expect that species' roles in the metanetwork will translate into different conservation values for maintaining functioning of seed-dispersal networks.</p>
Analysing landscape effects on dispersal networks and gene flow with genetic graphs
<p>Graph-theoretic approaches have relevant applications in landscape genetic analyses. When species form populations in discrete habitat patches, genetic graphs can be used i) to identify direct dispersal paths followed by propagules or ii) to quantify landscape effects on multigenerational gene flow. However, the influence of their construction parameters remains to be explored. Using a simulation approach, we constructed genetic graphs using several pruning methods (geographical distance thresholds, topological constraints, statistical inference) and genetic distances to weight graph links (F<sub>ST</sub>, D<sub>PS</sub>, Euclidean genetic distances). We then compared the capacity of these different graphs to i) identify the precise topology of the dispersal network and ii) to infer landscape resistance to gene flow from the relationship between cost-distances and genetic distances. Although not always clear-cut, our results showed that methods based on geographical distance thresholds seem to better identify dispersal networks in most cases. More interestingly, our study demonstrates that a subselection of pairwise distances through graph pruning (thereby reducing the number of data points) can counter-intuitively lead to improved inferences of landscape effects on dispersal. Finally, we showed that genetic distances such as the D<sub>PS</sub> or Euclidean genetic distances should be preferred over the F<sub>ST</sub> for landscape effect inference as they respond faster to landscape changes.</p>
Data from: Latest Ordovician (Hirnantian) brachiopod faunal lists used for non-matric multidimensional scaling (NMDS) and network analyses
<p><span>A total of 107 brachiopod genera of Hirnantian age among 42 localities worldwide are compiled into a binary dataset (Table S1; presence =1, absence = 0). The majority of the faunal lists was derived from the well-screened Hirnantian brachiopod faunal data of Rong et al. (2020). In this study, the Hirnantian faunal lists are updated for the following localities: </span><span>Anticosti Island, eastern Canada; </span><span>Edgewood region, American Mid-Continent; </span><span>Mackenzie Mountains, northwestern Canada. D</span><span>etailed discussions on these faunal update and references are provided in the main paper (section on Paleobiogeography of the Mackenzie Mountains Hirnantian fauna). </span></p>
Network analyses reveal the role of large snakes in connecting feeding guilds in a species-rich Amazonian snake community
<p class="normal">In ecological communities, interactions between consumers and resources lead to the emergence of ecological networks and a fundamental problem to solve is to understand which factors shape network structure. Empirical and theoretical studies on ecological networks suggest predator body size is a key factor structuring patterns of interaction. Because larger predators consume a wider resource range, including the prey consumed by smaller predators, we hypothesized that variation in body size favors the rise of nestedness. In contrast, if resource consumption requires specific adaptations, predators are expected to consume distinct sets of resources, thus favoring modularity. We investigate these predictions by characterising the trophic network of a species-rich Amazonian snake community (62 species). Our results revealed an intricate network pattern resulting from larger species feeding on higher diversity of prey, promoting nestedness, and specific lifestyles feeding on distinct resources, promoting modularity. Species removal simulations indicated that the nested structure is favored mainly by the presence of five species of the family Boidae, which because of their body size and generalist lifestyles connect modules in the network. Our study highlights the particular ways traits affect the structure of interactions among consumers and resources at the community level.</p>
Analyses, data and figures related to: "Connecting ships: Using dendrochronological network analysis to determine the wood provenance of Roman-period river barges found in the Lower Rhine region and visualise wood use patterns"
<p>Analyses, data and figures related to: "Connecting ships: using dendrochronological network analysis to determine the wood provenance of Roman-period river barges found in the Lower Rhine region and to visualise patterns of wood use" by Ronald M. Visser (Saxion University of Applied Sciences, Deventer, the Netherlands) and Yardeni Vorst (Vorst wood research, Zaandam, the Netherlands) submitted to the International Journal of Wood Culture</p>
Machine Learning and Network Analyses Reveals Disease Subtypes of Pancreatic Cancer and their Molecular Characteristics
<p>Supplementary information for the thesis chapter: Machine Learning and Network Analyses Reveals Disease Subtypes of Pancreatic Cancer and their Molecular Characteristics</p>
5-bus system and a real 221-bus low voltage network in the UK for analysing phase unbalance impacts on aggregated flexibility
<p>Two case studies for modelling flexibility services in low voltage distribution networks and quantifying the impacts of voltage unbalance limits and phase coordination constraints. The cases are in the OpenDSS format (.dss).<br>More details in the GitHub repository: https://github.com/AndreyChurkin/3FlexAnalyser.jl</p>
Data from: Three-dimensional trajectories and network analyses of group behaviour within chimney swift flocks during approaches to the roost
Chimney swifts (Chaetura pelagica) are highly manoeuvrable birds notable for roosting overnight in chimneys, in groups of hundreds or thousands of birds, before and during their autumn migration. At dusk, birds gather in large numbers from surrounding areas near a roost site. The whole flock then employs an orderly, but dynamic, circling approach pattern before rapidly entering a small aperture en masse. We recorded the three-dimensional trajectories of ≈1 800 individual birds during a 30 min period encompassing flock formation, circling, and landing, and used these trajectories to test several hypotheses relating to flock or group behaviour. Specifically, we investigated whether the swifts use local interaction rules based on topological distance (e.g. the n nearest neighbours, regardless of their distance) rather than physical distance (e.g. neighbours within x m, regardless of number) to guide interactions, whether the chimney entry zone is more or less cooperative than the surrounding flock, and whether the characteristic subgroup size is constant or varies with flock density. We found that the swift flock is structured around local rules based on physical distance, that subgroup size increases with density, and that there exist regions of the flock that are less cooperative than others, in particular the chimney entry zone.
Integrierte Antwortstrategien als Reaktion auf negative Electronic Word-of-Mouth. Eine Analyse von Nestlés Beschwerdemanagement auf deutschen und US-amerikanischen Social Network Sites
<p>Die hochgeladenen sieben Dokumente beinhalten das Codebuch der Arbeit, alle Beschwerden samt Codierungen sowie alle Korrelationen zwischen Beschwerden und Antwortstrategien.</p> <p>Des weiteren finden sich alle Beschwerden und Beschwerdeantworten der vier CSR-Themen <em>Tierleid, Privatisierung von Wasser/Wasserklau, Regenwaldzerstörung </em>und <em>Kinderarbeit. </em>Bei jeder Beschwerde sind zudem die passenden qualitativ ermittelten Kategorien grafisch dargestellt.</p>
Cytoscape files - Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation
<p>Cytoscape files of pathway enrichment analyses and PPI mapping associated with manuscript https://www.nature.com/articles/s41467-023-39241-7</p> <p><strong>Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics</strong> <strong>identify cancer-specific mechanisms of stress adaptation </strong></p> <p>Anna Rodina<sup>1,11</sup>, Chao Xu<sup>1,11</sup>, Chander S. Digwal<sup>1,11</sup>, Suhasini Joshi<sup>1,11</sup>, Anand R. Santhaseela<sup>1</sup>, Sadik Bay<sup>1</sup>, Swathi Merugu<sup>1</sup>, Aftab Alam<sup>1</sup>, Pengrong Yan<sup>1</sup>, Chenghua Yang<sup>1,12</sup>, Tanaya Roychowdhury<sup>1</sup>, Palak Panchal<sup>1</sup>, Liza Shrestha<sup>1</sup>, Yanlong Kang<sup>1</sup>, Sahil Sharma<sup>1</sup>, Yogita Patel<sup>2</sup>, Justina Almadovar<sup>1</sup>, Adriana Corben<sup>3,13</sup>, Mary Alpaugh<sup>1,14</sup>, Shanu Modi<sup>4</sup>, Monica L. Guzman<sup>5</sup>, Teng Fei<sup>6</sup>, Tony Taldone<sup>1</sup>, Stephen D. Ginsberg<sup>7,8</sup>, Hediye Erdjument-Bromage<sup>9</sup>, Thomas A. Neubert<sup>9</sup>, Katia Manova-Todorova<sup>10</sup>, Jason C. Young<sup>2</sup>,<strong> </strong>Meng-Fu Bryan Tsou<sup>10</sup><strong>, </strong>Tai Wang<sup>1,*</sup>, Gabriela Chiosis<sup>1,4,*</sup></p> <p><strong>Abstract </strong></p> <p>Systems-level assessments of protein-protein interaction (PPI) network dysfunctions are currently out-of-reach because approaches enabling proteome-wide identification, analysis, and modulation of context-specific PPI changes in native (unengineered) cells and tissues are lacking. Herein, we take advantage of first-in-class chemical binders of maladaptive scaffolding structures termed epichaperomes and develop an epichaperome-based ‘omics platform, epichaperomics, to identify PPI alterations in disease. We provide multiple lines of evidence, at both biochemical and functional levels, demonstrating the importance of these probes to identify and study PPI network dysfunctions and provide mechanistically and therapeutically relevant proteome-wide insights. As proof-of-principle, we derive systems-level insight into PPI dysfunctions of cancer cells which enabled the discovery of a context-dependent mechanism by which cancer cells enhance the fitness of mitotic protein networks. Importantly, our systems levels analyses support the use of epichaperome chemical binders as therapeutic strategies aimed at normalizing PPI networks. </p>
Data and code for: Generation and applications of simulated datasets to integrate social network and demographic analyses
<p class="MsoNormal"><span>Social networks are tied to population dynamics; interactions are driven by population density and demographic structure, while social relationships can be key determinants of survival and reproductive success. However, difficulties integrating models used in demography and network analysis have limited research at this interface. We introduce the R package genNetDem for simulating integrated network-demographic datasets. It can be used to create longitudinal social networks and/or capture-recapture datasets with known properties. It incorporates the ability to generate populations and their social networks, generate grouping events using these networks, simulate social network effects on individual survival, and flexibly sample these longitudinal datasets of social associations. By generating co-capture data with known statistical relationships it provides functionality for methodological research. We demonstrate its use with case studies testing how imputation and sampling design influence the success of adding network traits to conventional Cormack-Jolly-Seber (CJS) models. We show that incorporating social network effects in CJS models generates qualitatively accurate results, but with downward-biased parameter estimates when network position influences survival. Biases are greater when fewer interactions are sampled or fewer individuals are observed in each interaction. While our results indicate the potential of incorporating social effects within demographic models, they show that imputing missing network measures alone is insufficient to accurately estimate social effects on survival, pointing to the importance of incorporating network imputation approaches. genNetDem provides a flexible tool to aid these methodological advancements and help researchers test other sampling considerations in social network studies.</span></p>
Data from: The functional roles of species in metacommunities, as revealed by metanetwork analyses of bird-plant frugivory networks
Open the record for dataset details and reuse information.
Analysing landscape effects on dispersal networks and gene flow with genetic graphs
Open the record for dataset details and reuse information.
Data from: Latest Ordovician (Hirnantian) brachiopod faunal lists used for non-matric multidimensional scaling (NMDS) and network analyses
Open the record for dataset details and reuse information.
Network analyses reveal the role of large snakes in connecting feeding guilds in a species-rich Amazonian snake community
Open the record for dataset details and reuse information.
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.