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/.

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.

Real-time PCR investigation on the expression of sboA and ituD genes in Bacillus spp

Aims: To investigate the expression of sboA and ituD genes among strains of Bacillus spp. at different pH and temperature. Methods and Results: Different Bacillus strains from the Amazon basin and Bacillus subtilis ATCC 19659 were investigated for the production of subtilosin A and iturin A by qRT-PCR, analysing sboA and ituD gene expression under different culture conditions. Amazonian strains presented a general gene expression level lower than B. subtilis ATCC 19659 for sboA. In contrast, when analysing the expression of ituD gene, the strains from the Amazon, particularly P40 and P45B, exhibited higher levels of expression. Changes in pH (6 and 8) and temperature (37 and 42 degrees C) caused a decrease in sboA expression, but increased ituD expression among strains from Amazonian environment. Conclusions: Temperature and pH have an important influence on the expression of genes sboA (subtilosin A) and ituD (iturin A) among Bacillus spp. The strains P40 and P45B can be useful for the production of antimicrobial peptide iturin A. Significance and Impact of the Study: Monitoring the expression of essential biosynthetic genes by qRT-PCR is a valuable tool for optimization of the production of antimicrobial peptides.

Real-Time Voltage Regulation in Power Distribution System Using Fuzzy Control

Two different fuzzy approaches to voltage control in electric power distribution systems are introduced in this paper. The real-time controller in each case would act on power transformers equipped with under-load tap changers. Learning systems are employed to turn the voltage-control relays into adaptive devices. The scope of this study has been limited to the power distribution substation, and the voltage measurements and control actions are carried out on the secondary bus. The capacity of fuzzy systems to handle approximate data, together with their unique ability to interpret qualitative information, make it possible to design voltage-control strategies that satisfy the requirements of the Brazilian regulatory bodies and the real concerns of the electric power distribution companies. Fuzzy control systems based on these two strategies have been implemented and the test results were highly satisfactory.

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.

Mechanistic approach to predict real machining time for milling free-form geometries applying high feed rate

An accurate estimate of machining time is very important for predicting delivery time, manufacturing costs, and also to help production process planning. Most commercial CAM software systems estimate the machining time in milling operations simply by dividing the entire tool path length by the programmed feed rate. This time estimate differs drastically from the real process time because the feed rate is not always constant due to machine and computer numerical controlled (CNC) limitations. This study presents a practical mechanistic method for milling time estimation when machining free-form geometries. The method considers a variable called machine response time (MRT) which characterizes the real CNC machine`s capacity to move in high feed rates in free-form geometries. MRT is a global performance feature which can be obtained for any type of CNC machine configuration by carrying out a simple test. For validating the methodology, a workpiece was used to generate NC programs for five different types of CNC machines. A practical industrial case study was also carried out to validate the method. The results indicated that MRT, and consequently, the real machining time, depends on the CNC machine`s potential: furthermore, the greater MRT, the larger the difference between predicted milling time and real milling time. The proposed method achieved an error range from 0.3% to 12% of the real machining time, whereas the CAM estimation achieved from 211% to 1244% error. The MRT-based process is also suggested as an instrument for helping in machine tool benchmarking.

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.

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.

FOREIGN INVESTMENT AND THE BRAZILIAN REAL ESTATE MARKET

This article discusses the main aspects of the Brazilian real estate market in order to illustrate if it would be attractive for a typical American real estate investor to buy office-building portfolios in Brazil. The article emphasizes: [i] - the regulatory frontiers, comparing investment securitization, using a typical American REIT structure, with the Brazilian solution, using the Fundo de Investimento Imobiliario - FII; [ii] - the investment quality attributes in the Brazilian market, using an office building prototype, and [iii] - the comparison of [risk vs. yield] generated by an investment in the Brazilian market, using a FII, benchmarked against an existing REIT (OFFICE SUB-SECTOR) in the USA market. We conclude that investing dollars exchanged for Reais [the Brazilian currency] in a FII with a triple A office-building portfolio in the Sao Paulo marketplace will yield an annual income and a premium return above an American REIT investment. The highly aggressive scenario, along with the strong persistent exchange rate detachment to the IGP-M variations, plus instabilities affecting the generation of income, and even if we adopt a 300-point margin for the Brazil-Risk level, demonstrates that an investment opportunity in the Brazilian market, in the segment we have analyzed, outperforms an equivalent investment in the American market.

DESIGN OF CONCRETE PLATFORMS OFFSHORE USING THE THREE-LAYER SHELL THEORY

The concrete offshore platforms, which are subjected a several loading combinations and, thus, requires an analysis more generic possible, can be designed using the concepts adopted to shell elements, but the resistance must be verify in particular cross-sections to shear forces. This work about design of shell elements will be make using the three-layer shell theory. The elements are subject to combined loading of membrane and plate, totalizing eight components of internal forces, which are three membrane forces, three moments (two out-of-plane bending moments and one in-plane, or torsion, moment) and two shear forces. The design method adopted, utilizing the iterative process proposed by Lourenco & Figueiras (1993) obtained from equations of equilibrium developed by Gupta (1896) , will be compared to results of experimentally tested shell elements found in the literature using the program DIANA.

Role of price and enforcement in water allocation: Insights from Game Theory

As many countries are moving toward water sector reforms, practical issues of how water management institutions can better effect allocation, regulation, and enforcement of water rights have emerged. The problem of nonavailability of water to tailenders on an irrigation system in developing countries, due to unlicensed upstream diversions is well documented. The reliability of access or equivalently the uncertainty associated with water availability at their diversion point becomes a parameter that is likely to influence the application by users for water licenses, as well as their willingness to pay for licensed use. The ability of a water agency to reduce this uncertainty through effective water rights enforcement is related to the fiscal ability of the agency to monitor and enforce licensed use. In this paper, this interplay across the users and the agency is explored, considering the hydraulic structure or sequence of water use and parameters that define the users and the agency`s economics. The potential for free rider behavior by the users, as well as their proposals for licensed use are derived conditional on this setting. The analyses presented are developed in the framework of the theory of ""Law and Economics,`` with user interactions modeled as a game theoretic enterprise. The state of Ceara, Brazil, is used loosely as an example setting, with parameter values for the experiments indexed to be approximately those relevant for current decisions. The potential for using the ideas in participatory decision making is discussed. This paper is an initial attempt to develop a conceptual framework for analyzing such situations but with a focus on the reservoir-canal system water rights enforcement.

Galerkin finite element method for incompressible thermofluid flows framed within the bond graph theory

In this paper a bond graph methodology is used to model incompressible fluid flows with viscous and thermal effects. The distinctive characteristic of these flows is the role of pressure, which does not behave as a state variable but as a function that must act in such a way that the resulting velocity field has divergence zero. Velocity and entropy per unit volume are used as independent variables for a single-phase, single-component flow. Time-dependent nodal values and interpolation functions are introduced to represent the flow field, from which nodal vectors of velocity and entropy are defined as state variables. The system for momentum and continuity equations is coincident with the one obtained by using the Galerkin method for the weak formulation of the problem in finite elements. The integral incompressibility constraint is derived based on the integral conservation of mechanical energy. The weak formulation for thermal energy equation is modeled with true bond graph elements in terms of nodal vectors of temperature and entropy rates, resulting a Petrov-Galerkin method. The resulting bond graph shows the coupling between mechanical and thermal energy domains through the viscous dissipation term. All kind of boundary conditions are handled consistently and can be represented as generalized effort or flow sources. A procedure for causality assignment is derived for the resulting graph, satisfying the Second principle of Thermodynamics. (C) 2007 Elsevier B.V. All rights reserved.

Robust integration of real time optimization with linear model predictive control

Here, we study the stable integration of real time optimization (RTO) with model predictive control (MPC) in a three layer structure. The intermediate layer is a quadratic programming whose objective is to compute reachable targets to the MPC layer that lie at the minimum distance to the optimum set points that are produced by the RTO layer. The lower layer is an infinite horizon MPC with guaranteed stability with additional constraints that force the feasibility and convergence of the target calculation layer. It is also considered the case in which there is polytopic uncertainty in the steady state model considered in the target calculation. The dynamic part of the MPC model is also considered unknown but it is assumed to be represented by one of the models of a discrete set of models. The efficiency of the methods presented here is illustrated with the simulation of a low order system. (C) 2010 Elsevier Ltd. All rights reserved.

Real time optimization (RTO) with model predictive control (MPC)

This paper studies a simplified methodology to integrate the real time optimization (RTO) of a continuous system into the model predictive controller in the one layer strategy. The gradient of the economic objective function is included in the cost function of the controller. Optimal conditions of the process at steady state are searched through the use of a rigorous non-linear process model, while the trajectory to be followed is predicted with the use of a linear dynamic model, obtained through a plant step test. The main advantage of the proposed strategy is that the resulting control/optimization problem can still be solved with a quadratic programming routine at each sampling step. Simulation results show that the approach proposed may be comparable to the strategy that solves the full economic optimization problem inside the MPC controller where the resulting control problem becomes a non-linear programming problem with a much higher computer load. (C) 2010 Elsevier Ltd. All rights reserved.

Scatter search for a real-life heterogeneous fleet vehicle routing problem with time windows and split deliveries in Brazil

In this paper, we consider a real-life heterogeneous fleet vehicle routing problem with time windows and split deliveries that occurs in a major Brazilian retail group. A single depot attends 519 stores of the group distributed in 11 Brazilian states. To find good solutions to this problem, we propose heuristics as initial solutions and a scatter search (SS) approach. Next, the produced solutions are compared with the routes actually covered by the company. Our results show that the total distribution cost can be reduced significantly when such methods are used. Experimental testing with benchmark instances is used to assess the merit of our proposed procedure. (C) 2008 Published by Elsevier B.V.