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333 results for “functional network”
Functional composition of plant communities mediates biomass effects on ecosystem service recovery across an experimental dryland restoration network
<p>Land degradation can result in a loss of critical ecosystem services that we often seek to restore through re-establishment of desired plant communities. Trait-based approaches have the potential to target specific ecosystem services based on associations between the functional composition of plant communities and ecosystem properties that serve as indicators of those services. The effect of functional composition on ecosystem recovery may depend on the amount of restored plant biomass, itself a supporting service frequently targeted in restoration efforts. Yet, interactions between functional composition and biomass are not formally integrated into trait-based analytical frameworks. We tested the hypothesis that functional composition of plant communities both drives, and interacts with, biomass production to influence indicators of soil functioning and weed suppression across a network of degraded dryland restoration experiments. This networked approach allowed us to identify generalized effects of functional composition on ecosystem recovery across a range of dryland climate conditions. Climate had a substantial effect on ecosystem indicators, with weed cover and soil surface stability increasing in more arid climates, water infiltration increasing with precipitation, and aggregate structure increasing with less freezing. After accounting for climate effects across study sites, we found significant effects of community-weighted mean (CWM) trait values on biomass, particularly a positive effect of leaf carbon-to-nitrogen ratio, and of CWM-biomass interactions on other ecosystem indicators. Cover of exotic species was reduced in restored communities with a combination of low leaf dry matter content and high biomass, soil water infiltration increased with lower specific root length and high biomass, and soil aggregate stability increased with higher root dry matter content and high biomass, among other effects. Functional diversity had no significant effects on any ecosystem indicators. Synthesis: The influence of community functional composition on ecosystem properties increases with community biomass, particularly in disturbed or low productivity systems. This suggests that active management should not only focus on trait values that optimize individual ecosystem indicators, but also how those functional strategies are complementary or counter to those that increase biomass.</p>
Supplementary table of PRIDE datasets analyzed for "FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data"
<p>Our proteomics dataset comes from The PRoteomics IDEntifications (PRIDE) database, the world’s largest data repository of mass spectrometry-based proteomics data. Specifically, we used 633 human proteomics project experiments with a total of 32,546 runs and reanalyzed them using ionbot with an FDR threshold of 0.01 [16], resulting in a total of 154,885,151 peptide spectrum matches for 18,846 proteins. Here is the full list of projects, runs, and general statistics.</p>
Structure, function, and control of the musculoskeletal network - Data
<p>Supplementary data for: Structure, function, and control of the musculoskeletal network</p> <p>Table S8: The assigned homunculus categories and data driven community assignments of muscles.</p> <p>Table S9: The hypergraph of muscles and bones from the Hosford muscle tables used in the main text.</p> <p>Table S10: The hypergraph of muscles and bones from Grant's atlas used in the supplementary text.</p> <p> </p> <p>Data for Figures:</p> <p>2e</p> <p>3a, 3b</p> <p>4b, 4c, 4d</p> <p>S4a-h</p> <p>S5</p> <p>S6a, S6b</p> <p>S7a, S7b</p> <p>S8</p> <p>S9</p> <p>S10</p> <p>S11</p> <p>S12</p> <p> </p>
TNF SIGNALING NETWORK FUNCTIONS
<p>Tumor Necrosis Factor (TNF) inhibitors are a class of medications that target and neutralize TNF, a pro-inflammatory cytokine that plays a key role in the immune response and inflammation. TNF is involved in the pathogenesis of various autoimmune and inflammatory diseases, such as rheumatoid arthritis, psoriasis, ankylosing spondylitis, and inflammatory bowel disease. By inhibiting TNF, these drugs can effectively reduce inflammation, decrease joint damage, and improve clinical symptoms in patients with these conditions. TNF inhibitors work by blocking the interaction of TNF with its receptors, thereby preventing the cascade of inflammatory processes that lead to tissue damage. Understanding the mechanisms and therapeutic effects of TNF inhibitors is essential for optimizing the management of chronic inflammatory diseases.</p>
A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology
<p>Source Data and Supplementary Data associated with the paper “A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology” (DOI: https://doi.org/10.1101/2023.03.06.531441).</p>
Mapping trait versus species turnover reveals spatiotemporal variation in functional redundancy and network robustness in a plant‐pollinator community
<p>1. Functional overlap among species (redundancy) is considered important in shaping competitive and mutualistic interactions that determine how communities respond to environmental change. Most studies view functional redundancy as static, yet traits within species – which ultimately shape functional redundancy – can vary over seasonal or spatial gradients. We therefore have limited understanding of how trait turnover within and between species could lead to changes in functional redundancy or how loss of traits could differentially impact mutualistic interactions depending on where and when the interactions occur in space and time.</p> <p>2. Using an Arctic bumblebee community as a case study, and 1,277 individual measures from 14 species over three annual seasons, we quantified how inter- and intraspecific body-size turnover compared to species turnover with elevation and over the season. Coupling every individual and their trait with a plant visitation, we investigated how grouping individuals by a morphological trait or by species identity altered our assessment of network structure and how this differed in space and time. Finally, we tested how the sensitivity of the network in space and time differed when simulating extinction of nodes representing either morphological trait similarity or traditional species groups. This allowed us to explore the degree to which trait-based groups increase or decrease interaction redundancy relative to species-based nodes.</p> <p>3. We found that i) groups of taxonomically and morphologically similar bees turn over in space and time independently from each other, with trait turnover being larger over the season; ii) networks composed of nodes representing species versus morphologically similar bees were structured differently; and iii) simulated loss of bee trait groups caused faster coextinction of bumblebee species and flowering plants than when bee taxonomic groups were lost. Crucially, the magnitude of these effects varied in space and time, highlighting the importance of considering spatiotemporal context when studying the relative importance of taxonomic and trait contributions to interaction network architecture.</p> <p>4. Our finding that functional redundancy varies spatiotemporally demonstrates how considering the traits of individuals within networks is needed to understand the impacts of environmental variation and extinction on ecosystem functioning and resilience.</p>
Functional and taxonomic diversity indices of riparian plants in river networks
<p>1. The River Continuum Concept (RCC) predicts a gradual shift of organisms' functional adaptations along the longitudinal (upstream-downstream) gradient, as well as the maximization of the biotic diversity in mid-reaches. Although this theoretical framework was originally developed for stream macroinvertebrates, we tested whether such a pattern can be also observed in riparian plant communities.</p> <p>2. We studied the cover of plant species in riparian forests across two river networks. We analyzed the taxonomic and functional diversity indices, as well as community-weighted means of functional traits in relation to the plots' position in the catchments.</p> <p>3. The observed patterns were largely in line with the predictions of RCC. We discovered a significant decrease in the specific leaf area and an increase in the herbaceous plants' height in communities along a river gradient. There was also a shift in the dispersal syndromes, towards a higher importance of zoochory in the lower reaches.</p> <p>4. The functional richness and divergence displayed unimodal patterns of increasing values in the mid-reaches. The patterns of taxonomic diversity were similar, but some plots in the lowest reaches were more diverse than expected, forming an additional increase in diversity.</p> <p>5. The study shows that plant communities in natural riparian forests show high connectivity along the longitudinal gradient, which along with the environmental gradients creates patterns that are known from theoretical predictions.</p>
Dataset1 for "General framework for E(3)-equivariant neural network representation of density functional theory Hamiltonian"
<p>Supporting data for the paper "General framework for E(3)-equivariant neural network representation of density functional theory Hamiltonian". </p> <p>Contains atomic structures and Hamiltonian matrices of monolayer graphene, monolayer MoS<sub>2</sub>, bilayer graphene and bilayer bismuthene.</p> <p>Detailed descriptions about the format of data and instructions on how to reproduce the results in the paper can be found in README.md.</p>
Dataset2 for "General framework for E(3)-equivariant neural network representation of density functional theory Hamiltonian"
<p>Supporting data for the paper "General framework for E(3)-equivariant neural network representation of density functional theory Hamiltonian". </p> <p>Contains atomic structures and Hamiltonian matrices of bilayer bismuth selenide. </p> <p>Detailed descriptions about the format of data and instructions on how to reproduce the results in the paper can be found in README.md.</p>
Dataset3 for "General framework for E(3)-equivariant neural network representation of density functional theory Hamiltonian"
<p>Supporting data for the paper "General framework for E(3)-equivariant neural network representation of density functional theory Hamiltonian". </p> <p>Contains atomic structures and Hamiltonian matrices of bilayer bismuth telluride. </p> <p>Detailed descriptions about the format of data and instructions on how to reproduce the results in the paper can be found in README.md.</p>
Marmoset Functional Maps, "A Vocalization-Processing Network in Marmosets"
<p>Marmoset data and functional maps used in the article "A vocalization-processing network in marmosets". (Jafari et al., 2023)</p>
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>
The Effect of Acupuncture Treatment on Cognitive Functions and Brain Networks for Long COVID
ClinicalTrials.gov study NCT07355751. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Brain functional networks associated with social bonding in monogamous voles
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Functional connectivity in human auditory networks and the origins of variation in the transmission of musical systems
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The structure and ecological function of the interactions between plants and arbuscular mycorrhizal fungi through multilayer networks
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Data from: A global genetic interaction network maps a wiring diagram of cellular function
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Widespread resilience of animal species, functional diversity, and predator-prey networks to an unprecedented gigafire
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Data from: The functional roles of species in metacommunities, as revealed by metanetwork analyses of bird-plant frugivory networks
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Tissue-type specific accumulation of the plastoglobular proteome, transcriptional networks and plastoglobular functions
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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.