scispace - formally typeset
Search or ask a question
Topic

Interaction network

About: Interaction network is a research topic. Over the lifetime, 2700 publications have been published within this topic receiving 113372 citations.


Papers
More filters
Journal ArticleDOI
08 Jun 2016-PeerJ
TL;DR: By means of a fine-resolution temporal analysis, this work evidenced for the first time how temporal changes in the interaction network structure respond to the arrival of migratory species into the system and to fruit availability.
Abstract: Background. Ecological communities are dynamic collections whose composition and structure change over time, making up complex interspecific interaction networks. Mutualistic plant-animal networks can be approached through complex network analysis; these networks are characterized by a nested structure consisting of a core of generalist species, which endows the network with stability and robustness against disturbance. Those mutualistic network structures can vary as a consequence of seasonal fluctuations and food availability, as well as the arrival of new species into the system that might disorder the mutualistic network structure (e.g., a decrease in nested pattern). However, there is no assessment on how the arrival of migratory species into seasonal tropical systems can modify such patterns. Emergent and fine structural temporal patterns are adressed here for the first time for plant-frugivorous bird networks in a highly seasonal tropical environment. Methods. In a plant-frugivorous bird community, we analyzed the temporal turnover of bird species comprising the network core and periphery of ten temporal interaction networks resulting from different bird migration periods. Additionally, we evaluated how fruit abundance and richness, as well as the arrival of migratory birds into the system, explained the temporal changes in network parameters such as network size, connectance, nestedness, specialization, interaction strength asymmetry and niche overlap. The analysis included data from 10 quantitative plant-frugivorous bird networks registered from November 2013 to November 2014. Results. We registered a total of 319 interactions between 42 plant species and 44 frugivorous bird species; only ten bird species were part of the network core. We witnessed a noteworthy turnover of the species comprising the network periphery during migration periods, as opposed to the network core, which did not show significant temporal changes in species composition. Our results revealed that migration and fruit richness explain the temporal variations in network size, connectance, nestedness and interaction strength asymmetry. On the other hand, fruit abundance only explained connectance and nestedness. Discussion. By means of a fine-resolution temporal analysis, we evidenced for the first time how temporal changes in the interaction network structure respond to the arrival of migratory species into the system and to fruit availability. Additionally, few migratory bird species are important links for structuring networks, while most of them were peripheral species. We showed the relevance of studying bird-plant interactions at fine temporal scales, considering changing scenarios of species composition with a quantitative network approach.

50 citations

Posted Content
TL;DR: The proposed Multi-scale Interaction Network (MINet) uses multiple paths with different scales and balances the computational resources between the scales and outperforms point-based, image- based, and projection-based methods in terms of accuracy, number of parameters, and runtime.
Abstract: Real-time semantic segmentation of LiDAR data is crucial for autonomously driving vehicles, which are usually equipped with an embedded platform and have limited computational resources. Approaches that operate directly on the point cloud use complex spatial aggregation operations, which are very expensive and difficult to optimize for embedded platforms. They are therefore not suitable for real-time applications with embedded systems. As an alternative, projection-based methods are more efficient and can run on embedded platforms. However, the current state-of-the-art projection-based methods do not achieve the same accuracy as point-based methods and use millions of parameters. In this paper, we therefore propose a projection-based method, called Multi-scale Interaction Network (MINet), which is very efficient and accurate. The network uses multiple paths with different scales and balances the computational resources between the scales. Additional dense interactions between the scales avoid redundant computations and make the network highly efficient. The proposed network outperforms point-based, image-based, and projection-based methods in terms of accuracy, number of parameters, and runtime. Moreover, the network processes more than 24 scans per second on an embedded platform, which is higher than the framerates of LiDAR sensors. The network is therefore suitable for autonomous vehicles.

50 citations

Journal ArticleDOI
23 Oct 2014-PLOS ONE
TL;DR: This first study to evaluate plant-herbivore interaction networks on a small spatio-temporal scale identified the ecological factors structuring this network such as habitat complexity and seasonality and offers new evidence on the role of abiotic and biotic factors in the variation of the properties of species interaction networks.
Abstract: Despite the dynamic nature of ecological interactions, most studies on species networks offer static representations of their structure, constraining our understanding of the ecological mechanisms involved in their spatio-temporal stability. This is the first study to evaluate plant-herbivore interaction networks on a small spatio-temporal scale. Specifically, we simultaneously assessed the effect of host plant availability, habitat complexity and seasonality on the structure of plant-herbivore networks in a coastal tropical ecosystem. Our results revealed that changes in the host plant community resulting from seasonality and habitat structure are reflected not only in the herbivore community, but also in the emergent properties (network parameters) of the plant-herbivore interaction network such as connectance, selectiveness and modularity. Habitat conditions and periods that are most stressful favored the presence of less selective and susceptible herbivore species, resulting in increased connectance within networks. In contrast, the high degree of selectivennes (i.e. interaction specialization) and modularity of the networks under less stressful conditions was promoted by the diversification in resource use by herbivores. By analyzing networks at a small spatio-temporal scale we identified the ecological factors structuring this network such as habitat complexity and seasonality. Our research offers new evidence on the role of abiotic and biotic factors in the variation of the properties of species interaction networks.

49 citations

Journal ArticleDOI
TL;DR: The microarray data analysis based on biological networks contains two main research aspects: identification of active components in biological networks and assessment of gene sets significance.
Abstract: Microarray technology, which permits rapid and large-scale screening for patterns of gene expressions, usually generates a large amount of data. How to mine the biological meanings under these data is one of the main challenges in bioinformatics. Compared to the pure mathematical techniques, those methods incorporated with some prior biological knowledge generally bring better interpretations. Recently, a new analysis, in which the knowledge of biological networks such as metabolic network and protein interaction network is introduced, is widely applied to microarray data analysis. The microarray data analysis based on biological networks contains two main research aspects: identification of active components in biological networks and assessment of gene sets significance. In this paper, we briefly review the progress of these two categories of analyses, especially some representative methods. * Supported by the National Program on Key Basic Research Projects (No. 2004CB518606), the Fundamental R...

49 citations

Book ChapterDOI
TL;DR: In vitro and cell-based methods that exploit SAHB compounds to determine the functional consequences of BH3 interactions in regulating apoptosis are described.
Abstract: The BCL-2 family of apoptotic proteins regulates the critical balance between cellular life and death and, thus, has become the focus of intensive basic science inquiry and a fundamental target for therapeutic development in oncology and other diseases. Classified based on the presence of conserved alpha-helical motifs and pro- and anti-apoptotic functionalities, BCL-2 proteins participate in a complex interaction network that determines cellular fate. The identification of BCL-2 homology domain 3 (BH3) as a critical death helix that engages and regulates BCL-2 family proteins has inspired the development of molecular tools to decode and drug the interaction network. Stabilized Alpha-Helices of BCL-2 domains (SAHBs) are structurally reinforced, protease-resistant, and cell-permeable compounds that retain the specificity of native BH3 death ligands and, therefore, serve as ideal reagents to dissect BCL-2 family interactions in vitro and in vivo. Here, we describe the in vitro and cell-based methods that exploit SAHB compounds to determine the functional consequences of BH3 interactions in regulating apoptosis.

49 citations


Network Information
Related Topics (5)
Genome
74.2K papers, 3.8M citations
83% related
Regulation of gene expression
85.4K papers, 5.8M citations
81% related
Cluster analysis
146.5K papers, 2.9M citations
80% related
Gene
211.7K papers, 10.3M citations
79% related
Transcription factor
82.8K papers, 5.4M citations
78% related
Performance
Metrics
No. of papers in the topic in previous years
YearPapers
202337
202290
2021183
2020221
2019201
2018163