Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.

The impact of measurement errors in the identification of regulatory networks

Background: There are several studies in the literature depicting measurement error in gene expression data and also, several others about regulatory network models. However, only a little fraction describes a combination of measurement error in mathematical regulatory networks and shows how to identify these networks under different rates of noise. Results: This article investigates the effects of measurement error on the estimation of the parameters in regulatory networks. Simulation studies indicate that, in both time series (dependent) and non-time series (independent) data, the measurement error strongly affects the estimated parameters of the regulatory network models, biasing them as predicted by the theory. Moreover, when testing the parameters of the regulatory network models, p-values computed by ignoring the measurement error are not reliable, since the rate of false positives are not controlled under the null hypothesis. In order to overcome these problems, we present an improved version of the Ordinary Least Square estimator in independent (regression models) and dependent (autoregressive models) data when the variables are subject to noises. Moreover, measurement error estimation procedures for microarrays are also described. Simulation results also show that both corrected methods perform better than the standard ones (i.e., ignoring measurement error). The proposed methodologies are illustrated using microarray data from lung cancer patients and mouse liver time series data. Conclusions: Measurement error dangerously affects the identification of regulatory network models, thus, they must be reduced or taken into account in order to avoid erroneous conclusions. This could be one of the reasons for high biological false positive rates identified in actual regulatory network models.

Structure, stability, depolarized light scattering, and vibrational spectra of fullerenols from all-electron density-functional-theory calculations

We have investigated the stability, electronic properties, Rayleigh (elastic), and Raman (inelastic) depolarization ratios, infrared and Raman absorption vibrational spectra of fullerenols [C(60)(OH)(n)] with different degrees of hydroxylation by using all-electron density-functional-theory (DFT) methods. Stable arrangements of these molecules were found by means of full geometry optimizations using Becke's three-parameter exchange functional with the Lee, Yang, and Parr correlation functional. This DFT level has been combined with the 6-31G(d,p) Gaussian-type basis set, as a compromise between accuracy and capability to treat highly hydroxylated fullerenes, e.g., C(60)(OH)(36). Thus, the molecular properties of fullerenols were systematically analyzed for structures with n=1, 2, 3, 4, 8, 10, 16, 18, 24, 32, and 36. From the electronic structure analysis of these molecules, we have evidenced an important effect related to the weak chemical reactivity of a possible C(60)(OH)(24) isomer. To investigate Raman scattering and the vibrational spectra of the different fullerenols, frequency calculations are carried out within the harmonic approximation. In this case a systematic study is only performed for n=1-4, 8, 10, 16, 18, and 24. Our results give good agreements with the expected changes in the spectral absorptions due to the hydroxylation of fullerenes.

Music and faith: The religious scene in the Brazilian phonographic market

This text discusses the phonographic segment of religious music in Brazil in its two main manifestations, linked respectively to the Catholic and Protestant traditions. The text offers a brief history of both traditions, as well as a description of their main recording companies and artists of greatest prominence. In its final part. the text presents the strategies that bring together recording companies and independent artists, as well as ponders over Brazil`s independent musical production as a whole.

MUSICAL ANALYSIS OF THE PRELUDE N.1, LA COLOMBE, BY OLIVIER MESSIAEN

This work proposes an association between musical analysis techniques developed during the twentieth and the twenty-first centuries, presented by authors like Felix Salzer and Joseph Straus, and the musical theory concepts presented by Olivier Messiaen, for the analysis of Prelude n(o) 1, La Colombe. The analysis contributes to broaden the theory concepts presented by the composer. In the Conclusion we trace lines of an authorial sonority by Olivier Messiaen.

Modeling associations between genetic markers using Bayesian networks

Motivation: Understanding the patterns of association between polymorphisms at different loci in a population ( linkage disequilibrium, LD) is of fundamental importance in various genetic studies. Many coefficients were proposed for measuring the degree of LD, but they provide only a static view of the current LD structure. Generative models (GMs) were proposed to go beyond these measures, giving not only a description of the actual LD structure but also a tool to help understanding the process that generated such structure. GMs based in coalescent theory have been the most appealing because they link LD to evolutionary factors. Nevertheless, the inference and parameter estimation of such models is still computationally challenging. Results: We present a more practical method to build GM that describe LD. The method is based on learning weighted Bayesian network structures from haplotype data, extracting equivalence structure classes and using them to model LD. The results obtained in public data from the HapMap database showed that the method is a promising tool for modeling LD. The associations represented by the learned models are correlated with the traditional measure of LD D`. The method was able to represent LD blocks found by standard tools. The granularity of the association blocks and the readability of the models can be controlled in the method. The results suggest that the causality information gained by our method can be useful to tell about the conservability of the genetic markers and to guide the selection of subset of representative markers.

H(infinity) filtering for rectangular discrete-time descriptor systems

This paper deals with the H(infinity) recursive estimation problem for general rectangular time-variant descriptor systems in discrete time. Riccati-equation based recursions for filtered and predicted estimates are developed based on a data fitting approach and game theory. In this approach, the nature determines a state sequence seeking to maximize the estimation cost, whereas the estimator tries to find an estimate that brings the estimation cost to a minimum. A solution exists for a specified gamma-level if the resulting cost is positive. In order to present some computational alternatives to the H(infinity) filters developed, they are rewritten in information form along with the respective array algorithms. (C) 2009 Elsevier Ltd. All rights reserved.

Fault Detection in Power Distribution Systems Using Automated Integration of Computational Intelligence Tools

The main purpose of this paper is to present architecture of automated system that allows monitoring and tracking in real time (online) the possible occurrence of faults and electromagnetic transients observed in primary power distribution networks. Through the interconnection of this automated system to the utility operation center, it will be possible to provide an efficient tool that will assist in decisionmaking by the Operation Center. In short, the desired purpose aims to have all tools necessary to identify, almost instantaneously, the occurrence of faults and transient disturbances in the primary power distribution system, as well as to determine its respective origin and probable location. The compilations of results from the application of this automated system show that the developed techniques provide accurate results, identifying and locating several occurrences of faults observed in the distribution system.

Experimental results on the nonlinear H(infinity) control via quasi-LPV representation and game theory for wheeled mobile robots

In this paper, nonlinear dynamic equations of a wheeled mobile robot are described in the state-space form where the parameters are part of the state (angular velocities of the wheels). This representation, known as quasi-linear parameter varying, is useful for control designs based on nonlinear H(infinity) approaches. Two nonlinear H(infinity) controllers that guarantee induced L(2)-norm, between input (disturbances) and output signals, bounded by an attenuation level gamma, are used to control a wheeled mobile robot. These controllers are solved via linear matrix inequalities and algebraic Riccati equation. Experimental results are presented, with a comparative study among these robust control strategies and the standard computed torque, plus proportional-derivative, controller.

Timoshenko versus Euler beam theory: Pitfalls of a deterministic approach

The selection criteria for Euler-Bernoulli or Timoshenko beam theories are generally given by means of some deterministic rule involving beam dimensions. The Euler-Bernoulli beam theory is used to model the behavior of flexure-dominated (or ""long"") beams. The Timoshenko theory applies for shear-dominated (or ""short"") beams. In the mid-length range, both theories should be equivalent, and some agreement between them would be expected. Indeed, it is shown in the paper that, for some mid-length beams, the deterministic displacement responses for the two theories agrees very well. However, the article points out that the behavior of the two beam models is radically different in terms of uncertainty propagation. In the paper, some beam parameters are modeled as parameterized stochastic processes. The two formulations are implemented and solved via a Monte Carlo-Galerkin scheme. It is shown that, for uncertain elasticity modulus, propagation of uncertainty to the displacement response is much larger for Timoshenko beams than for Euler-Bernoulli beams. On the other hand, propagation of the uncertainty for random beam height is much larger for Euler beam displacements. Hence, any reliability or risk analysis becomes completely dependent on the beam theory employed. The authors believe this is not widely acknowledged by the structural safety or stochastic mechanics communities. (C) 2010 Elsevier Ltd. All rights reserved.

Improved finite element for 3D laminate frame analysis including warping for any cross-section

The most ordinary finite element formulations for 3D frame analysis do not consider the warping of cross-sections as part of their kinematics. So the stiffness, regarding torsion, should be directly introduced by the user into the computational software and the bar is treated as it is working under no warping hypothesis. This approach does not give good results for general structural elements applied in engineering. Both displacement and stress calculation reveal sensible deficiencies for both linear and non-linear applications. For linear analysis, displacements can be corrected by assuming a stiffness that results in acceptable global displacements of the analyzed structure. However, the stress calculation will be far from reality. For nonlinear analysis the deficiencies are even worse. In the past forty years, some special structural matrix analysis and finite element formulations have been proposed in literature to include warping and the bending-torsion effects for 3D general frame analysis considering both linear and non-linear situations. In this work, using a kinematics improvement technique, the degree of freedom ""warping intensity"" is introduced following a new approach for 3D frame elements. This degree of freedom is associated with the warping basic mode, a geometric characteristic of the cross-section, It does not have a direct relation with the rate of twist rotation along the longitudinal axis, as in existent formulations. Moreover, a linear strain variation mode is provided for the geometric non-linear approach, for which complete 3D constitutive relation (Saint-Venant Kirchhoff) is adopted. The proposed technique allows the consideration of inhomogeneous cross-sections with any geometry. Various examples are shown to demonstrate the accuracy and applicability of the proposed formulation. (C) 2009 Elsevier Inc. All rights reserved.

A boundary element formulation for analysis of elastoplastic plates with geometrical nonlinearity

In this paper a new boundary element method formulation for elastoplastic analysis of plates with geometrical nonlinearities is presented. The von Mises criterion with linear isotropic hardening is considered to evaluate the plastic zone. Large deflections are assumed but within the context of small strain. To derive the boundary integral equations the von Karman`s hypothesis is taken into account. An initial stress field is applied to correct the true stresses according to the adopted criterion. Isoparametric linear elements are used to approximate the boundary unknown values while triangular internal cells with linear shape function are adopted to evaluate the domain value influences. The nonlinear system of equations is solved by using an implicit scheme together with the consistent tangent operator derived along the paper. Numerical examples are presented to demonstrate the accuracy and the validity of the proposed formulation.

BEM formulation for von Karman plates

This work deals with nonlinear geometric plates in the context of von Karman`s theory. The formulation is written such that only the boundary in-plane displacement and deflection integral equations for boundary collocations are required. At internal points, only out-of-plane rotation, curvature and in-plane internal force representations are used. Thus, only integral representations of these values are derived. The nonlinear system of equations is derived by approximating all densities in the domain integrals as single values, which therefore reduces the computational effort needed to evaluate the domain value influences. Hyper-singular equations are avoided by approximating the domain values using only internal nodes. The solution is obtained using a Newton scheme for which a consistent tangent operator was derived. (C) 2009 Elsevier Ltd. All rights reserved.

Enhanced aeroelastic energy harvesting by exploiting combined nonlinearities: theory and experiment

Converting aeroelastic vibrations into electricity for low power generation has received growing attention over the past few years. In addition to potential applications for aerospace structures, the goal is to develop alternative and scalable configurations for wind energy harvesting to use in wireless electronic systems. This paper presents modeling and experiments of aeroelastic energy harvesting using piezoelectric transduction with a focus on exploiting combined nonlinearities. An airfoil with plunge and pitch degrees of freedom (DOF) is investigated. Piezoelectric coupling is introduced to the plunge DOF while nonlinearities are introduced through the pitch DOF. A state-space model is presented and employed for the simulations of the piezoaeroelastic generator. A two-state approximation to Theodorsen aerodynamics is used in order to determine the unsteady aerodynamic loads. Three case studies are presented. First the interaction between piezoelectric power generation and linear aeroelastic behavior of a typical section is investigated for a set of resistive loads. Model predictions are compared to experimental data obtained from the wind tunnel tests at the flutter boundary. In the second case study, free play nonlinearity is added to the pitch DOF and it is shown that nonlinear limit-cycle oscillations can be obtained not only above but also below the linear flutter speed. The experimental results are successfully predicted by the model simulations. Finally, the combination of cubic hardening stiffness and free play nonlinearities is considered in the pitch DOF. The nonlinear piezoaeroelastic response is investigated for different values of the nonlinear-to-linear stiffness ratio. The free play nonlinearity reduces the cut-in speed while the hardening stiffness helps in obtaining persistent oscillations of acceptable amplitude over a wider range of airflow speeds. Such nonlinearities can be introduced to aeroelastic energy harvesters (exploiting piezoelectric or other transduction mechanisms) for performance enhancement.