Feature selection environment for genomic applications

Background: Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction). There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e. g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application. Results: The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes ( targets or predictors) is also implemented in the system. Conclusion: The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.

Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview

Background: DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes. Results: Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools. Conclusions: DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks.

Haplotype distribution of five nuclear genes based on network genealogies and Bayesian inference indicates that Trypanosoma cruzi hybrid strains are polyphyletic

Chagas disease is still a major public health problem in Latin America. Its causative agent, Trypanosoma cruzi, can be typed into three major groups, T. cruzi I, T. cruzi II and hybrids. These groups each have specific genetic characteristics and epidemiological distributions. Several highly virulent strains are found in the hybrid group; their origin is still a matter of debate. The null hypothesis is that the hybrids are of polyphyletic origin, evolving independently from various hybridization events. The alternative hypothesis is that all extant hybrid strains originated from a single hybridization event. We sequenced both alleles of genes encoding EF-1 alpha, actin and SSU rDNA of 26 T. cruzi strains and DHFR-TS and TR of 12 strains. This information was used for network genealogy analysis and Bayesian phylogenies. We found T. cruzi I and T. cruzi II to be monophyletic and that all hybrids had different combinations of T. cruzi I and T. cruzi II haplotypes plus hybrid-specific haplotypes. Bootstrap values (networks) and posterior probabilities (Bayesian phylogenies) of clades supporting the monophyly of hybrids were far below the 95% confidence interval, indicating that the hybrid group is polyphyletic. We hypothesize that T. cruzi I and T. cruzi II are two different species and that the hybrids are extant representatives of independent events of genome hybridization, which sporadically have sufficient fitness to impact on the epidemiology of Chagas disease.

Monitoring stress tolerance and occurrences of upper respiratory illness in basketball players by means of psychometric tools and salivary biomarkers

The aim of the study was to evaluate the possible relationships between stress tolerance, training load, banal infections and salivary parameters during 4 weeks of regular training in fifteen basketball players. The Daily Analysis of Life Demands for Athletes` questionnaire (sources and symptoms of stress) and the Wisconsin Upper Respiratory Symptom Survey were used on a weekly basis. Salivary cortisol and salivary immunoglobulin A (SIgA) were collected at the beginning (before) and after the study, and measured by enzyme-linked immunosorbent assay (ELISA). Ratings of perceived exertion (training load) were also obtained. The results from ANOVA with repeated measures showed greater training loads, number of upper respiratory tract infection episodes and negative sensation to both symptoms and sources of stress, at week 2 (p < 0.05). Significant increases in cortisol levels and decreases in SIgA secretion rate were noted (before to after). Negative sensations to symptoms of stress at week 4 were inversely and significantly correlated with SIgA secretion rate. A positive and significant relationship between sources and symptoms of stress at week 4 and cortisol levels were verified. In summary, an approach incorporating in conjunction psychometric tools and salivary biomarkers could be an efficient means of monitoring reaction to stress in sport. Copyright (C) 2010 John Wiley & Sons, Ltd.

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.

Connection Admission Control for a WDM Optical Network Based on Traffic Monitoring and Bandwidth Release

We proposed a connection admission control (CAC) to monitor the traffic in a multi-rate WDM optical network. The CAC searches for the shortest path connecting source and destination nodes, assigns wavelengths with enough bandwidth to serve the requests, supervises the traffic in the most required nodes, and if needed activates a reserved wavelength to release bandwidth according to traffic demand. We used a scale-free network topology, which includes highly connected nodes ( hubs), to enhance the monitoring procedure. Numerical results obtained from computational simulations show improved network performance evaluated in terms of blocking probability.

Performance analysis of an optical network employing waveband and traffic grooming

This paper analyses an optical network architecture composed by an arrangement of nodes equipped with multi-granular optical cross-connects (MG-OXCs) in addition to the usual optical cross-connects (OXCs). Then, selected network nodes can perform both waveband as well as traffic grooming operations and our goal is to assess the improvement on network performance brought by these additional capabilities. Specifically, the influence of the MG-OXC multi-granularity on the blocking probability is evaluated for 16 classes of service over a network based on the NSFNet topology. A mechanism of fairness in bandwidth capacity is also added to the connection admission control to manage the blocking probabilities of all kind of bandwidth requirements. Comprehensive computational simulation are carried out to compare eight distinct node architectures, showing that an adequate combination of waveband and single-wavelength ports of the MG-OXCs and OXCs allow a more efficient operation of a WDM optical network carrying multi-rate traffic.

Neural network model for designing automotive devices using SMD LED

The advantages offered by the electronic component LED (Light Emitting Diode) have resulted in a quick and extensive application of this device in the replacement of incandescent lights. In this combined application, however, the relationship between the design variables and the desired effect or result is very complex and renders it difficult to model using conventional techniques. This paper consists of the development of a technique using artificial neural networks that makes it possible to obtain the luminous intensity values of brake lights using SMD (Surface Mounted Device) LEDs from design data. This technique can be utilized to design any automotive device that uses groups of SMD LEDs. The results of industrial applications using SMD LED are presented to validate the proposed technique.

Neural network-based H(infinity) control for fully actuated and underactuated cooperative manipulators

This paper develops H(infinity) control designs based on neural networks for fully actuated and underactuated cooperative manipulators. The neural networks proposed in this paper only adapt the uncertain dynamics of the robot manipulators. They work as a complement of the nominal model. The H(infinity) performance index includes the position errors as well the squeeze force errors between the manipulator end-effectors and the object, which represents a complete disturbance rejection scenario. For the underactuated case, the squeeze force control problem is more difficult to solve due to the loss of some degrees of manipulator actuation. Results obtained from an actual cooperative manipulator, which is able to work as a fully actuated and an underactuated manipulator, are presented. (C) 2008 Elsevier Ltd. All rights reserved.

Hybrid fault diagnosis scheme implementation for power distribution systems automation

Power distribution automation and control are import-ant tools in the current restructured electricity markets. Unfortunately, due to its stochastic nature, distribution systems faults are hardly avoidable. This paper proposes a novel fault diagnosis scheme for power distribution systems, composed by three different processes: fault detection and classification, fault location, and fault section determination. The fault detection and classification technique is wavelet based. The fault-location technique is impedance based and uses local voltage and current fundamental phasors. The fault section determination method is artificial neural network based and uses the local current and voltage signals to estimate the faulted section. The proposed hybrid scheme was validated through Alternate Transient Program/Electromagentic Transients Program simulations and was implemented as embedded software. It is currently used as a fault diagnosis tool in a Southern Brazilian power distribution company.

Implementation of a Control Loop Experiment in a Network-Based Control System With LonWorks Technology and IP Networks

Considering the increasing popularity of network-based control systems and the huge adoption of IP networks (such as the Internet), this paper studies the influence of network quality of service (QoS) parameters over quality of control parameters. An example of a control loop is implemented using two LonWorks networks (CEA-709.1) interconnected by an emulated IP network, in which important QoS parameters such as delay and delay jitter can be completely controlled. Mathematical definitions are provided according to the literature, and the results of the network-based control loop experiment are presented and discussed.

Ultrasound, eddy current and magnetic Barkhausen noise as tools for sigma phase detection on a UNS S31803 duplex stainless steel

Sigma phase is a deleterious one which can be formed in duplex stainless steels during heat treatment or welding. Aiming to accompany this transformation, ferrite and sigma percentage and hardness were measured on samples of a UNS S31803 duplex stainless steel submitted to heat treatment. These results were compared to measurements obtained from ultrasound and eddy current techniques, i.e., velocity and impedance, respectively. Additionally, backscattered signals produced by wave propagation were acquired during ultrasonic inspection as well as magnetic Barkhausen noise during magnetic inspection. Both signal types were processed via a combination of detrended-fluctuation analysis (DFA) and principal component analysis (PCA). The techniques used were proven to be sensitive to changes in samples related to sigma phase formation due to heat treatment. Furthermore, there is an advantage using these methods since they are nondestructive. (C) 2010 Elsevier B.V. All rights reserved.

Comparison between detailed model simulation and artificial neural network for forecasting building energy consumption

There are several ways to attempt to model a building and its heat gains from external sources as well as internal ones in order to evaluate a proper operation, audit retrofit actions, and forecast energy consumption. Different techniques, varying from simple regression to models that are based on physical principles, can be used for simulation. A frequent hypothesis for all these models is that the input variables should be based on realistic data when they are available, otherwise the evaluation of energy consumption might be highly under or over estimated. In this paper, a comparison is made between a simple model based on artificial neural network (ANN) and a model that is based on physical principles (EnergyPlus) as an auditing and predicting tool in order to forecast building energy consumption. The Administration Building of the University of Sao Paulo is used as a case study. The building energy consumption profiles are collected as well as the campus meteorological data. Results show that both models are suitable for energy consumption forecast. Additionally, a parametric analysis is carried out for the considered building on EnergyPlus in order to evaluate the influence of several parameters such as the building profile occupation and weather data on such forecasting. (C) 2008 Elsevier B.V. All rights reserved.

MODELLING AND CONTROL OF ERSW PROCESSES BY NEURONAL NETWORK

A study on the use of artificial intelligence (AI) techniques for the modelling and subsequent control of an electric resistance spot welding process (ERSW) is presented. The ERSW process is characterized by the coupling of thermal, electrical, mechanical, and metallurgical phenomena. For this reason, early attempts to model it using computational methods established as the methods of finite differences, finite element, and finite volumes, ask for simplifications that lead the model obtained far from reality or very costly in terms of computational costs, to be used in a real-time control system. In this sense, the authors have developed an ERSW controller that uses fuzzy logic to adjust the energy transferred to the weld nugget. The proposed control strategies differ in the speed with which it reaches convergence. Moreover, their application for a quality control of spot weld through artificial neural networks (ANN) is discussed.

Multi-actuated functionally graded piezoelectric micro-tools design: A multiphysics topology optimization approach

Micro-tools offer significant promise in a wide range of applications Such as cell Manipulation, microsurgery, and micro/nanotechnology processes. Such special micro-tools consist of multi-flexible structures actuated by two or more piezoceramic devices that must generate output displacements and forces lit different specified points of the domain and at different directions. The micro-tool Structure acts as a mechanical transformer by amplifying and changing the direction of the piezoceramics Output displacements. The design of these micro-tools involves minimization of the coupling among movements generated by various piezoceramics. To obtain enhanced micro-tool performance, the concept of multifunctional and functionally graded materials is extended by, tailoring elastic and piezoelectric properties Of the piezoceramics while simultaneously optimizing the multi-flexible structural configuration using multiphysics topology optimization. The design process considers the influence of piezoceramic property gradation and also its polarization sign. The method is implemented considering continuum material distribution with special interpolation of fictitious densities in the design domain. As examples, designs of a single piezoactuator, an XY nano-positioner actuated by two graded piezoceramics, and a micro-gripper actuated by three graded piezoceramics are considered. The results show that material gradation plays an important role to improve actuator performance, which may also lead to optimal displacements and coupling ratios with reduced amount of piezoelectric material. The present examples are limited to two-dimensional models because many of the applications for Such micro-tools are planar devices. Copyright (c) 2008 John Wiley & Sons, Ltd.