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325 results for “network structure”

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zenodo36/100

Data for: Reconstructing Cosmological Initial Conditions from Late-Time Structure with Convolutional Neural Networks

Trained models and evaluation data for the revised submitted paper "Reconstructing Cosmological Initial Conditions from Late-Time Structure with Convolutional Neural Networks," Christopher J. Shallue & Daniel J. Eisenstein (2022)

opencc-by-4.0Jul 2022View details →

dryad36/100

Orchid-mycorrhizal fungi interactions reveal a duality in their network structure in two European regions differing in climate

Network analysis is an effective tool to describe and quantify the ecological interactions between plants and root-associated fungi. Mycoheterotrophic plants, such as orchids, critically rely on mycorrhizal fungi for nutrients to survive, therefore, investigating the structure of those intimate interactions brings new insights into the plant community assembly and coexistence. So far, there is little consensus on the structure of those interactions, described either as nested (generalist interactions), modular (highly specific interactions) or of both topologies. Biotic factors (e.g., mycorrhizal specificity) were shown to influence the network structure, while there is less evidence of abiotic factor effects. By using next-generation sequencing of the orchid mycorrhizal fungal (OMF) community associated with 238 plant individuals belonging to 17 orchid species, we assessed the structure of four orchid-OMF networks in two European regions under contrasting climatic conditions (Mediterranean vs Continental). Each network contained four to 12 co-occurring orchid species, including up to eight species shared among the sites. All four networks were both nested and modular, and fungal communities were different between co-occurring orchid species, despite multiple sharing of fungi across some orchids. Co-occurring orchid species growing in Mediterranean climates were associated with more dissimilar fungal communities, consistent with a greater modular structure compared to the Continental ones. The OMF diversity was comparable among orchid species since most orchids were associated with multiple rarer fungi and with only a few highly dominant ones in the roots. Our results provide useful highlights on potential factors involved in structuring plant-mycorrhizal fungi interactions in different climatic conditions.

opencc-zeroMar 2023View details →

zenodo36/100

Agta hunter-gatherer oral microbiomes are shaped by contact network structure

Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter-gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar to Central African Bayaka hunter-gatherers than to neighbouring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that large interaction networks including strong links between close kin, spouses, and even unrelated friends, can significantly predict bacterial transmission networks across Agta camps. Finally, we show that more central individuals to social networks are also bacterial supersharers. We conclude that hunter-gatherer social microbiomes are predominantly pathogenic and were shaped by evolutionary tradeoffs between extensive sociality and disease spread.

opencc-by-4.0Dec 2030View details →

zenodo36/100

Data for "Structure and drivers of social networks and their links with health in older adults"

Data, supplementary material and scripts for the paper "Structure and drivers of social networks and their links with health in older adults" Social network is an important factor in promoting healthy aging. However, the mechanisms linking social capital to health are complex. Moreover, most of the social network analysis studies on older adults consider only participants’ relationships and not how these relationships are themselves connected. In this study, we went further than current ego-centered network studies by determining global social network metrics and the structure of relationships among older adult participants of the RECORD Cohort using the Veritas-Social questionnaire. The aim of this study is to identify key dimensions of social networks of older adults, and to evaluate how these dimensions relate to depressive symptoms, life satisfaction, and well-being. Using Principal Component Analyses (PCA), we identified four social network dimensions with psychological meanings. Dimension 1 (homophily) was positively linked with perceived accessibility to services in one’s residential neighborhood but negatively linked with the level of study. Dimension 2 (social integration) as Dimension 3 (social support) was only linked to the number of people living with ego. Dimension 4 was linked with perceived accessibility to local services. Finally, and rather surprisingly, we found that none of the four network dimensions, even the degree, was linked to the three health status metrics.

opencc-by-4.0Mar 2023View details →

zenodo36/100

unarXive: All arXiv Publications Pre-Processed for NLP, Including Structured Full-Text and Citation Network (open subset)

<h2>Description</h2>unarXive is a scholarly data set containing publications' structured full-text, annotated in-text citations, linked non-text content (mathematical notation, figure/table captions) and a citation network.The data is generated from all LaTeX sources on <a href="https://arxiv.org/">arXiv</a> and therefore of higher quality than data generated from PDF files.Typical uses are<ul><li>Training of ML models (citation recommendation, summarization, LLMs)</li><li>Citation context analysis</li><li>Bibliographic analyses</li></ul><h2>Access</h2>┏━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃  <a href="https://github.com/IllDepence/unarXive/raw/master/doc/unarXive_data_sample.tar.gz">D O W N L O A D   S A M P L E</a>   ┃ ┗━━━━━━━━━━━━━━━━━━━━━━━━━━┛Regarding the full data set, please note the following:<blockquote>Note: this Zenodo record is the "open subset" of unarXive, which contains all permissively licensed papers from arXiv.org. You can find the <a href="https://doi.org/10.5281/zenodo.7752754">full version here</a>.</blockquote>The code used for generating the data set is <a href="https://github.com/IllDepence/unarXive">publicly available</a>.

opencc-by-sa-4.0Mar 2023View details →

dryad36/100

Data from: Network structure of avian mixed-species flocks decays with elevation and latitude across the Andes

Birds in mixed-species flocks benefit from greater foraging efficiency and reduced predation but also face costs related to competition and activity matching. Because this cost-benefit trade-off is context-dependent (e.g., abiotic conditions, habitat quality), the structure of flocks is expected to vary along elevational, latitudinal, and disturbance gradients. Specifically, we predicted that the connectivity and cohesion of flocking networks would (1) decline towards tropical latitudes and lower elevations, where competition and activity matching costs are higher, and (2) increase with lower forest cover and greater human disturbance. We analysed the structure of 84 flock networks across the Andes and assessed the effect of elevation, latitude, forest cover and human disturbance on network characteristics. We found that Andean flocks are overall open-membership systems (unstructured), though the extent of network structure varied across gradients. Elevation was the main predictor of structure, with more connected and less modular flocks upslope. As expected, flocks in areas with higher forest cover were less cohesive, with better-defined flock subtypes. Flocks also varied across latitude and disturbance gradients as predicted, but effect sizes were small. Our findings indicate that the unstructured nature of Andean flocks might arise as a strategy to cope with harsh environmental conditions.

opencc-zeroDec 2022View details →

dryad36/100

The structure and ecological function of the interactions between plants and arbuscular mycorrhizal fungi through multilayer networks

<ol> <li>Arbuscular mycorrhizas are one of the most frequent mutualisms in terrestrial ecosystems. Although studies on plant mutualistic interaction networks suggest that they may leave their imprint on plant community structure and dynamics, this has not been explicitly assessed. Thus, in the context of plant-fungi interactions, studies explicitly linking plant-mycorrhizal fungi interaction networks with key ecological functions of plant communities, such as recruitment, are lacking. </li> <li>In this study, we analyse, in two Mediterranean forest communities of southern Iberian Peninsula, how plant-AMF networks modulate plant-plant recruitment interaction networks. We use a new approach integrating plant-AMF and plant recruitment networks into a single multilayer structure. We also develop a new metric (Interlayer Node Neighbourhood Integration, INNI) to explore the impact of a given node on the structure across layers.</li> <li>Similarity of plant species in their AMF communities is positively related to the observed frequency of recruitment interactions in the field. Results reveal that properties of plant-AMF networks, such as plant degree and centrality, contribute to explaining properties of the plant recruitment network, such as in- and out-degree (i.e. sapling bank and canopy service) and its modular structure. However, these relationships differed between the two forest communities. Finally, we identify particular AMF that contribute to integrating the neighbourhood of recruitment interactions between plants.</li> <li>This multilayer network approach is useful to explore the role of plant-AMF interactions on recruitment, a key ecosystem function enhanced by fungi. Results provide evidence that the complex structure of plant-AMF interactions impacts functional and structurally plant-plant interactions, which in turn may potentially influence plant community dynamics, through their effects on the structure of the recruitment network.</li> </ol>

opencc-zeroDec 2022View details →

dryad36/100

Social network and fitness data from age-structured populations of forked fungus beetles

We investigated the relationships between age, social behavior, and fitness at three levels of organization: the individual, the local social environment, and the population. Replicate groups of forked fungus beetles (Bolitotherus cornutus) were engineered to have either young- or old- biased age structures, and both social and reproductive behaviors were recorded.

opencc-zeroMay 2023View details →

dryad36/100

Data for: Honey bees (Apis mellifera) modify plant-pollinator network structure, but do not alter wild species' interactions

Honey bees (Apis mellifera) are widely used for honey production and crop pollination, raising concern for wild pollinators, as honey bees may compete with wild pollinators for floral resources. The first sign of competition, before changes appear in wild pollinator abundance or diversity, may be changes to wild pollinator interactions with plants. Such changes for a community can be measured by looking at changes to metrics of resource use overlap in plant-pollinator interaction networks. Studies of honey bee effects on plant-pollinator networks have usually not distinguished whether honey bees alter wild pollinator interactions, or if they merely alter total network structure by adding their own interactions. To test this question, we experimentally introduced honey bees to a Canadian grassland and measured plant-pollinator interactions at varying distances from the introduced hives. We found that honey bees increased the network metrics of pollinator and plant functional complementarity and decreased interaction evenness. However, in networks constructed from just wild pollinator interactions, honey bee abundance did not affect any of the metrics calculated. Thus, all network structural changes to the full network (including honey bee interactions) were due only to honey bee-plant interactions, and not to honey bees causing changes in wild pollinator-plant interactions. Given widespread and increasing use of honey bees, it is important to establish whether they affect wild pollinator communities. Our results suggest that honey bees did not alter wild pollinator foraging patterns in this system, even in a year that was drier than the 20-year average.

opencc-zeroJun 2023View details →

dryad36/100