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PubMed1998

On the piecewise analysis of networks of linear threshold neurons.

The computational abilities of recurrent networks of neurons with a linear activation function above threshold are analyzed. These networks selectively realise a linear mapping of their input. Using this property, the dynamics as well as the number and the stability of stationary states can be investigated. The important property of the boundedness of neural activities can be guaranteed by global inhibition. If used together with self-excitation, the global inhibition gives rise to a multi stable winner-take-all (WTA) mechanism. A condition for a neuron to be a potential winner of the competing dynamics is derived. The network becomes a largest input selector when the self-excitation is marginal.Slowing down the global inhibition produces oscillations. The study of oscillations of random networks suggests that all cyclic trajectories of linear threshold networks are a result of the existence of partitions with undamped linear oscillations. Chaotic dynamics were never encountered in computer simulations and perhaps do not exist at all in small networks.

Journal Article↗
PubMed2006

Perturbation avalanches and criticality in gene regulatory networks.

Boolean networks are simplified models of gene regulatory networks. We derive an approximation of the size distribution of perturbation avalanches in Boolean networks based on known results in the theory of branching processes. We show numerically that the approximation works well for different kinds of Boolean networks. It has been suggested that gene regulatory networks may be dynamically critical. To study this, as an application of the presented theory we present a novel method for estimating an order parameter from microarray data. According to the available data and our method, we find that gene regulatory networks appear to be stable and reside near the phase transition between order and chaos.

Animals↗
PubMed2003

Computer simulation of water in cytochrome c oxidase.

Statistical mechanics and molecular dynamics simulations have been carried out to study the distribution and dynamics of internal water molecules in bovine heart cytochrome c oxidase (CcO). CcO is found to be capable of holding plenty of water, which in subunit I alone amounts to about 165 molecules. The dynamic characterization of these water molecules is carried out. The nascent water molecules produced in the redox reaction at the heme a(3)-CuB binuclear site form an intriguing chain structure. The chain begins at the position of Glu242 at the end of the D channel, and has a fork structure, one branch of which leads to the binuclear center, and the other to the propionate d of heme a(3). The branch that leads to the binuclear center has dynamic access both to the site where the formation of water occurs, and to delta-nitrogen of His291. From the binuclear center, the chain continues to run into the K channel. The stability of this hydrogen bond network is examined dynamically. The catalytic site is located at the hydrophobic region, and the nascent water molecules are produced at the top of the energy hill. The energy gradient is utilized as the mechanism of water removal from the protein. The water exit channels are explored using high-temperature dynamics simulations. Two putative channels for water exit from the catalytic site have been identified. One is leading directly toward Mg(2+) site. However, this channel is only open when His291 is dissociated from CuB. If His291 is bound to CuB, the only channel for water exit is the one that originates at E242 and leads toward the middle of the membrane. This is the same channel that is presumably used for oxygen supply.

Animals↗
PubMed2003

Analysis and modelling of signal transduction pathways in systems biology.

There is general agreement that a systems approach is needed for a better understanding of causal and functional relationships that generate the dynamics of biological networks and pathways. These observations have been the basis for efforts to get the engineering and physical sciences involved in life sciences. The emergence of systems biology as a new area of research is evidence for these developments. Dynamic modelling and simulation of signal transduction pathways is an important theme in systems biology and is getting growing attention from researchers with an interest in the analysis of dynamic systems. This paper introduces systems biology in terms of the analysis and modelling of signal transduction pathways. Focusing on mathematical representations of cellular dynamics, a number of emerging challenges and perspectives are discussed.

Computational Biology↗
PubMed2006

Synchronization in uncertain complex networks.

We consider the problem of synchronization in uncertain generic complex networks. For generic complex networks with unknown dynamics of nodes and unknown coupling functions including uniform and nonuniform inner couplings, some simple linear feedback controllers with updated strengths are designed using the well-known LaSalle invariance principle. The state of an uncertain generic complex network can synchronize an arbitrary assigned state of an isolated node of the network. The famous Lorenz system is stimulated as the nodes of the complex networks with different topologies. We found that the star coupled and scale-free networks with nonuniform inner couplings can be in the state of synchronization if only a fraction of nodes are controlled.

Action Potentials↗
PubMed2003

Empowered women, social networks and the contribution of qualitative research: broadening our understanding of underlying causes for food and nutrition insecurity.

OBJECTIVE: To investigate underlying causes for food and nutrition insecurity in black South African households and to gain understanding of the factors contributing to better nutrition security, with emphasis on household organisation, gender and intra-household dynamics and social networks. DESIGN, SETTING AND SUBJECTS: Within a larger cross-sectional survey that investigated the impact of urbanisation on the health of black South Africans, 166 people, mostly women, were interviewed on household food security. Methods used were structured face-to-face interviews, in-depth interviews, observation, interviews with key informants and a sociodemographic questionnaire. Information was collected from 1998 to 2000 in 15 rural and urban areas of the North West Province, South Africa. RESULTS: Three-quarters of households in this sample are chronically food-insecure. Families are disrupted, due to migrant work, poverty and increasing societal violence, and half of households are female-headed. Certain categories of female-headed households and households based on partnership relationships, despite more limited resources, achieve a better or an equal economic status and better nutrition security than those households led by men, with the latter often being considered an economic liability. The reliance on and fostering of social ties and networks appear to be of central significance. CONCLUSION: Gender and intra-household relations, as well as social networks and income from informal sector activities, are often not uncovered by conventional statistical methods. Qualitative research can reveal the unexpected and furthermore empowers people, as their voices are heard.

Adult↗
PubMed2005

Spatial and temporal development of chondrocyte-seeded agarose constructs in free-swelling and dynamically loaded cultures.

Dynamic deformational loading has been shown to significantly increase the development of material properties of chondrocyte-seeded agarose hydrogels, however little is known about the spatial development of the material properties within these constructs. In this study, a technique that combines video microscopy and optimized digital image correlation, was applied to assess the spatial development of material properties in tissue-engineered cartilage constructs cultured in free-swelling and dynamically-loaded conditions (3h/day, 5 days/week, and maintained in free-swelling conditions when not being loaded) over a 6-week period. Although homogeneous at day 0, both free-swelling and dynamically loaded samples progressively developed stiffer outer edges and a softer central region. The distribution of GAGs and collagens were shown to mimic this profile. These results indicate that although dynamic loading augments the development of bulk properties in these samples, possibly by overcoming some of the diffusion limitation and nutrient transport issues, the overall profile of construct properties in the axial direction remains qualitatively the same as in free-swelling culture conditions. Poisson's ratio of these constructs increased over time in culture with increased fixed charged density contributed by the GAGs, but this increase was significantly less in dynamically loaded samples by day 42. Polarized light microscopy of Picrosirius Red labeled samples, at an angle perpendicular to the direction of loading, suggests that these differences in Poisson's ratio may be due to improved organization of collagen network in the dynamically loaded samples.

Animals↗
PubMed2003

Unravelling Nature's networks.

Dramatic progress has been made recently in determining the genetic and molecular composition of cells. This has prompted the development of new approaches to the challenge of understanding how basic cellular mechanisms are coordinated to produce the dazzling complexity of living systems. To face this challenge fully, it is critical not only to know what genes and proteins are expressed in cells, but also to understand the spatiotemporal dynamics of their networks of interactions. The sheer scale and complexity of cellular interaction networks necessitates a multi-disciplinary effort in which sophisticated experimental techniques are employed in combination with computational analysis and mathematical modelling. Such approaches are beginning to provide insight into basic structures and mechanisms, and promise to become critical to the post-genomic mission of understanding the cell as a complex dynamical system.

Cells↗
PubMed1979

Effect of boundaries on the response of a neural network.

The effect an abrupt boundary has upon the dynamical response of a neural network is investigated. The retina of the Limulus eye is used as a model system for studying this effect. A theoretical technique is presented for the quantitative prediction of the manner in which this neural network responds in the vicinity of its boundary. Corresponding experimental measurements of the response to moving stimuli by single optic neurons located near retinal boundaries are presented. Theory and experiment show detailed quantitative agreement.

Animals↗
PubMed2006

Synchronizing weighted complex networks.

Real networks often consist of local units, which interact with each other via asymmetric and heterogeneous connections. In this work, we explore the constructive role played by such a directed and weighted wiring for the synchronization of networks of coupled dynamical systems. The stability condition for the synchronous state is obtained from the spectrum of the respective coupling matrices. In particular, we consider a coupling scheme in which the relative importance of a link depends on the number of shortest paths through it. We illustrate our findings for networks with different topologies: scale free, small world, and random wirings.

Action Potentials↗
PubMed1992

A neural network model rapidly learning gains and gating of reflexes necessary to adapt to an arm's dynamics.

Effects of dynamic coupling, gravity, inertia and the mechanical impedances of the segments of a multi-jointed arm are shown to be neutralizable through a reflex-like operating three layer static feedforward network. The network requires the proprioceptively mediated actual state variables (here angular velocity and position) of each arm segment. Added neural integrators (and/or differentiators) can make the network exhibit dynamic properties. Then, actual feedback is not necessary and the network can operate in a pure feedforward fashion. Feedforward of an additional load can easily be implemented into the network using "descendent gating", and a negative feedback control loop added to the feedforward control reduces errors due to external noise. A training, which combines a least squared error based simultaneous learning rule (LSQ-rule) with a "self-imitation algorithm" based on direct inverse modeling, enables the network to acquire the whole inverse dynamics, limb parameters included, during one short training movement. The considerations presented also hold for multi-jointed manipulators.

Animals↗
PubMed1992

Bayesian belief networks in quantitative histopathology.

Bayesian belief networks have a dynamic range and numeric response characteristics that make them uniquely suitable for descriptive classification schemes. Features showing considerable overlap of tolerance regions may be used, in a cumulative manner, to derive unequivocal classification decisions. The numeric response characteristics of Bayesian belief networks are analyzed, and their application as control modules in automated scene segmentation in histopathology is demonstrated.

Bayes Theorem↗
PubMed1996

Aids, violence and behavioral coding: information theory, risk behavior and dynamic process on core-group sociogeographic networks.

Elsewhere we have presented a traveling-wave analysis of HIV transmission on a tightly self-interactive, geographically-focused core group social network (Wallace R. Soc. Sci. Med. 32, 847, 1991; Soc. Sci. Med. 33, 1155, 1991; Environ. Plan. A. 26, 767, 1994; Wallace R. and Fullilove M. Environ. Plan. A. 23, 1701 1991). Here we reanalyze the problem in probability space and recover a close analog of the Shannon Coding Theorem of information theory. Subsequent direct application of information-theoretic methods provides striking insight regarding the spread of disease along the sociogeographic networks of marginalized subgroups, suggesting that 'risk behaviors' for infection may constitute essential components of a behavioral code for the transmission of information within the noisy channel of a marginalized community's social networks. The code's form, including the incorporation of risk behaviors, arises as a direct consequence of the external oppressive forces which structure marginalization. This viewpoint suggests an explanation of the sometime-observed rapid transmission of both infection and of control strategies for infection along the same network, but suggests further that if risk behaviors are indeed parts of a behavioral code for the transmission of group norms, statements of individual worth or resource sharing, then high rates of relapse are inevitable, given the persistence of the external oppression which gives those behaviors symbolic value. We suggest that violent acts in particular may emerge as key behavioral symbols for 'sending a message' in socially disorganized communities, implying that school-based or other individual-oriented harm reduction strategies for violence prevention, in the absence of a comprehensive, multifactorial reform program, cannot significantly reverse the effects of continuing economic and social constraints or of public policies of planned shrinkage and benign neglect, factors primarily responsible for the disorganization of urban minority communities within the United States.

Acquired Immunodeficiency Syndrome↗
PubMed2000

Cortical dynamics of memory.

Memory networks are formed in the cerebral cortex by associative processes, following Hebbian principles of synaptic modulation. Sensory and motor memory networks are made of elementary representations in cell assemblies of primary sensory and motor cortex (phyletic memory). Higher-order individual memories, e.g. episodic, semantic, conceptual - are represented in hierarchically organized neuronal networks of the cortex of association. Perceptual memories are organized in posterior (post-rolandic) cortex, motor (executive) memories in cortex of the frontal lobe. Memory networks overlap and interact profusely with one another, such that a cellular assembly can be part of many memories or networks. Working memory essentially consists in the temporary activation of a memory network, as needed for the execution of successive acts in a temporal structure of behavior. That activation of the network is maintained by recurrent excitation through reentrant circuits. The recurrent reentry may occur within local circuits as well as between separate cortical areas. In either case. recurrence binds together the associated components of the network and thus of the memory it represents.

Animals↗
PubMedDate not supplied

Rule-dynamical generalization of McCulloch-Pitts neuron networks.

A new aspect for neuronal networks is presented. The aspect is based on the concept of ruledynamics which was originally proposed by one of the authors, Aizawa. The concept of ruledynamics were modeled on the two states cellular automata of neighborhood-three (CA(2/3)). A brief review of ruledynamics is also presented, because most publications of the authors so far have been in Japanese. Our concise assertion in the present paper is that a neuronal network realizes a kind of ruledynamics. This assertion is a speculation on the comparison of McCulloch-Pitts neuron networks with ruledynamics on CA(2/3). A trial is originally shown to demonstrate that a McCulloch-Pitts neuron network can be imitated by an extended version of ruledynamics on CA(2/3).

Models, Neurological↗
PubMed2001

Feature extraction and classification of breast cancer on dynamic magnetic resonance imaging using artificial neural network.

A neural network system was designed to extract and analyze the quantitative data from time-intensity profile. These data was used to predict the outcome of biopsy in a group of patients with histopathologically proved breast lesions. The performance of an artificial neural network (ANN) was compared with radiologists using a database with 120 patients' records each of which consisted of 14 quantitative parameters mostly derived directly from time-intensity profile. The network was trained and tested using the jackknife method and its performance was then compared with that of the radiologists in terms of sensitivity, specificity and accuracy using receiver operating characteristic curve (ROC) analysis. The network was able to classify correctly 107 of 120 original cases and yielded a better diagnostic accuracy (89%), compared with that of the radiologist (79%) by performing a constructive association between extracted quantitative data and corresponding pathological results (r=0.72, P<0.001).

Adolescent↗
PubMed2004

Electron hopping dynamics in monolayer-protected au cluster network polymer films by rotated disk electrode voltammetry.

Electrons are transported within polymeric films of alkanethiolate monolayer-protected Au clusters (MPCs) by electron hopping (self-exchange) between the metal cores. The surrounding monolayers, the molecular linkers that generate the network polymer film, or both, presumably serve as tunneling bridges in the electron transfers. This paper introduces a steady-state electrochemical method for measuring electron hopping rates in solvent-wetted and swollen, ionically conductive MPC films. The films are network polymer films of nanoparticles, coated on a rotated disk electrode that is contacted by a solution of a redox species (decamethylferrocene, CpFe). Controlling the electrode potential such that the film mediates oxidation of the redox probe can force control of the overall current onto the rate of electron hopping within the film, which is characterized as the apparent electron diffusion coefficient D(E). D(E) is translated into an apparent electron hopping rate k(ET) by a cubic lattice model. The experiment is applied to MPC network polymer films linked by alpha,omega-alkanedithiolates and by metal ion-carboxylate connections. We evaluate the dependencies of apparent hopping rate on CpFe concentration, film thickness, electrode potential relative to the CpFe formal potential, film-swelling solvent, and temperature. The apparent hopping rates are in the 10(4)-10(5) s(-)(1) range, which is slower than those for the same kind of MPC films, but in a dry (nonswollen) state measured by electronic conductivities.

Journal Article↗