64 research outputs found
Measuring Information Transfer
An information theoretic measure is derived that quantifies the statistical
coherence between systems evolving in time. The standard time delayed mutual
information fails to distinguish information that is actually exchanged from
shared information due to common history and input signals. In our new
approach, these influences are excluded by appropriate conditioning of
transition probabilities. The resulting transfer entropy is able to distinguish
driving and responding elements and to detect asymmetry in the coupling of
subsystems.Comment: 4 pages, 4 Figures, Revte
Lyapunov spectral analysis of a nonequilibrium Ising-like transition
By simulating a nonequilibrium coupled map lattice that undergoes an
Ising-like phase transition, we show that the Lyapunov spectrum and related
dynamical quantities such as the dimension correlation length~ are
insensitive to the onset of long-range ferromagnetic order. As a function of
lattice coupling constant~ and for certain lattice maps, the Lyapunov
dimension density and other dynamical order parameters go through a minimum.
The occurrence of this minimum as a function of~ depends on the number of
nearest neighbors of a lattice point but not on the lattice symmetry, on the
lattice dimensionality or on the position of the Ising-like transition. In
one-space dimension, the spatial correlation length associated with magnitude
fluctuations and the length~ are approximately equal, with both
varying linearly with the radius of the lattice coupling.Comment: 29 pages of text plus 15 figures, uses REVTeX macros. Submitted to
Phys. Rev. E
Theory and computation of covariant Lyapunov vectors
Lyapunov exponents are well-known characteristic numbers that describe growth
rates of perturbations applied to a trajectory of a dynamical system in
different state space directions. Covariant (or characteristic) Lyapunov
vectors indicate these directions. Though the concept of these vectors has been
known for a long time, they became practically computable only recently due to
algorithms suggested by Ginelli et al. [Phys. Rev. Lett. 99, 2007, 130601] and
by Wolfe and Samelson [Tellus 59A, 2007, 355]. In view of the great interest in
covariant Lyapunov vectors and their wide range of potential applications, in
this article we summarize the available information related to Lyapunov vectors
and provide a detailed explanation of both the theoretical basics and numerical
algorithms. We introduce the notion of adjoint covariant Lyapunov vectors. The
angles between these vectors and the original covariant vectors are
norm-independent and can be considered as characteristic numbers. Moreover, we
present and study in detail an improved approach for computing covariant
Lyapunov vectors. Also we describe, how one can test for hyperbolicity of
chaotic dynamics without explicitly computing covariant vectors.Comment: 21 pages, 5 figure
HERMES: Towards an Integrated Toolbox to Characterize Functional and Effective Brain Connectivity
The analysis of the interdependence between time series has become an important field of research in the last years, mainly as a result of advances in the characterization of dynamical systems from the signals they produce, the introduction of concepts such as generalized and phase synchronization and the application of information theory to time series analysis. In neurophysiology, different analytical tools stemming from these concepts have added to the ‘traditional’ set of linear methods, which includes the cross-correlation and the coherency function in the time and frequency domain, respectively, or more elaborated tools such as Granger Causality. This increase in the number of approaches to tackle the existence of functional (FC) or effective connectivity (EC) between two (or among many) neural networks, along with the mathematical complexity of the corresponding time series analysis tools, makes it desirable to arrange them into a unified-easy-to-use software package. The goal is to allow neuroscientists, neurophysiologists and researchers from related fields to easily access and make use of these analysis methods from a single integrated toolbox. Here we present HERMES (http://hermes.ctb.upm.es), a toolbox for the Matlab® environment (The Mathworks, Inc), which is designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. We believe that this toolbox will be very helpful to all the researchers working in the emerging field of brain connectivity analysis
Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium
Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These “memory” effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesis and estimate the capacity of these systems and growth dynamics to ‘remember’ 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy
Resveratrol and Cancer: Focus on in vivo Evidence
Resveratrol is a naturally occurring polyphenol that provides a number of anti-aging health benefits including improved metabolism, cardioprotection, and cancer prevention. Much of the work on resveratrol and cancer comes from in vitro studies looking at resveratrol actions on cancer cells and pathways. There are, however, comparatively fewer studies that have investigated resveratrol treatment and cancer outcomes in vivo, perhaps limited by its poor bioavailability when taken orally. Although research in cell culture has shown promising and positive effects of resveratrol, evidence from rodents and humans is inconsistent. This review highlights the in vivo effects of resveratrol treatment on breast, colorectal, liver, pancreatic, and prostate cancers. Resveratrol supplementation in animal models of cancer has shown positive, neutral as well as negative outcomes depending on resveratrol route of administration, dose, tumor model, species, and other factors. Within a specific cancer type, there is variability between studies with respect to strain, age, and sex of animal used, timing and method of resveratrol supplementation, and dose of resveratrol used to study cancer endpoints. Together, the data suggest that many factors need to be considered before resveratrol can be used for human cancer prevention or therapy
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