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dynamical network

Lucia Russo, Paola Russo, Constantinos I Siettos
Based on complex network theory, we propose a computational methodology which addresses the spatial distribution of fuel breaks for the inhibition of the spread of wildland fires on heterogeneous landscapes. This is a two-level approach where the dynamics of fire spread are modeled as a random Markov field process on a directed network whose edge weights are determined by a Cellular Automata model that integrates detailed GIS, landscape and meteorological data. Within this framework, the spatial distribution of fuel breaks is reduced to the problem of finding network nodes (small land patches) which favour fire propagation...
2016: PloS One
Shi-Peng Chen, Chih-Hsien Kuo, Hsueh-Han Lu, Hui-Shan Lo, Kai-Wun Yeh
IbNAC1 is known to activate the defense system by reprogramming a genetic network against herbivory in sweet potato. This regulatory activity elevates plant defense potential but relatively weakens plants by IbNAC1-mediated JA response. The mechanism controlling IbNAC1 expression to balance plant vitality and survival remains unclear. In this study, a wound-responsive G-box cis-element in the IbNAC1 promoter from -1484 to -1479 bp was identified. From a screen of wound-activated transcriptomic data, one transcriptional activator, IbbHLH3, and one repressor, IbbHLH4, were selected that bind to and activate or repress, respectively, the G-box motif in the IbNAC1 promoter to modulate the IbNAC1-mediated response...
October 2016: PLoS Genetics
Benjamin W Mooneyham, Michael D Mrazek, Alissa J Mrazek, Kaita L Mrazek, Dawa T Phillips, Jonathan W Schooler
During tasks that require continuous engagement, the mind alternates between mental states of focused attention and mind-wandering. Existing research has assessed the functional connectivity of intrinsic brain networks underlying the experience and training of these mental states using "static" approaches that assess connectivity across an entire task. To disentangle the functional connectivity between brain regions as the mind fluctuates between discrete brain states, we employed a dynamic functional connectivity approach that characterized brain activity using a sliding window...
October 25, 2016: Journal of Cognitive Neuroscience
Hao Liu, Wei Ye, Hai-Feng Chen
Acetylcholinesterase is a potent enzyme that regulates neurotransmission by rapidly hydrolyzing the neurotransmitter acetylcholine in synapses of the nervous system. As drug target of anti-AD, it has catalytic and peripheral anionic sites. However, the regulation relation between these two sites is unclear. Therefore, we constructed dynamics fluctuation network based on all-atom molecular dynamics simulations to reveal the regulation mechanism. The results suggest that the correlation network in double site system (hAChE/TZ5) is distinctly different from that in the free state and single site systems (hAChE/huprine and hAChE/1YL)...
October 25, 2016: Chemical Biology & Drug Design
Lydia Laninga-Wijnen, Zeena Harakeh, Christian Steglich, Jan K Dijkstra, René Veenstra, Wilma Vollebergh
This study examined whether peer norms for aggression within the classroom impact friendship selection, maintenance, and socialization processes related to aggression across the 1st year of secondary school (N = 1,134 students from 51 classes, Mage  = 12.66). As hypothesized, longitudinal social network analyses indicated that friendship selection and influence processes related to aggression depended on the popularity norm within the classroom (i.e., the class-level association between popularity and aggression) rather than the descriptive norm (aggregated average of aggressive behavior)...
October 25, 2016: Child Development
Jie Zhou, Yong Zou, Shuguang Guan, Zonghua Liu, S Boccaletti
Networks whose structure of connections evolves in time constitute a big challenge in the study of synchronization, in particular when the time scales for the evolution of the graph topology are comparable with (or even longer than) those pertinent to the units' dynamics. We here focus on networks with a slow-switching structure, and show that the necessary conditions for synchronization, i.e. the conditions for which synchronization is locally stable, are determined by the time average of the largest Lyapunov exponents of transverse modes of the switching topologies...
October 25, 2016: Scientific Reports
Mark Wilson
The study of the structure and dynamics of network-forming materials is reviewed. Experimental techniques used to extract key structural information are briefly considered. Strategies for building simulation models, based on both targeting key (experimentally-accessible) materials and on systematically controlling key model parameters, are discussed. As an example of the first class of materials, a key target system, SiO2, is used to highlight how the changing structure with applied pressure can be effectively modelled (in three dimensions) and used to link to both experimental results and simple structural models...
October 25, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Long Liang, Christopher Jones, Shaohua Chen, Bo Sun, Yang Jiao
Collagen networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the transmission of forces generated by contractile cells in 3D collagen-I networks. Specifically, the graph (bond-node) representations of collagen networks with collagen concentrations of 1, 2 and 4 mg ml(-1) are derived from confocal microscopy data and used to model the network microstructure. Cell contraction is modeled by applying correlated displacements at specific nodes of the network, representing the focal adhesion sites...
October 25, 2016: Physical Biology
Nikos A Afratis, Konstantina Karamanou, Zoi Piperigkou, Demitrios H Vynios, Achilleas D Theocharis
Glycosaminoglycans are integral part of the dynamic extracellular matrix (ECM) network that control crucial biochemical and biomechanical signals required for tissue morphogenesis, differentiation, homeostasis and cancer development. Breast cancer cells communicate with stromal ones to modulate ECM mainly through release of soluble effectors during cancer progression. The intracellular cross-talk between cell surface receptors and estrogen receptors is important for the regulation of breast cancer cell properties and production of ECM molecules...
October 24, 2016: Glycoconjugate Journal
Castrese Morrone, Riccardo Miggiano, Mario Serpe, Alberto Massarotti, Anna Valenti, Giovanni Del Monaco, Mosè Rossi, Franca Rossi, Menico Rizzi, Giuseppe Perugino, Maria Ciaramella
BACKGROUND: Alkylated DNA-protein alkyltransferases (AGTs) are conserved proteins that repair alkylation damage in DNA by using a single-step mechanism leading to irreversible alkylation of the catalytic cysteine in the active site. Trans-alkylation induces inactivation and destabilization of the protein, both in vitro and in vivo, likely triggering conformational changes. A complete picture of structural rearrangements occurring during the reaction cycle is missing, despite considerable interest raised by the peculiarity of AGT reaction, and the contribution of a functional AGT in limiting the efficacy of chemotherapy with alkylating drugs...
October 21, 2016: Biochimica et Biophysica Acta
Money Gupta, Rashi Chauhan, Yamuna Prasad, Gulshan Wadhwa, Chakresh Kumar Jain
The lack of complete treatments and appearance of multiple drug-resistance strains of Burkholderia cepacia complex (Bcc) are causing an increased risk of lung infections in cystic fibrosis patients. Bcc infection is a big risk to human health and demands an urgent need to identify new therapeutics against these bacteria. Network biology has emerged as one of the prospective hope in identifying novel drug targets and hits. We have applied protein-protein interaction methodology to identify new drug-target candidates (orthologs) in Burkhloderia cepacia GG4, which is an important strain for studying the quorum-sensing phenomena...
October 8, 2016: Computational Biology and Chemistry
Yuchen Gao, Xin Xiong, Spencer Wong, Emeric J Charles, Wendell A Lim, Lei S Qi
The ability to dynamically manipulate the transcriptome is important for studying how gene networks direct cellular functions and how network perturbations cause disease. Nuclease-dead CRISPR-dCas9 transcriptional regulators, while offering an approach for controlling individual gene expression, remain incapable of dynamically coordinating complex transcriptional events. Here, we describe a flexible dCas9-based platform for chemical-inducible complex gene regulation. From a screen of chemical- and light-inducible dimerization systems, we identified two potent chemical inducers that mediate efficient gene activation and repression in mammalian cells...
October 24, 2016: Nature Methods
Qichao Zhang, Dongbin Zhao, Ding Wang
In this paper, the robust control problem for a class of continuous-time nonlinear system with unmatched uncertainties is investigated using an event-based control method. First, the robust control problem is transformed into a corresponding optimal control problem with an augmented control and an appropriate cost function. Under the event-based mechanism, we prove that the solution of the optimal control problem can asymptotically stabilize the uncertain system with an adaptive triggering condition. That is, the designed event-based controller is robust to the original uncertain system...
October 18, 2016: IEEE Transactions on Neural Networks and Learning Systems
Tanya T Nguyen, Sanja Kovacevic, Sheena I Dev, Kun Lu, Thomas T Liu, Lisa T Eyler
Objective: Disturbances in functional connectivity have been suggested to contribute to cognitive and emotion processing deficits observed in bipolar disorder (BD). Functional connectivity between medial prefrontal cortex (mPFC) and other brain regions may be particularly abnormal. The goal of the present study was to characterize the temporal dynamics of the default mode network (DMN) connectivity in BD and examine its association with cognition. Method: In a preliminary study, euthymic BD (n = 15) and healthy comparison (HC, n = 19) participants underwent resting-state functional MRI, using high-resolution sequences adapted from the Human Connectome Project, and completed neuropsychological measures of processing speed and executive function...
October 24, 2016: Neuropsychology
Shouying Huang, Jifa Jiang
In this paper, we develop and analyze an SIS epidemic model with a general nonlinear incidence rate, as well as degree-dependent birth and natural death, on heterogeneous networks. We analytically derive the epidemic threshold R0 which completely governs the disease dynamics: when R0 < 1, the disease-free equilibrium is globally asymptotically stable, i.e., the disease will die out; when R0 > 1, the disease is permanent. It is interesting that the threshold value R0 bears no relation to the functional form of the nonlinear incidence rate and degree-dependent birth...
August 1, 2016: Mathematical Biosciences and Engineering: MBE
Enrico Ubaldi, Nicola Perra, Márton Karsai, Alessandro Vezzani, Raffaella Burioni, Alessandro Vespignani
The dynamic of social networks is driven by the interplay between diverse mechanisms that still challenge our theoretical and modelling efforts. Amongst them, two are known to play a central role in shaping the networks evolution, namely the heterogeneous propensity of individuals to i) be socially active and ii) establish a new social relationships with their alters. Here, we empirically characterise these two mechanisms in seven real networks describing temporal human interactions in three different settings: scientific collaborations, Twitter mentions, and mobile phone calls...
October 24, 2016: Scientific Reports
Hui Liu, Fan Zhang, Shital Kumar Mishra, Shuigeng Zhou, Jie Zheng
Modeling of signaling pathways is crucial for understanding and predicting cellular responses to drug treatments. However, canonical signaling pathways curated from literature are seldom context-specific and thus can hardly predict cell type-specific response to external perturbations; purely data-driven methods also have drawbacks such as limited biological interpretability. Therefore, hybrid methods that can integrate prior knowledge and real data for network inference are highly desirable. In this paper, we propose a knowledge-guided fuzzy logic network model to infer signaling pathways by exploiting both prior knowledge and time-series data...
October 24, 2016: Scientific Reports
Yuanhua Qiao, Xiaojie Liu, Jun Miao, Lijuan Duan
In this paper, a two-layer network is built to simulate the mechanism of visual selection and shifting based on the mapping dynamic model for instantaneous frequency. Unlike the differential equation model using limit cycle to simulate neuron oscillation, we build an instantaneous frequency mapping dynamic model to describe the change of the neuron frequency to avoid the difficulty of generating limit cycle. The activity of the neuron is rebuilt based on the instantaneous frequency and in this work, we use the first layer of neurons to implement image segmentation and the second layer of neurons to act as visual selector...
October 24, 2016: Journal of Integrative Neuroscience
B Bellana, Z-X Liu, N B Diamond, C L Grady, M Moscovitch
The default mode network (DMN) has been identified reliably during rest, as well as during the performance of tasks such as episodic retrieval and future imagining. It remains unclear why this network is engaged across these seemingly distinct conditions, though many hypotheses have been proposed to account for these effects. Prior to generating hypotheses explaining common DMN involvement, the degree of commonality in the DMN across these conditions, within individuals, must be statistically determined to test whether or not the DMN is truly a unitary network, equally engaged across rest, retrieval and future imagining...
October 24, 2016: Human Brain Mapping
Joakim Esbjörnsson, Mattias Mild, Anne Audelin, Jannik Fonager, Helena Skar, Louise Bruun Jørgensen, Kirsi Liitsola, Per Björkman, Göran Bratt, Magnus Gisslén, Anders Sönnerborg, Claus Nielsen, Patrik Medstrand, Jan Albert
Increased knowledge about HIV-1 transmission dynamics in different transmission groups and geographical regions is fundamental for assessing and designing prevention efforts against HIV-1 spread. Since the first reported cases of HIV infection during the early 1980s, the HIV-1 epidemic in the Nordic countries has been dominated by HIV-1 subtype B and MSM transmission. HIV-1 pol sequences and clinical data of 51 per cent of all newly diagnosed HIV-1 infections in Sweden, Denmark, and Finland in the period 2000-2012 (N = 3,802) were analysed together with a large reference sequence dataset (N = 4,537) by trend analysis and phylogenetics...
January 2016: Virus Evolution
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