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https://www.readbyqxmd.com/read/28426669/a-dynamic-genetic-hormonal-regulatory-network-model-explains-multiple-cellular-behaviors-of-the-root-apical-meristem-of-arabidopsis-thalian
#1
Mónica L García-Gómez, Eugenio Azpeitia, Elena R Álvarez-Buylla
The study of the concerted action of hormones and transcription factors is fundamental to understand cell differentiation and pattern formation during organ development. The root apical meristem of Arabidopsis thaliana is a useful model to address this. It has a stem cell niche near its tip conformed of a quiescent organizer and stem or initial cells around it, then a proliferation domain followed by a transition domain, where cells diminish division rate before transiting to the elongation zone; here, cells grow anisotropically prior to their final differentiation towards the plant base...
April 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28415379/chimeras-and-clusters-in-networks-of-hyperbolic-chaotic-oscillators
#2
A V Cano, M G Cosenza
We show that chimera states, where differentiated subsets of synchronized and desynchronized dynamical elements coexist, can emerge in networks of hyperbolic chaotic oscillators subject to global interactions. As local dynamics we employ Lozi maps, which possess hyperbolic chaotic attractors. We consider a globally coupled system of these maps and use two statistical quantities to describe its collective behavior: the average fraction of elements belonging to clusters and the average standard deviation of state variables...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28415236/globally-attracting-synchrony-in-a-network-of-oscillators-with-all-to-all-inhibitory-pulse-coupling
#3
Carmen C Canavier, Ruben A Tikidji-Hamburyan
The synchronization tendencies of networks of oscillators have been studied intensely. We assume a network of all-to-all pulse-coupled oscillators in which the effect of a pulse is independent of the number of oscillators that simultaneously emit a pulse and the normalized delay (the phase resetting) is a monotonically increasing function of oscillator phase with the slope everywhere less than 1 and a value greater than 2φ-1, where φ is the normalized phase. Order switching cannot occur; the only possible solutions are globally attracting synchrony and cluster solutions with a fixed firing order...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28405191/cognitive-architecture-with-evolutionary-dynamics-solves-insight-problem
#4
Anna Fedor, István Zachar, András Szilágyi, Michael Öllinger, Harold P de Vladar, Eörs Szathmáry
In this paper, we show that a neurally implemented a cognitive architecture with evolutionary dynamics can solve the four-tree problem. Our model, called Darwinian Neurodynamics, assumes that the unconscious mechanism of problem solving during insight tasks is a Darwinian process. It is based on the evolution of patterns that represent candidate solutions to a problem, and are stored and reproduced by a population of attractor networks. In our first experiment, we used human data as a benchmark and showed that the model behaves comparably to humans: it shows an improvement in performance if it is pretrained and primed appropriately, just like human participants in Kershaw et al...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28381275/quantitative-evaluation-and-reversion-analysis-of-the-attractor-landscapes-of-an-intracellular-regulatory-network-for-colorectal-cancer
#5
Yunseong Kim, Sea Choi, Dongkwan Shin, Kwang-Hyun Cho
BACKGROUND: Cancer reversion, converting the phenotypes of a cancer cell into those of a normal cell, has been sporadically observed throughout history. However, no systematic analysis has been attempted so far. RESULTS: To investigate this from a systems biological perspective, we have constructed a logical network model of colorectal tumorigenesis by integrating key regulatory molecules and their interactions from previous experimental data. We identified molecular targets that can reverse cancerous cellular states to a normal state by systematically perturbing each molecular activity in the network and evaluating the resulting changes of the attractor landscape with respect to uncontrolled proliferation, EMT, and stemness...
April 5, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28364765/modeling-the-network-dynamics-of-pulse-coupled-neurons
#6
Sarthak Chandra, David Hathcock, Kimberly Crain, Thomas M Antonsen, Michelle Girvan, Edward Ott
We derive a mean-field approximation for the macroscopic dynamics of large networks of pulse-coupled theta neurons in order to study the effects of different network degree distributions and degree correlations (assortativity). Using the ansatz of Ott and Antonsen [Chaos 18, 037113 (2008)], we obtain a reduced system of ordinary differential equations describing the mean-field dynamics, with significantly lower dimensionality compared with the complete set of dynamical equations for the system. We find that, for sufficiently large networks and degrees, the dynamical behavior of the reduced system agrees well with that of the full network...
March 2017: Chaos
https://www.readbyqxmd.com/read/28363113/the-attractor-recurrent-neural-network-based-on-fuzzy-functions-an-effective-model-for-the-classification-of-lung-abnormalities
#7
Mohammad Bagher Khodabakhshi, Mohammad Hassan Moradi
The respiratory system dynamic is of high significance when it comes to the detection of lung abnormalities, which highlights the importance of presenting a reliable model for it. In this paper, we introduce a novel dynamic modelling method for the characterization of the lung sounds (LS), based on the attractor recurrent neural network (ARNN). The ARNN structure allows the development of an effective LS model. Additionally, it has the capability to reproduce the distinctive features of the lung sounds using its formed attractors...
March 23, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28356477/moving-slowly-is-hard-for-humans-limitations-of-dynamic-primitives
#8
Se-Woong Park, Hamal Marino, Steven K Charles, Dagmar Sternad, Neville Hogan
Mounting evidence suggests that human motor control uses dynamic primitives, attractors of dynamic neural networks which require minimal central supervision. However, advantages for control may be offset by compromised versatility. Extending recent results showing that humans could not sustain discrete motions as duration decreased, this study tested whether smoothly rhythmic performance could be maintained as duration increased. Participants performed horizontal movements between two targets, paced by sounds that increased from 1s to 6s by 200ms per cycle and then decreased again...
March 29, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28348638/cardioprotection-effects-of-sevoflurane-by-regulating-the-pathway-of-neuroactive-ligand-receptor-interaction-in-patients-undergoing-coronary-artery-bypass-graft-surgery
#9
Jinquan Wang, Jian Cheng, Chao Zhang, Xiaojun Li
This study was designed to identify attractor modules and further reveal the potential biological processes involving in sevoflurane-induced anesthesia in patients treated with coronary artery bypass graft (CABG) surgery. Microarray profile data (ID: E-GEOD-4386) on atrial samples obtained from patients receiving anesthetic gas sevoflurane prior to and following CABG procedure were downloaded from EMBL-EBI database for further analysis. Protein-protein interaction (PPI) networks of baseline and sevoflurane groups were inferred and reweighted according to Spearman correlation coefficient (SCC), followed by systematic modules inference using clique-merging approach...
2017: Computational and Mathematical Methods in Medicine
https://www.readbyqxmd.com/read/28327650/erratum-the-combination-of-the-functionalities-of-feedback-circuits-is-determinant-for-the-attractors-number-and-size-in-pathway-like-boolean-networks
#10
Eugenio Azpeitia, Stalin Muñoz, Daniel González-Tokman, Mariana Esther Martínez-Sánchez, Nathan Weinstein, Aurélien Naldi, Elena R Álvarez-Buylla, David A Rosenblueth, Luis Mendoza
No abstract text is available yet for this article.
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28323150/systematic-expression-profiling-analysis-mines-dys-regulated-modules-in-active-tuberculosis-based-on-re-weighted-protein-protein-interaction-network-and-attract-algorithm
#11
Ying Sun, Yan Weng, Ying Zhang, Xiang Yan, Lei Guo, Jia Wang, Xin Song, Ying Yuan, Fu-Ye Chang, Chun-Ling Wang
About 90% of tuberculosis (TB) patients latently infected with Mycobacterium tuberculosis (Mtb) show no symptoms, yet have a 10% chance in lifetime to progress active TB. Nevertheless, current diagnosis approaches need improvement in efficiency and sensitivity. The objective of this work was to detect potential signatures for active TB to further improve the understanding of the biological roles of functional modules involved in this disease. First, targeted networks of active TB and control groups were established via re-weighting protein-protein interaction (PPI) networks using Pearson's correlation coefficient (PCC)...
March 18, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28303791/integer-programming-based-method-for-observability-of-singleton-attractors-in-boolean-networks
#12
Xiaoqing Cheng, Yushan Qiu, Wenpin Hou, Wai-Ki Ching
Boolean network (BN) is a popular mathematical model for revealing the behaviour of a genetic regulatory network. Furthermore, observability, an important network feature, plays a significant role in understanding the underlying network. Several studies have been done on analysis of observability of BNs and complex networks. However, the observability of attractor cycles, which can serve as biomarker detection, has not yet been addressed in the literature. This is an important, interesting and challenging problem that deserves a detailed study...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28303788/dynamics-and-robustness-of-the-cardiac-progenitor-cell-induced-pluripotent-stem-cell-network-during-cell-phenotypes-transition
#13
Yuangen Yao, Chengzhang Ma, Haiyou Deng, Quan Liu, Wei Cao, Rong Gui, Tianquan Feng, Ming Yi
Robustness is a fundamental characteristic of biological systems since all living systems need to adapt to internal or external perturbations, unpredictable environments, stochastic events and unreliable components, and so on. A long-term challenge in systems biology is to reveal the origin of robustness underlying molecular regulator network. In this study, a simple Boolean model is used to investigate the global dynamic properties and robustness of cardiac progenitor cell (CPC) induced pluripotent stem cell network that governs reprogramming and directed differentiation process...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28302453/brain-rhythm-attractor-breakdown-in-alzheimer-s-disease-functional-and-pathologic-implications
#14
Elissaios Karageorgiou, Keith A Vossel
This perspective binds emerging evidence on the bidirectional relationship between Alzheimer's disease (AD) and sleep disorders through a model of brain rhythm attractor breakdown. This approach explains behavioral-cognitive changes in AD across the sleep-wake cycle and supports a causal association between early brainstem tau pathology and subsequent cortical amyloid-β accumulation. Specifically, early tau dysregulation within brainstem-hypothalamic nuclei leads to breakdown of sleep-wake attractor networks, with patients displaying an attenuated range of behavioral and electrophysiological activity patterns, a "twilight zone" of constant activity between deep rest and full alertness...
March 14, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28297946/cluster-synchronization-in-networks-of-identical-oscillators-with-%C3%AE-function-pulse-coupling
#15
Bolun Chen, Jan R Engelbrecht, Renato Mirollo
We study a network of N identical leaky integrate-and-fire model neurons coupled by α-function pulses, weighted by a coupling parameter K. Studies of the dynamics of this system have mostly focused on the stability of the fully synchronized and the fully asynchronous splay states, which naturally depends on the sign of K, i.e., excitation vs inhibition. We find that there is also a rich set of attractors consisting of clusters of fully synchronized oscillators, such as fixed (N-1,1) states, which have synchronized clusters of sizes N-1 and 1, as well as splay states of clusters with equal sizes greater than 1...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28297900/transient-dynamics-and-their-control-in-time-delay-autonomous-boolean-ring-networks
#16
Johannes Lohmann, Otti D'Huys, Nicholas D Haynes, Eckehard Schöll, Daniel J Gauthier
Biochemical systems with switch-like interactions, such as gene regulatory networks, are well modeled by autonomous Boolean networks. Specifically, the topology and logic of gene interactions can be described by systems of continuous piecewise-linear differential equations, enabling analytical predictions of the dynamics of specific networks. However, most models do not account for time delays along links associated with spatial transport, mRNA transcription, and translation. To address this issue, we have developed an experimental test bed to realize a time-delay autonomous Boolean network with three inhibitory nodes, known as a repressilator, and use it to study the dynamics that arise as time delays along the links vary...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28280579/measure-for-degree-heterogeneity-in-complex-networks-and-its-application-to-recurrence-network-analysis
#17
Rinku Jacob, K P Harikrishnan, R Misra, G Ambika
We propose a novel measure of degree heterogeneity, for unweighted and undirected complex networks, which requires only the degree distribution of the network for its computation. We show that the proposed measure can be applied to all types of network topology with ease and increases with the diversity of node degrees in the network. The measure is applied to compute the heterogeneity of synthetic (both random and scale free (SF)) and real-world networks with its value normalized in the interval [Formula: see text]...
January 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28270783/semi-supervised-learning-of-cartesian-factors-a-top-down-model-of-the-entorhinal-hippocampal-complex
#18
András Lőrincz, András Sárkány
The existence of place cells (PCs), grid cells (GCs), border cells (BCs), and head direction cells (HCs) as well as the dependencies between them have been enigmatic. We make an effort to explain their nature by introducing the concept of Cartesian Factors. These factors have specific properties: (i) they assume and complement each other, like direction and position and (ii) they have localized discrete representations with predictive attractors enabling implicit metric-like computations. In our model, HCs make the distributed and local representation of direction...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28261066/ring-attractor-dynamics-emerge-from-a-spiking-model-of-the-entire-protocerebral-bridge
#19
Kyobi S Kakaria, Benjamin L de Bivort
Animal navigation is accomplished by a combination of landmark-following and dead reckoning based on estimates of self motion. Both of these approaches require the encoding of heading information, which can be represented as an allocentric or egocentric azimuthal angle. Recently, Ca(2+) correlates of landmark position and heading direction, in egocentric coordinates, were observed in the ellipsoid body (EB), a ring-shaped processing unit in the fly central complex (CX; Seelig and Jayaraman, 2015). These correlates displayed key dynamics of so-called ring attractors, namely: (1) responsiveness to the position of external stimuli; (2) persistence in the absence of external stimuli; (3) locking onto a single external stimulus when presented with two competitors; (4) stochastically switching between competitors with low probability; and (5) sliding or jumping between positions when an external stimulus moves...
2017: Frontiers in Behavioral Neuroscience
https://www.readbyqxmd.com/read/28256642/identifying-the-optimal-anticancer-targets-from-the-landscape-of-a-cancer-immunity-interaction-network
#20
Chunhe Li
Cancer immunotherapy, an approach of targeting immune cells to attack tumor cells, has been suggested to be a promising way for cancer treatment recently. However, the successful application of this approach warrants a deeper understanding of the intricate interplay between cancer cells and the immune system. Especially, the mechanisms of immunotherapy remain elusive. In this work, we constructed a cancer-immunity interplay network by incorporating interactions among cancer cells and some representative immune cells, and uncovered the potential landscape of the cancer-immunity network...
March 3, 2017: Physical Chemistry Chemical Physics: PCCP
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