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.

Neutron Activation Analysis: A Primary (Ratio) Method to Determine SI-Traceable Values of Element Content in Complex Samples

The metrological principles of neutron activation analysis are discussed. It has been demonstrated that this method can provide elemental amount of substance with values fully traceable to the SI. The method has been used by several laboratories worldwide in a number of CCQM key comparisons - interlaboratory comparison tests at the highest metrological level - supplying results equivalent to values from other methods for elemental or isotopic analysis in complex samples without the need to perform chemical destruction and dissolution of these samples. The CCOM accepted therefore in April 2007 the claim that neutron activation analysis should have the similar status as the methods originally listed by the CCOM as `primary methods of measurement`. Analytical characteristics and scope of application are given.

Compton suppression instrumental neutron activation analysis performance in determining trace- and minor-element contents in foodstuff

In 2003-2004, several food items were purchased from large commercial outlets in Coimbra, Portugal. Such items included meats (chicken, pork, beef), eggs, rice, beans and vegetables (tomato, carrot, potato, cabbage, broccoli, lettuce). Elemental analysis was carried out through INAA at the Technological and Nuclear Institute (ITN, Portugal), the Nuclear Energy Centre for Agriculture (CENA, Brazil), and the Nuclear Engineering Teaching Lab of the University of Texas at Austin (NETL, USA). At the latter two, INAA was also associated to Compton suppression. It can be concluded that by applying Compton suppression (1) the detection limits for arsenic, copper and potassium improved; (2) the counting-statistics error for molybdenum diminished; and (3) the long-lived zinc had its 1115-keV photopeak better defined. In general, the improvement sought by introducing Compton suppression in foodstuff analysis was not significant. Lettuce, cabbage and chicken (liver, stomach, heart) are the richest diets in terms of human nutrients.

THE SUMMATION OF VOLUNTARY AND ELECTRICAL ELICITED STIMULUS INCREASES JOINT TORQUE?

The aim of this study is to analyze the effect of neuromuscular electrical stimulation (NMES) on myoelectrical activity and on joint torque during isometric plantar flexion contraction. Ten healthy young adult subjects participate in this study. The electrodes for NMES are placed along posterior thigh along ciatic nerve trajectory. It is measured the myoelectrical activity and the isometric torque generated by ankle plantar flexion with an isokinetic dynamometer. The conditions of isometric contractions are maximum isometric voluntary contraction (MIVC), NMES, and association of both (MIVC+NMES). The results show lower torque during NMES and larger SOL activity compare to the others. Besides, in order to keep the same objective task (to produce the same level of torque), neuromuscular adaptations are necessary on the common drive.

Information from managing information systems as a fundamental element to support decision-making in hospitals

This article deals with the activity of defining information of hospital systems as fundamental for choosing the type of information systems to be used and also the organizational level to be supported. The use of hospital managing information systems improves the user`s decision -making process by allowing control report generation and following up the procedures made in the hospital as well.

Effects of joint immobilization on standing balance

We investigated the effect of joint immobilization on the postural sway during quiet standing. We hypothesized that the center of pressure (COP), rambling, and trembling trajectories would be affected by joint immobilization. Ten young adults stood on a force plate during 60 s without and with immobilized joints (only knees constrained, CK; knees and hips, CH; and knees, hips, and trunk, CT). with their eyes open (OE) or closed (CE). The root mean square deviation (RMS, the standard deviation from the mean) and mean speed of COP, rambling, and trembling trajectories in the anterior-posterior and medial-lateral directions were analyzed. Similar effects of vision were observed for both directions: larger amplitudes for all variables were observed in the CE condition. In the anterior-posterior direction, postural sway increased only when the knees, hips, and trunk were immobilized. For the medial-lateral direction, the RMS and the mean speed of the COP, rambling, and trembling displacements decreased after immobilization of knees and hips and knees, hips, and trunk. These findings indicate that the single inverted pendulum model is unable to completely explain the processes involved in the control of the quiet upright stance in the anterior-posterior and medial-lateral directions. (C) 2009 Elsevier B.V. All rights reserved.

Joint forces and torques when walking in shallow water

This study reports for the first time an estimation of the internal net joint forces and torques on adults` lower limbs and pelvis when walking in shallow water, taking into account the drag forces generated by the movement of their bodies in the water and the equivalent data when they walk on land. A force plate and a video camera were used to perform a two-dimensional gait analysis at the sagittal plane of 10 healthy young adults walking at comfortable speeds on land and in water at a chest-high level. We estimated the drag force on each body segment and the joint forces and torques at the ankle, knee, and hip of the right side of their bodies using inverse dynamics. The observed subjects` apparent weight in water was about 35% of their weight on land and they were about 2.7 times slower when walking in water. When the subjects walked in water compared with walking on land, there were no differences in the angular displacements but there was a significant reduction in the joint torques which was related to the water`s depth. The greatest reduction was observed for the ankle and then the knee and no reduction was observed for the hip. All joint powers were significantly reduced in water. The compressive and shear joint forces were on average about three times lower during walking in water than on land. These quantitative results substantiate the use of water as a safe environment for practicing low-impact exercises, particularly walking. (C) 2011 Elsevier Ltd. All rights reserved.

The four-element Chua`s circuit

A new circuit configuration, linearly conjugate to the standard Chua`s circuit, is presented. Its distinctive feature is that the equations now admit an additional parameter, which controls the dissipation in the network connected to the Chua diode. In the limiting case we obtain the simplest chaotic circuit, consisting of a piecewise-linear resistor and three lossless elements.

Aerodynamic study of three-dimensional larynx models using finite element methods

The airflow velocities and pressures are calculated from a three-dimensional model of the human larynx by using the finite element method. The laryngeal airflow is assumed to be incompressible, isothermal, steady, and created by fixed pressure drops. The influence of different laryngeal profiles (convergent, parallel, and divergent), glottal area, and dimensions of false vocal folds in the airflow are investigated. The results indicate that vertical and horizontal phase differences in the laryngeal tissue movements are influenced by the nonlinear pressure distribution across the glottal channel, and the glottal entrance shape influences the air pressure distribution inside the glottis. Additionally, the false vocal folds increase the glottal duct pressure drop by creating a new constricted channel in the larynx, and alter the airflow vortexes formed after the true vocal folds. (C) 2007 Elsevier Ltd. All rights reserved.

Finite element homogenization technique for the characterization of d(15) shear piezoelectric macro-fibre composites

A finite element homogenization method for a shear actuated d(15) macro-fibre composite (MFC) made of seven layers (Kapton, acrylic, electrode, piezoceramic fibre and epoxy composite, electrode, acrylic, Kapton) is proposed and used for the characterization of its effective material properties. The methodology is first validated for the MFC active layer only, made of piezoceramic fibre and epoxy, through comparison with previously published analytical results. Then, the methodology is applied to the seven-layer MFC. It is shown that the packaging reduces significantly the shear stiffness of the piezoceramic material and, thus, leads to significantly smaller effective electromechanical coupling coefficient k(15) and piezoelectric stress constant e(15) when compared to the piezoceramic fibre properties. However, it is found that the piezoelectric charge constant d(15) is less affected by the softer layers required by the MFC packaging.

Non-linear boundary element formulation applied to contact analysis using tangent operator

This work presents a non-linear boundary element formulation applied to analysis of contact problems. The boundary element method (BEM) is known as a robust and accurate numerical technique to handle this type of problem, because the contact among the solids occurs along their boundaries. The proposed non-linear formulation is based on the use of singular or hyper-singular integral equations by BEM, for multi-region contact. When the contact occurs between crack surfaces, the formulation adopted is the dual version of BEM, in which singular and hyper-singular integral equations are defined along the opposite sides of the contact boundaries. The structural non-linear behaviour on the contact is considered using Coulomb`s friction law. The non-linear formulation is based on the tangent operator in which one uses the derivate of the set of algebraic equations to construct the corrections for the non-linear process. This implicit formulation has shown accurate as the classical approach, however, it is faster to compute the solution. Examples of simple and multi-region contact problems are shown to illustrate the applicability of the proposed scheme. (C) 2011 Elsevier Ltd. All rights reserved.

Dual boundary element formulation applied to analysis of multi-fractured domains

This paper deals with analysis of multiple random crack propagation in two-dimensional domains using the boundary element method (BEM). BEM is known to be a robust and accurate numerical technique for analysing this type of problem. The formulation adopted in this work is based on the dual BEM, for which singular and hyper-singular integral equations are used. We propose an iterative scheme to predict the crack growth path and the crack length increment at each time step. The proposed scheme able us to simulate localisation and coalescence phenomena, which is the main contribution of this paper. Considering the fracture mechanics analysis, the displacement correlation technique is applied to evaluate the stress intensity factors. The propagation angle and the equivalent stress intensity factor are calculated using the theory of maximum circumferential stress. Examples of simple and multi-fractured domains, loaded up to the rupture, are considered to illustrate the applicability of the proposed scheme. (C) 2010 Elsevier Ltd. All rights reserved.

Coupled reliability and boundary element model for probabilistic fatigue life assessment in mixed mode crack propagation

Fatigue and crack propagation are phenomena affected by high uncertainties, where deterministic methods fail to predict accurately the structural life. The present work aims at coupling reliability analysis with boundary element method. The latter has been recognized as an accurate and efficient numerical technique to deal with mixed mode propagation, which is very interesting for reliability analysis. The coupled procedure allows us to consider uncertainties during the crack growth process. In addition, it computes the probability of fatigue failure for complex structural geometry and loading. Two coupling procedures are considered: direct coupling of reliability and mechanical solvers and indirect coupling by the response surface method. Numerical applications show the performance of the proposed models in lifetime assessment under uncertainties, where the direct method has shown faster convergence than response surface method. (C) 2010 Elsevier Ltd. All rights reserved.

Inverse analysis FOR two-dimensional structures using the boundary element method

Inverse analysis is currently an important subject of study in several fields of science and engineering. The identification of physical and geometric parameters using experimental measurements is required in many applications. In this work a boundary element formulation to identify boundary and interface values as well as material properties is proposed. In particular the proposed formulation is dedicated to identifying material parameters when a cohesive crack model is assumed for 2D problems. A computer code is developed and implemented using the BEM multi-region technique and regularisation methods to perform the inverse analysis. Several examples are shown to demonstrate the efficiency of the proposed model. (C) 2010 Elsevier Ltd. All rights reserved,

Analyzing static three-dimensional elastic domains with a new infinite boundary element formulation

A new two-dimensionally mapped infinite boundary element (IBE) is presented. The formulation is based on a triangular boundary element (BE) with linear shape functions instead of the quadrilateral IBEs usually found in the literature. The infinite solids analyzed are assumed to be three-dimensional, linear-elastic and isotropic, and Kelvin fundamental solutions are employed. One advantage of the proposed formulation over quadratic or higher order elements is that no additional degrees of freedom are added to the original BE mesh by the presence of the IBEs. Thus, the IBEs allow the mesh to be reduced without compromising the accuracy of the result. Two examples are presented, in which the numerical results show good agreement with authors using quadrilateral IBEs and analytical solutions. (C) 2010 Elsevier Ltd. All rights reserved.