keyword
MENU ▼
Read by QxMD icon Read
search

Attractor network

keyword
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
#1
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
#2
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
#3
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
#4
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
#5
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 13, 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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28255297/a-dynamic-bioinspired-neural-network-based-real-time-path-planning-method-for-autonomous-underwater-vehicles
#12
Jianjun Ni, Liuying Wu, Pengfei Shi, Simon X Yang
Real-time path planning for autonomous underwater vehicle (AUV) is a very difficult and challenging task. Bioinspired neural network (BINN) has been used to deal with this problem for its many distinct advantages: that is, no learning process is needed and realization is also easy. However, there are some shortcomings when BINN is applied to AUV path planning in a three-dimensional (3D) unknown environment, including complex computing problem when the environment is very large and repeated path problem when the size of obstacles is bigger than the detection range of sensors...
2017: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/28254369/applying-attractor-dynamics-to-infer-gene-regulatory-interactions-involved-in-cellular-differentiation
#13
Ahmadreza Ghaffarizadeh, Gregory J Podgorski, Nicholas S Flann
The dynamics of gene regulatory networks (GRNs) guide cellular differentiation. Determining the ways regulatory genes control expression of their targets is essential to understand and control cellular differentiation. The way a regulatory gene controls its target can be expressed as a gene regulatory function. Manual derivation of these regulatory functions is slow, error-prone and difficult to update as new information arises. Automating this process is a significant challenge and the subject of intensive effort...
February 27, 2017: Bio Systems
https://www.readbyqxmd.com/read/28223913/neuromorphic-implementation-of-attractor-dynamics-in-a-two-variable-winner-take-all-circuit-with-nmdars-a-simulation-study
#14
Hongzhi You, Da-Hui Wang
Neural networks configured with winner-take-all (WTA) competition and N-methyl-D-aspartate receptor (NMDAR)-mediated synaptic dynamics are endowed with various dynamic characteristics of attractors underlying many cognitive functions. This paper presents a novel method for neuromorphic implementation of a two-variable WTA circuit with NMDARs aimed at implementing decision-making, working memory and hysteresis in visual perceptions. The method proposed is a dynamical system approach of circuit synthesis based on a biophysically plausible WTA model...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28218914/persistently-active-neurons-in-human-medial-frontal-and-medial-temporal-lobe-support-working-memory
#15
Jan Kamiński, Shannon Sullivan, Jeffrey M Chung, Ian B Ross, Adam N Mamelak, Ueli Rutishauser
Persistent neural activity is a putative mechanism for the maintenance of working memories. Persistent activity relies on the activity of a distributed network of areas, but the differential contribution of each area remains unclear. We recorded single neurons in the human medial frontal cortex and medial temporal lobe while subjects held up to three items in memory. We found persistently active neurons in both areas. Persistent activity of hippocampal and amygdala neurons was stimulus-specific, formed stable attractors and was predictive of memory content...
February 20, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28209158/gene-regulatory-network-underlying-the-immortalization-of-epithelial-cells
#16
Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García, Elena R Alvarez-Buylla
BACKGROUND: Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of spontaneous immortalization. This process is characterized by a series of cell-state transitions, in which normal epithelial cells acquire first a senescent state which is later surpassed to attain a mesenchymal stem-like phenotype with a potentially tumorigenic behavior. In this paper we aim to provide a system-level mechanistic explanation to the emergence of these cell types, and to the time-ordered transition patterns that are common to neoplasias of epithelial origin...
February 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28186191/the-combination-of-the-functionalities-of-feedback-circuits-is-determinant-for-the-attractors-number-and-size-in-pathway-like-boolean-networks
#17
Eugenio Azpeitia, Stalin Muñoz, Daniel González-Tokman, Mariana Esther Martínez-Sánchez, Nathan Weinstein, Aurélien Naldi, Elena R Álvarez-Buylla, David A Rosenblueth, Luis Mendoza
Molecular regulation was initially assumed to follow both a unidirectional and a hierarchical organization forming pathways. Regulatory processes, however, form highly interlinked networks with non-hierarchical and non-unidirectional structures that contain statistically overrepresented circuits or motifs. Here, we analyze the behavior of pathways containing non-unidirectional (i.e. bidirectional) and non-hierarchical interactions that create motifs. In comparison with unidirectional and hierarchical pathways, our pathways have a high diversity of behaviors, characterized by the size and number of attractors...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28176397/a-scientific-theory-of-ars-memoriae-spatial-view-cells-in-a-continuous-attractor-network-with-linked-items
#18
Edmund T Rolls
The art of memory (ars memoriae) used since classical times includes using a well-known scene to associate each view or part of the scene with a different item in a speech. This memory technique is also known as the 'method of loci'. The new theory is proposed that this type of memory is implemented in the CA3 region of the hippocampus where there are spatial view cells in primates that allow a particular view to be associated with a particular object in an event or episodic memory. Given that the CA3 cells with their extensive recurrent collateral system connecting different CA3 cells, and associative synaptic modifiability, form an autoassociation or attractor network, the spatial view cells with their approximately Gaussian view fields become linked in a continuous attractor network...
February 8, 2017: Hippocampus
https://www.readbyqxmd.com/read/28159684/energy-landscape-analysis-of-the-subcortical-brain-network-unravels-system-properties-beneath-resting-state-dynamics
#19
Jiyoung Kang, Chongwon Pae, Hae-Jeong Park
The configuration of the human brain system at rest, which is in a transitory phase among multistable states, remains unknown. To investigate the dynamic systems properties of the human brain at rest, we constructed an energy landscape for the state dynamics of the subcortical brain network, a critical center that modulates whole brain states, using resting state fMRI. We evaluated alterations in energy landscapes following perturbation in network parameters, which revealed characteristics of the state dynamics in the subcortical brain system, such as maximal number of attractors, unequal temporal occupations, and readiness for reconfiguration of the system...
February 1, 2017: NeuroImage
https://www.readbyqxmd.com/read/28154501/computational-methods-for-asynchronous-basins
#20
Ian H Dinwoodie
For a Boolean network we consider asynchronous updates and define the exclusive asynchronous basin of attraction for any steady state or cyclic attractor. An algorithm based on commutative algebra is presented to compute the exclusive basin. Finally its use for targeting desirable attractors by selective intervention on network nodes is illustrated with two examples, one cell signalling network and one sensor network measuring human mobility.
December 2016: Discrete and Continuous Dynamical Systems. Series B
keyword
keyword
41275
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"