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Testing a semistochastic variant of the interactive activation model in different word recognition experiments.

A semistochastic variant of the interactive activation (IA) model of context effects in letter perception (McClelland & Rumelhart, 1981) was used to simulate response time distributions and means in different experiments investigating the effects of word frequency, neighborhood size and frequency, and orthographic priming in visual word recognition. The results provide evidence in favor of the connectivity assumption underlying the model but question the necessity of the interactivity assumption for simulating latencies in word recognition tasks. Together with those of a recent study by McClelland (1991), the present results suggest that 10 years after its appearance, the IA model's potential for testing hypotheses about the structure and dynamics of basic phenomena of human information processing in a variety of perceptual and cognitive tasks is not yet fully exploited.

Arousal↗

Initialization, noise, singularities, and scale in height ridge traversal for tubular object centerline extraction.

The extraction of the centerlines of tubular objects in two and three-dimensional images is a part of many clinical image analysis tasks. One common approach to tubular object centerline extraction is based on intensity ridge traversal. In this paper, we evaluate the effects of initialization, noise, and singularities on intensity ridge traversal and present multiscale heuristics and optimal-scale measures that minimize these effects. Monte Carlo experiments using simulated and clinical data are used to quantify how these "dynamic-scale" enhancements address clinical needs regarding speed, accuracy, and automation. In particular, we show that dynamic-scale ridge traversal is insensitive to its initial parameter settings, operates with little additional computational overhead, tracks centerlines with subvoxel accuracy, passes branch points, and handles significant image noise. We also illustrate the capabilities of the method for medical applications involving a variety of tubular structures in clinical data from different organs, patients, and imaging modalities.

Algorithms↗

Speed of feedforward and recurrent processing in multilayer networks of integrate-and-fire neurons.

The speed of processing in the visual cortical areas can be fast, with for example the latency of neuronal responses increasing by only approximately 10 ms per area in the ventral visual system sequence V1 to V2 to V4 to inferior temporal visual cortex. This has led to the suggestion that rapid visual processing can only be based on the feedforward connections between cortical areas. To test this idea, we investigated the dynamics of information retrieval in multiple layer networks using a four-stage feedforward network modelled with continuous dynamics with integrate-and-fire neurons, and associative synaptic connections between stages with a synaptic time constant of 10 ms. Through the implementation of continuous dynamics, we found latency differences in information retrieval of only 5 ms per layer when local excitation was absent and processing was purely feedforward. However, information latency differences increased significantly when non-associative local excitation was included. We also found that local recurrent excitation through associatively modified synapses can contribute significantly to processing in as little as 15 ms per layer, including the feedforward and local feedback processing. Moreover, and in contrast to purely feed-forward processing, the contribution of local recurrent feedback was useful and approximately this rapid even when retrieval was made difficult by noise. These findings suggest that cortical information processing can benefit from recurrent circuits when the allowed processing time per cortical area is at least 15 ms long.

Action Potentials↗

Action potential onset dynamics and the response speed of neuronal populations.

The result of computational operations performed at the single cell level are coded into sequences of action potentials (APs). In the cerebral cortex, due to its columnar organization, large number of neurons are involved in any individual processing task. It is therefore important to understand how the properties of coding at the level of neuronal populations are determined by the dynamics of single neuron AP generation. Here, we analyze how the AP generating mechanism determines the speed with which an ensemble of neurons can represent transient stochastic input signals. We analyze a generalization of the theta-neuron, the normal form of the dynamics of Type-I excitable membranes. Using a novel sparse matrix representation of the Fokker-Planck equation, which describes the ensemble dynamics, we calculate the transmission functions for small modulations of the mean current and noise noise amplitude. In the high-frequency limit the transmission function decays as omega(-gamma), where gamma surprisingly depends on the phase theta(s) at which APs are emitted. If at theta(s) the dynamics is insensitive to external inputs, the transmission function decays as (i) omega(-3) for the case of a modulation of a white noise input and as (ii) omega(-2) for a modulation of the mean input current in the presence of a correlated and uncorrelated noise as well as (iii) in the case of a modulated amplitude of a correlated noise input. If the insensitivity condition is lifted, the transmission function always decays as omega(-1), as in conductance based neuron models. In a physiologically plausible regime up to 1 kHz the typical response speed is, however, independent of the high-frequency limit and is set by the rapidness of the AP onset, as revealed by the full transmission function. In this regime modulations of the noise amplitude can be transmitted faithfully up to much higher frequencies than modulations in the mean input current. We finally show that the linear response approach used is valid for a large regime of stimulus amplitudes.

Action Potentials↗

Simulated maximum likelihood method for estimating kinetic rates in gene expression.

MOTIVATION: Kinetic rate in gene expression is a key measurement of the stability of gene products and gives important information for the reconstruction of genetic regulatory networks. Recent developments in experimental technologies have made it possible to measure the numbers of transcripts and protein molecules in single cells. Although estimation methods based on deterministic models have been proposed aimed at evaluating kinetic rates from experimental observations, these methods cannot tackle noise in gene expression that may arise from discrete processes of gene expression, small numbers of mRNA transcript, fluctuations in the activity of transcriptional factors and variability in the experimental environment. RESULTS: In this paper, we develop effective methods for estimating kinetic rates in genetic regulatory networks. The simulated maximum likelihood method is used to evaluate parameters in stochastic models described by either stochastic differential equations or discrete biochemical reactions. Different types of non-parametric density functions are used to measure the transitional probability of experimental observations. For stochastic models described by biochemical reactions, we propose to use the simulated frequency distribution to evaluate the transitional density based on the discrete nature of stochastic simulations. The genetic optimization algorithm is used as an efficient tool to search for optimal reaction rates. Numerical results indicate that the proposed methods can give robust estimations of kinetic rates with good accuracy.

Algorithms↗

Biased intrachromosomal gene conversion in a chromosome lineage.

A model for the evolution of a family of tandemly repeated genes in a single chromosome lineage under intrachromosomal gene conversion [43] is analyzed further and extended. Direct and diffusion approximations are derived for the exact fixation probabilities, mean time to fixation or loss, and mean conditional fixation time of Nagylaki and Petes [43]. The distribution of the number of variant repeats under the joint action of gene conversion and reversible mutation is investigated; exact and approximate expressions are derived for the stationary distribution. It is shown that conversional bias greatly increases the amount of sequence homogeneity at equilibrium. The diffusion processes studied here also apply to selection and mutation in a finite population, and some new results are established for that classical problem.

Alleles↗

A parity-dependent immigration-birth-death-emigration process.

An immigration-birth-death-emigration process is studied when the immigration, birth, death, and emigration parameters depend on two parity classes of individuals, namely, zero and nonzero parity. The expected number of individuals in the population at time t and that of emigrants in (0,t) of both parity classes are obtained using the probability generating function (pgf) technique. The explicit expression for the pgf of the process is derived when the parameters are parity-independent. Population extinction and some limiting results are also discussed.

Candida albicans↗

Brownian motion, fluctuation and life.

The measurements of dynamic behaviors of biomolecules in relation to their functions have been allowed using single molecule measurements. Thermal Brownian motion causes random step motion of motor proteins and structural fluctuation of protein molecules between multiple states. In hierarchic structure of life, the fluctuation is modulated. Random fluctuation is biased to directional motion and reactions as a result of interaction of proteins. The fluctuation of kinetic state of signaling proteins results in polarization and localization of cells. A recognition process in brain is also explained by the equation analogous to biochemical reaction at the molecular level. Thus dynamic processes originated from thermal motion may play an important role in activation processes in life.

Actins↗

A model for the oscillatory motion of single dynein molecules.

Axonemal dynein is the molecular motor responsible for the rhythmic beating of eukaryotic cilia and flagella. An individual axonemal dynein molecule is capable of both unidirectional and oscillatory motion along a microtubule (Nature 393 (1998) 711). We propose a model which links the physical motion of a two-headed dynein molecule to its ATP hydrolysis cycle, and which exhibits both processive and oscillatory behaviors. A mathematical analysis of the model is used to make experimentally testable predictions.

Animals↗

Distinct roles of transcription factors TFIIIB and TFIIIC in RNA polymerase III transcription reinitiation.

Eukaryotic RNA polymerase (Pol) III is recruited to target promoters by a stable preinitiation complex containing transcription factors TFIIIC and TFIIIB. After the first transcription cycle, reinitiation proceeds through facilitated recycling, a process by which the terminating Pol III rapidly reloads onto the same transcription unit. Here, we show that Pol III is repeatedly recaptured in vitro by the first transcribed gene, even in the presence of a juxtaposed competitor promoter complex, thus suggesting that facilitated recycling is not merely due to a stochastic reassociation process favored by the small size of class III genes. The transcription factor requirements for facilitated reinitiation were investigated by taking advantage of Pol III templates that support both TFIIIC-dependent and TFIIIC-independent transcription. A TFIIIC-less transcription system, in which TFIIIB was reconstituted from recombinant TATA box-binding protein and Brf1 proteins and a crude fraction containing the Bdp1 component, was sufficient to direct efficient Pol III recycling on short ( approximately 100 bp) class III genes. Unexpectedly, however, on longer (>300 bp) transcription units, reinitiation in the presence of TFIIIB alone was compromised, and TFIIIC was further required to reestablish a high reinitiation rate. Transcription reinitiation was also severely impaired when recombinant Bdp1 protein replaced the corresponding crude fraction in reconstituted TFIIIB. The data reveal an unexpected complexity in the Pol III reinitiation mechanism and suggest the existence of a handing-back network between Pol III, TFIIIC, and TFIIIB on actively transcribed class III genes.

DNA-(Apurinic or Apyrimidinic Site) Lyase↗

Flow correlated percolation during vascular remodeling in growing tumors.

A theoretical model based on the molecular interactions between a growing tumor and a dynamically evolving blood vessel network describes the transformation of the regular vasculature in normal tissues into a highly inhomogeneous tumor specific capillary network. The emerging morphology, characterized by the compartmentalization of the tumor into several regions differing in vessel density, diameter, and necrosis, is in accordance with experimental data for human melanoma. Vessel collapse due to a combination of severely reduced blood flow and solid stress exerted by the tumor leads to a correlated percolation process that is driven towards criticality by the mechanism of hydrodynamic vessel stabilization.

Blood Vessels↗

The unified neutral theory of biodiversity: do the numbers add up?

Hubbell's unified neutral theory is a zero-sum ecological drift model in which population sizes change at random in a process resembling genetic drift, eventually leading to extinction. Diversity is maintained within the community by speciation. Hubbell's model makes predictions about the distribution of species abundances within communities and the turnover of species from place to place (beta diversity). However, ecological drift cannot be tested adequately against these predictions without independent estimates of speciation rates, population sizes, and dispersal distances. A more practical prediction from ecological drift is that time to extinction of a population of size N is approximately 2N generations. I test this prediction here using data for passerine birds (Passeriformes). Waiting times to speciation and extinction were estimated from genetic divergence between sister populations and a lineage-through-time plot for endemic South American suboscine passerines. Population sizes were estimated from local counts of birds in two large forest plots extrapolated to the area of wet tropical forest in South America and from atlas data on European passerines. Waiting times to extinction (ca. 2 Ma) are much less than twice the product of average population size (4.0 and 14.4 x 10(6) individuals in South America and Europe) and generation length (five and three years) for songbirds, that is, 40 and 86 Ma, respectively. Thus, drift is too slow to account for turnover in regional avifaunas. Presumably, other processes, involving external drivers, such as climate and physiographic change, and internal drivers, such as evolutionary change in antagonistic interactions, predominate. Hubbell's model is historical and geographic, and his perspective importantly links local and regional process and pattern. Ecological reality can be added to the mix while retaining Hubbell's concept of continuity of communities in space and time.

Biodiversity↗

Software sensor for on-line estimation of the microbial activity in activated sludge systems.

This paper considers the design of a software sensor (or soft-sensor) for the on-line estimation of the biological activities of a colony of aerobic micro-organisms acting on activated sludge processes, where the carbonaceous waste degradation and nitrification processes are taken into account. These bioactivities are intimately related to the dissolved oxygen concentration. Two factors that affect the dynamics of the dissolved oxygen are the respiration rate or the oxygen uptake rate (OUR) and the oxygen transfer function (K(l)a). These items are challenging topics for the application of recursive identification due the nonlinear characteristic of the oxygen transfer function, and to the time-varying feature of the respiration rate. In this work, OUR and the oxygen transfer function are estimated through a software sensor, which is based on a modified version of the discrete extended Kalman filter. Numerical simulations are carried out in a predenitrifying activated sludge process benchmark and the obtained results demonstrate the applicability and efficiency of the proposed methodology, which should provide a valuable tool to supervise and control activated sludge processes.

Algorithms↗

Fuzzy control of multivariable process by modified error decoupling.

In this paper, a control concept for the squared (equal number of inputs and outputs) multivariable process systems is given. The proposed control system consists of two parts, single loop fuzzy controllers in each loop and a centralized decoupling unit. The fuzzy control system uses feedback control to minimize the error in the loop and the decoupler uses an adaptive technique to mitigate loop interactions. The decoupler predicts the interacting loop changes and modifies the input (error) of the loop controller. The controller was tested on the simulation model of "single component vaporizer" process. The results indicate that the decoupling controller shows better performance for set point and load changes.

Algorithms↗

Metapopulation dynamics with quasi-local competition.

Stepping-stone models for the ecological dynamics of metapopulations are often used to address general questions about the effects of spatial structure on the nature and complexity of population fluctuations. Such models describe an ensemble of local and spatially isolated habitat patches that are connected through dispersal. Reproduction and hence the dynamics in a given local population depend on the density of that local population, and a fraction of every local population disperses to neighboring patches. In such models, interesting dynamic phenomena, e.g. the persistence of locally unstable predator-prey interactions, are only observed if the local dynamics in an isolated patch exhibit non-equilibrium behavior. Therefore, the scope of these models is limited. Here we extend these models by making the biologically plausible assumption that reproductive success in a given local habitat not only depends on the density of the local population living in that habitat, but also on the densities of neighboring local populations. This would occur if competition for resources occurs between neighboring populations, e.g. due to foraging in neighboring habitats. With this assumption of quasi-local competition the dynamics of the model change completely. The main difference is that even if the dynamics of the local populations have a stable equilibrium in isolation, the spatially uniform equilibrium in which all local populations are at their carrying capacity becomes unstable if the strength of quasi-local competition reaches a critical level, which can be calculated analytically. In this case the metapopulation reaches a new stable state, which is, however, not spatially uniform anymore and instead results in an irregular spatial pattern of local population abundance. For large metapopulations, a huge number of different, spatially non-uniform equilibrium states coexist as attractors of the metapopulation dynamics, so that the final state of the system depends critically on the initial conditions. The existence of a large number of attractors has important consequences when environmental noise is introduced into the model. Then the metapopulation performs a random walk in the space of all attractors. This leads to large and complicated population fluctuations whose power spectrum obeys a red-shifted power law. Our theory reiterates the potential importance of spatial structure for ecological processes and proposes new mechanisms for the emergence of non-uniform spatial patterns of abundance and for the persistence of complicated temporal population fluctuations.

Competitive Behavior↗

Estimation in degradation models with explanatory variables.

Influence of covariates on degradation is modelled. Models which include dependence of the intensity of the process of traumatic events on the degradation level are also discussed. Estimation of reliability and degradation characteristics from data with covariates is considered in dynamic environments.

Equipment Failure↗

Texture segregation and visual search: a comparison of the effects of random variations along irrelevant dimensions.

The effects of irrelevant variations in the color and depth of elements on participants' ability to detect and discriminate elements defined by a difference in orientation were compared. Consistent with previous research, it was found that there was no effect or small effects if the targets were single elements in visual search tasks and that there were large effects for targets defined by several elements defining an area in visual segmentation tasks. It is suggested that the reason for the discrepancy between the 2 paradigms lies in the need for grouping processes in segmentation experiments. This notion was examined in 3 additional experiments that manipulated grouping processes through task demands and stimulus design. The data provide tentative support for this notion.

Adult↗