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Statistical characteristics of climbing fiber spikes necessary for efficient cerebellar learning.

Mean firing rates (MFRs), with analogue values, have thus far been used as information carriers of neurons in most brain theories of learning. However, the neurons transmit the signal by spikes, which are discrete events. The climbing fibers (CFs), which are known to be essential for cerebellar motor learning, fire at the ultra-low firing rates (around 1 Hz), and it is not yet understood theoretically how high-frequency information can be conveyed and how learning of smooth and fast movements can be achieved. Here we address whether cerebellar learning can be achieved by CF spikes instead of conventional MFR in an eye movement task, such as the ocular following response (OFR), and an arm movement task. There are two major afferents into cerebellar Purkinje cells: parallel fiber (PF) and CF, and the synaptic weights between PFs and Purkinje cells have been shown to be modulated by the stimulation of both types of fiber. The modulation of the synaptic weights is regulated by the cerebellar synaptic plasticity. In this study we simulated cerebellar learning using CF signals as spikes instead of conventional MFR. To generate the spikes we used the following four spike generation models: (1) a Poisson model in which the spike interval probability follows a Poisson distribution, (2) a gamma model in which the spike interval probability follows the gamma distribution, (3) a max model in which a spike is generated when a synaptic input reaches maximum, and (4) a threshold model in which a spike is generated when the input crosses a certain small threshold. We found that, in an OFR task with a constant visual velocity, learning was successful with stochastic models, such as Poisson and gamma models, but not in the deterministic models, such as max and threshold models. In an OFR with a stepwise velocity change and an arm movement task, learning could be achieved only in the Poisson model. In addition, for efficient cerebellar learning, the distribution of CF spike-occurrence time after stimulus onset must capture at least the first, second and third moments of the temporal distribution of error signals.

Action Potentials↗

Methodology of ECG interpretation in the Louvain program.

The Louvain program performs the analysis and interpretation of the vectorcardiogram (VCG) to increase the clinical utility of ECG analysis. Among its original features, there are (1) a high-resolution vector-loop display for visual analysis, (2) quantitative analysis of the spatial VCG using age-sex stratified limits, (3) separate software for adult and pediatric series and (4) complementary deterministic and statistical methods of diagnostic classification. Using objective, ECG-independent evidence as a reference standard, the Louvain program has shown satisfactory levels of diagnostic accuracy in most basic categories. However, its usefulness is especially marked in "borderline" or "complex" situations, where the 12-lead ECG cannot provide a clear answer. It corresponds to the concept of "computer-assisted ECG interpretation" as opposed to "computer ECG analysis".

Adult↗

Mathematical modelling, simulation and prediction of tumour-induced angiogenesis.

Angiogenesis, the formation of blood vessels from a pre-existing vasculature, is a process whereby capillary sprouts are formed in response to externally supplied chemical stimuli. The sprouts then grow and develop, driven by endothelial cell migration and proliferation, and organise themselves into a dendritic structure. Angiogenesis occurs during embryogenesis, wound healing, arthritis and during the growth of solid tumours. In this paper we present a novel mathematical model which describes the formation of the capillary sprout network in response to chemical stimuli (tumour angiogenesis factors, TAF) supplied by a solid tumour. The model also takes into account endothelial cell-extracellular matrix interactions via the inclusion of fibronectin in the model. The model consists of a system of nonlinear partial differential equations describing the response in space and time of endothelial cells to the TAF and the fibronectin (migration, proliferation, anastomosis, branching). Using the discretized system of partial differential equations, we use a deterministic cellular automata (DCA) model, which enables us to track individual endothelial cells and incorporate branching explicity into the model. Numerical simulations are presented which are in very good qualitative agreement with experimental observations. Certain experiments are suggested which could be used to test the hypotheses of the model and various extensions and developments of the model with particular applications to anti-angiogenesis strategies are discussed.

Animals↗

Improving conformational searches by geometric screening.

MOTIVATION: Conformational searches in molecular docking are a time-consuming process with wide range of applications. Favorable conformations of the ligands that successfully bind with receptors are sought to form stable ligand-receptor complexes. Usually a large number of conformations are generated and their binding energies are examined. We propose adding a geometric screening phase before an energy minimization procedure so that only conformations that geometrically fit in the binding site will be prompted for energy calculation. RESULTS: Geometric screening can drastically reduce the number of conformations to be examined from millions (or higher) to thousands (or lower). The method can also handle cases when there are more variables than geometric constraints. An early-stage implementation is able to finish the geometric filtering of conformations for molecules with up to nine variables in 1 min. To the best of our knowledge, this is the first time such results are reported deterministically. CONTACT: mzhang@mdanderson.org.

Algorithms↗

Modelling and simulation of a schistosomiasis infection with biological control.

A mathematical model is developed for a schistosomiasis infection that involves human and intermediate snail hosts as well as an additional mammalian host and a competitor snail species. The model consists of a system of eight differential equations for the infected and susceptible subpopulations. The deterministic system is generalized to a stochastic system of differential equations to account for the random behavior of demographic changes in the population levels. Values for the parameters in the model are estimated and the populations are computationally simulated under various conditions. Results of the simulations indicate several interesting features such as the rapidity by which an invading competing snail species can change the dynamics of a schistosomiasis infection.

Animals↗

Adaptive stochastic-deterministic chemical kinetic simulations.

MOTIVATION: Biochemical signaling pathways and genetic circuits often involve very small numbers of key signaling molecules. Computationally expensive stochastic methods are necessary to simulate such chemical situations. Single-molecule chemical events often co-exist with much larger numbers of signaling molecules where mass-action kinetics is a reasonable approximation. Here, we describe an adaptive stochastic method that dynamically chooses between deterministic and stochastic calculations depending on molecular count and propensity of forward reactions. The method is fixed timestep and has first order accuracy. We compare the efficiency of this method with exact stochastic methods. RESULTS: We have implemented an adaptive stochastic-deterministic approximate simulation method for chemical kinetics. With an error margin of 5%, the method solves typical biologically constrained reaction schemes more rapidly than exact stochastic methods for reaction volumes >1-10 micro m(3). We have developed a test suite of reaction cases to test the accuracy of mixed simulation methods. AVAILABILITY: Simulation software used in the paper is freely available from http://www.ncbs.res.in/kinetikit/download.html

Algorithms↗

Using mark-recapture methodology to estimate the size of a population at risk for sexually transmitted diseases.

To study the spread of sexually transmitted diseases (STDs) using social/sexual mixing models, one must have quantitative information about sexual mixing. An unavoidable complication in gathering such information by survey is that members of the surveyed population will almost certainly have sexual contacts outside that population. The number of these outsiders may be substantial and, hence, important for the modelling process. In this paper, we develop a mark-recapture model for estimating the size of the population at risk for contracting a STD due to direct sexual contact with a specified population targeted by a survey. This mark-recapture methodology provides a reliable method of estimating the number of outsiders. Because not everyone in the targeted population may be sexually active, the size of the sexually active subset, used as the number marked in our tag-recapture formulation, must be estimated, which introduces extra variability. We derive an estimator of the variance of the estimated total number at risk that accounts for this extra variability and an expression for the bias of that estimator. We extend the methodology to stratified surveys and illustrate its use with data collected from a population of university undergraduates to estimate sexual mixing parameters of a deterministic model of the spread of STDs.

Analysis of Variance↗

Migration and mutation in stochastic models of gene frequency change. I. The island model.

Migration has in the past been introduced deterministically into stochastic gene frequency models. Migration at rate m then reduces the between-population variability by a factor of (1 - m)2 each generation. We show that with stochastic migration, whether of fixed or variable numbers of individuals, a positive term delta m is added to the variance. As a result of the delta m term, the equilibrium value of the between-population variability is increased compared to the corresponding value for deterministic migration by a factor of approximately (1 - m)-2 for small m. An equivalent result is derived for mutation, using the infinite allele model for a single population. We show in addition that these results may be derived much more simply by use of identity-by-descent probability methods, but only if a modified definition of the probability of identity-by-descent is used, involving the sampling with instead of without replacement of pairs of genes from the population.

Diploidy↗

Demography in an increasingly variable world.

Recent advances in stochastic demography provide unique insights into the probable effects of increasing environmental variability on population dynamics, and these insights can be substantially different compared with those from deterministic models. Stochastic variation in structured population models influences estimates of population growth rate, persistence and resilience, which ultimately can alter community composition, species interactions, distributions and harvesting. Here, we discuss how understanding these demographic consequences of environmental variation will have applications for anticipating changes in populations resulting from anthropogenic activities that affect the variance in vital rates. We also highlight new tools for anticipating the consequences of the magnitude and temporal patterning of environmental variability.

Animals↗

Whole-tree methods for detecting differential diversification rates.

Prolific cladogenesis, adaptive radiation, species selection, key innovations, and mass extinctions are a few examples of biological phenomena that lead to differential diversification among lineages. Central to the study of differential diversification rates is the ability to distinguish chance variation from that which requires deterministic explanation. To detect diversification rate variation among lineages, we propose a number of methods that incorporate information on the topological distribution of species diversity from all internal nodes of a phylogenetic tree. These whole-tree methods (M(Pi), M(Sigma), and M(R)) are explicitly connected to a null model of random diversification--the equal-rates Markov (ERM) random branching model--and an alternative model of differential diversification: M(Pi) is based on the product of individual nodal ERM probabilities; M(Sigma) is based on the sum of individual nodal ERM probabilities, and M(R) is based on a transformation of ERM probabilities that corresponds to a formalized system that orders trees by their relative symmetry. These methods have been implemented in a freely available computer program, SYMMETREE, to detect clades with variable diversification rates, thereby allowing the study of biological processes correlated with and possibly causal to shifts in diversification rate. Application of these methods to several published phylogenies demonstrates their ability to contend with relatively large, incompletely resolved trees. These topology-based methods do not require estimates of relative branch lengths, which should facilitate the analysis of phylogenies, such as supertrees, for which such data are unreliable or unavailable.

Animals↗

Measuring the complexity of time series: an application to neurophysiological signals.

Measures of signal complexity can be used to distinguish neurophysiological activation from noise in those neuroimaging techniques where we record variations of brain activity with time, e.g., fMRI, EEG, ERP. In this paper we explore a recently developed approach to calculate a quantitative measure of deterministic signal complexity and information content: The Renyi number. The Renyi number is by definition an entropy, i.e., a classically used measure of disorder in physical systems, and is calculated in this paper over the basis of the time frequency representation (TFRs) of the measured signals. When calculated in this form, the Renyi entropy (RE) indirectly characterizes the complexity of a signal by providing an approximate counting of the number of separated elementary atoms that compose the time series in the time frequency plane. In this sense, this measure conforms closely to our visual notion of complexity since low complexity values are obtained for signals formed by a small number of "components". The most remarkable properties of this measure are twofold: 1) It does not rely on assumptions about the time series such as stationarity or gaussianity and 2) No model of the neural process under study is required, e.g., no hemodynamic response model for fMRI. The method is illustrated in this paper using fMRI, intracranial ERPs and intracranial potentials estimated from scalp recorded ERPs through an inverse solution (ELECTRA). The main theoretical and practical drawbacks of this measure, especially its dependence of the selected TFR, are discussed. Also the capability of this approach to produce, with less restrictive hypothesis, results comparable to those obtained with more standard methods but is emphasized.

Algorithms↗

Interrupting neural pathways that transduce stressful information into physiological responses.

Stressor-stimuli evoke a noradrenergic process in the frontal lobes, the amplitude of which depends on both the individual's experience with the stimulus and his or her genetic background. Novel and noxious stimuli evoke large frontocortical responses and benign ones evoke relatively larger reactions in persons with a family history of cardiovascular disease. Blockade of neural projections from the frontal cortex and amygdala to the brainstem cardiovascular centers will normalize blood-pressure elevations in experimental hypertension and prevent lethal arrhythmias in animals with a myocardial infarction. The anti-mortality effect of the cardiac drugs known as beta-blockers is exerted by inhibition of cerebral beta-receptors, not peripheral ones. A new putative neuropeptide, NLX, may have the same desirable cardiovascular effects, but without the side-effects that limit clinical usefulness. The neural regulation of the heart during stress can be detected by a new deterministic measure of low-dimensional chaos in heartbeat intervals. In both animals and humans undergoing myocardial infarction, this deterministic measure correctly predicts lethal arrhythmogenesis, minutes to hours prior to the event. Thus an approach combining both brain and heart studies (i.e., "neurocardiology") has led to an understanding of how stressor-stimuli evoke autonomic reactions. This, in turn, has led to new methods in the diagnosis and treatment of cardiovascular disorders.

Animals↗

Propensity of a circadian clock to adjust to the 24h day-night light cycle and its sensitivity to molecular noise.

The circadian clock of Drosophila melanogaster and its tendency to adjust to the day-night light cycle is simulated by deterministic and stochastic methods. The robustness of the locking to the light-cycle with respect to molecular noise is studied. It is found that within the model studied, the molecular noise in the stochastic simulation erases the finer injection-locking structures, stronger injection signals are needed and the locking has the character of prolonged locked time intervals with cycle slips in between. The simulations are compared to a simple injection-locking model with noise that seems to describe the overall behavior well.

Algorithms↗

Sustained oscillations in stochastic systems.

Many non-linear deterministic models for interacting populations present damped oscillations towards the corresponding equilibrium values. However, simulations produced with related stochastic models usually present sustained oscillations which preserve the natural frequency of the damped oscillations of the deterministic model but showing non-vanishing amplitudes. The relation between the amplitude of the stochastic oscillations and the values of the equilibrium populations is not intuitive in general but scales with the square root of the populations when the ratio between different populations is kept fixed. In this work, we explain such phenomena for the case of a general epidemic model. We estimate the stochastic fluctuations of the populations around the equilibrium point in the epidemiological model showing their (approximated) relation with the mean values.

Models, Biological↗

COAST: Controllable approximative stochastic reaction algorithm.

We present an approximative algorithm for stochastic simulations of chemical reaction systems, called COAST, based on three different modeling levels: for small numbers of particles an exact stochastic model; for intermediate numbers an approximative, but computationally more efficient stochastic model based on discrete Gaussian distributions; and for large numbers the deterministic reaction kinetics. In every simulation time step, the subdivision of the reaction channels into the three different modeling levels is done automatically, where all approximations applied can be controlled by a single error parameter for which an appropriate value can easily be found. Test simulations show that the results of COAST simulations agree well with the outcomes of exact algorithms; however, the asymptotic run times of COAST are asymptotically proportional to smaller powers of the particle numbers than exact algorithms.

Algorithms↗

Augmented moment method for stochastic ensembles with delayed couplings. II. FitzHugh-Nagumo model.

Dynamics of FitzHugh-Nagumo (FN) neuron ensembles with time-delayed couplings subject to white noises, has been studied by using both direct simulations and a semianalytical augmented moment method (AMM) which has been proposed in a preceding paper [H. Hasegawa, Phys. Rev. E 70, 021911 (2004)]. For N-unit FN neuron ensembles, AMM transforms original 2N-dimensional stochastic delay differential equations (SDDEs) to infinite-dimensional deterministic DEs for means and correlation functions of local and global variables. Infinite-order recursive DEs are terminated at the finite level m in the level-m AMM (AMMm), yielding 8(m+1)-dimensional deterministic DEs. When a single spike is applied, the oscillation may be induced if parameters of coupling strength, delay, noise intensity and/or ensemble size are appropriate. Effects of these parameters on the emergence of the oscillation and on the synchronization in FN neuron ensembles have been studied. The synchronization shows the fluctuation-induced enhancement at the transition between nonoscillating and oscillating states. Results calculated by AMM5 are in fairly good agreement with those obtained by direct simulations.

Action Potentials↗

Linearity of cortical receptive fields measured with natural sounds.

How do cortical neurons represent the acoustic environment? This question is often addressed by probing with simple stimuli such as clicks or tone pips. Such stimuli have the advantage of yielding easily interpreted answers, but have the disadvantage that they may fail to uncover complex or higher-order neuronal response properties. Here, we adopt an alternative approach, probing neuronal responses with complex acoustic stimuli, including animal vocalizations. We used in vivo whole-cell methods in the rat auditory cortex to record subthreshold membrane potential fluctuations elicited by these stimuli. Most neurons responded robustly and reliably to the complex stimuli in our ensemble. Using regularization techniques, we estimated the linear component, the spectrotemporal receptive field (STRF), of the transformation from the sound (as represented by its time-varying spectrogram) to the membrane potential of the neuron. We find that the STRF has a rich dynamical structure, including excitatory regions positioned in general accord with the prediction of the classical tuning curve. However, whereas the STRF successfully predicts the responses to some of the natural stimuli, it surprisingly fails completely to predict the responses to others; on average, only 11% of the response power could be predicted by the STRF. Therefore, most of the response of the neuron cannot be predicted by the linear component, although the response is deterministically related to the stimulus. Analysis of the systematic errors of the STRF model shows that this failure cannot be attributed to simple nonlinearities such as adaptation to mean intensity, rectification, or saturation. Rather, the highly nonlinear response properties of auditory cortical neurons must be attributable to nonlinear interactions between sound frequencies and time-varying properties of the neural encoder.

Acoustic Stimulation↗

Reliability of a fly motion-sensitive neuron depends on stimulus parameters.

The variability of responses of sensory neurons constrains how reliably animals can respond to stimuli in the outside world. We show for a motion-sensitive visual interneuron of the fly that the variability of spike trains depends on the properties of the motion stimulus, although differently for different stimulus parameters. (1) The spike count variances of responses to constant and to dynamic stimuli lie in the same range. (2) With increasing stimulus size, the variance may slightly decrease. (3) Increasing pattern contrast reduces the variance considerably. For all stimulus conditions, the spike count variance is much smaller than the mean spike count and does not depend much on the mean activity apart from very low activities. Using a model of spike generation, we analyzed how the spike count variance depends on the membrane potential noise and the deterministic membrane potential fluctuations at the spike initiation zone of the neuron. In a physiologically plausible range, the variance is affected only weakly by changes in the dynamics or the amplitude of the deterministic membrane potential fluctuations. In contrast, the amplitude and dynamics of the membrane potential noise strongly influence the spike count variance. The membrane potential noise underlying the variability of the spike responses in the motion-sensitive neuron is concluded to be affected considerably by the contrast of the stimulus but by neither its dynamics nor its size.

Action Potentials↗