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.

A Study on Unconditionally Stable FDTD Methods for the Modeling of Metamaterials

We assess the performance of three unconditionally stable finite-difference time-domain (FDTD) methods for the modeling of doubly dispersive metamaterials: 1) locally one-dimensional FDTD; 2) locally one-dimensional FDTD with Strang splitting; and (3) alternating direction implicit FDTD. We use both double-negative media and zero-index media as benchmarks.

Power quality analysis applying a hybrid methodology with wavelet transforms and neural networks

A hybrid system to automatically detect, locate and classify disturbances affecting power quality in an electrical power system is presented in this paper. The disturbances characterized are events from an actual power distribution system simulated by the ATP (Alternative Transients Program) software. The hybrid approach introduced consists of two stages. In the first stage, the wavelet transform (WT) is used to detect disturbances in the system and to locate the time of their occurrence. When such an event is flagged, the second stage is triggered and various artificial neural networks (ANNs) are applied to classify the data measured during the disturbance(s). A computational logic using WTs and ANNs together with a graphical user interface (GU) between the algorithm and its end user is then implemented. The results obtained so far are promising and suggest that this approach could lead to a useful application in an actual distribution system. (C) 2009 Elsevier Ltd. All rights reserved.

A hybrid system for upper limb movement restoration in quadriplegics

Generally, quadriplegic individuals have difficulties performing object manipulation. Toward satisfactory manipulation, reach and grasp movements must be performed with voluntary control, and for that, grasp force feedback is essential. A hybrid system aiming at partial upper limb sensory-motor restoration for quadriplegics was built. Such device is composed of an elbow dynamic orthosis that provides elbow flexion/extension (range was approximately from 20 degrees to 120 degrees, and average angular speed was approximately 15 degrees/s) with forearm support, a wrist static orthosis and neuromuscular electrical stimulation for grasping generation, and a glove with force sensors that allows grasping force feedback. The glove presents two user interface modes: visual by light emitting diodes or audio emitted by buzzer. Voice control of the entire system (elbow dynamic orthosis and electrical stimulator) is performed by the patient. The movements provided by the hybrid system, combined with the scapular and shoulder movements performed by the patient, can aid quadriplegic individuals in tasks that involve reach and grasp movements.

Dynamic behavior analysis of drill-threading process when machining AISI Al-Si-Cu(4) alloy

Conventional threading operations involve two distinct machining processes: drilling and threading. Therefore, it is time consuming for the tools must be changed and the workpiece has to be moved to another machine. This paper presents an analysis of the combined process (drilling followed by threading) using a single tool for both operations: the tap-milling tool. Before presenting the methodology used to evaluate this hybrid tool, the ODS (operating deflection shapes) basics is shortly described. ODS and finite element modeling (FEM) were used during this research to optimize the process aiming to achieve higher stable machining conditions and increasing the tool life. Both methods allowed the determination of the natural frequencies and displacements of the machining center and optimize the workpiece fixture system. The results showed that there is an excellent correlation between the dynamic stability of the machining center-tool holder and the tool life, avoiding a tool premature catastrophic failure. Nevertheless, evidence showed that the tool is very sensitive to work conditions. Undoubtedly, the use of ODS and FEM eliminate empiric decisions concerning the optimization of machining conditions and increase drastically the tool life. After the ODS and FEM studies, it was possible to optimize the process and work material fixture system and machine more than 30,000 threaded holes without reaching the tool life limit and catastrophic fail.

A state-space modeling approach for active structural acoustic control

The demands for improvement in sound quality and reduction of noise generated by vehicles are constantly increasing, as well as the penalties for space and weight of the control solutions. A promising approach to cope with this challenge is the use of active structural-acoustic control. Usually, the low frequency noise is transmitted into the vehicle`s cabin through structural paths, which raises the necessity of dealing with vibro-acoustic models. This kind of models should allow the inclusion of sensors and actuators models, if accurate performance indexes are to be accessed. The challenge thus resides in deriving reasonable sized models that integrate structural, acoustic, electrical components and the controller algorithm. The advantages of adequate active control simulation strategies relies on the cost and time reduction in the development phase. Therefore, the aim of this paper is to present a methodology for simulating vibro-acoustic systems including this coupled model in a closed loop control simulation framework that also takes into account the interaction between the system and the control sensors/actuators. It is shown that neglecting the sensor/actuator dynamics can lead to inaccurate performance predictions.

Analysis of a semi-rigid connection for precast concrete

This paper presents a study of a specific type of beam-to-column connection for precast concrete structures. Furthermore, an analytical model to determine the strength and the stiffness of the connection, based on test results of two prototypes, is proposed. To evaluate the influence of the strength and stiffness of the connection on the behaviour of the structure, the results of numerical simulations of a typical multi-storey building with semi-rigid connections are also presented and compared with the results using pinned and rigid connections. The main conclusions are: (a) the proposed design model can reasonably evaluate the studied connection strength; (b) the evaluation of strength is more accurate than that of stiffness; (c) for a typical structure, it is possible to increase the number of storeys of the structure from two to four with lower horizontal displacement at the top, and only a small increase of the column base bending moment by replacing the pinned connections with semi-rigid ones; and (d) although there is significant uncertainty in the connection stiffness, the results show that the displacements at the top of the structure, and the column base moments present low susceptibility deviations to this parameter.

A hybrid Particle Swarm Optimization - Simplex algorithm (PSOS) for structural damage identification

This study proposes a new PSOS-model based damage identification procedure using frequency domain data. The formulation of the objective function for the minimization problem is based on the Frequency Response Functions (FRFs) of the system. A novel strategy for the control of the Particle Swarm Optimization (PSO) parameters based on the Nelder-Mead algorithm (Simplex method) is presented; consequently, the convergence of the PSOS becomes independent of the heuristic constants and its stability and confidence are enhanced. The formulated hybrid method performs better in different benchmark functions than the Simulated Annealing (SA) and the basic PSO (PSO(b)). Two damage identification problems, taking into consideration the effects of noisy and incomplete data, were studied: first, a 10-bar truss and second, a cracked free-free beam, both modeled with finite elements. In these cases, the damage location and extent were successfully determined. Finally, a non-linear oscillator (Duffing oscillator) was identified by PSOS providing good results. (C) 2009 Elsevier Ltd. All rights reserved

A hybrid-Trefftz formulation for plane elasticity with selective enrichment of the approximations

This work is related to the so-called non-conventional finite element formulations. Essentially, a methodology for the enrichment of the initial approximation which is typical of the meshless methods and based on the clouds concept is introduced in the hybrid-Trefftz formulation for plane elasticity. The formulation presented allows for the approximation and direct enrichment of two independent fields: stresses in the domains and displacements on the boundaries of the elements. Defined by a set of elements and interior boundaries sharing a common node, the cloud notion is employed to select the enrichment support for the approximation fields. The numerical analysis performed reveals an excellent performance of the resulting formulation, characterized by the good approximation ability and a reduced computational effort. Copyright (C) 2009 John Wiley & Sons, Ltd.

Parametrical study of masonry walls subjected to in-plane loading through numerical modeling

This paper deals with the numerical assessment of the influence of parameters such as pre-compression level, aspect ratio, vertical and horizontal reinforcement ratios and boundary conditions on the lateral strength of masonry walls under in-plane loading. The numerical study is performed through the software DIANA (R) based on the Finite Element Method. The validation of the numerical model is carried out from a database of available experimental results on masonry walls tested under cyclic lateral loading. Numerical results revealed that boundary conditions play a central role on the lateral behavior of masonry walls under in-plane loading and determine the influence of level of pre-compression as well as the reinforcement ratio on the wall strength. The lateral capacity of walls decreases with the increase of aspect ratio and with the decrease of pre-compression. Vertical steel bars appear to have almost no influence in the shear strength of masonry walls and horizontal reinforcement only increases the lateral strength of masonry walls if the shear response of the walls is determinant for failure, which is directly related to the boundary conditions. (C) 2011 Elsevier Ltd. All rights reserved.

Assessment of groundwater recharge and water fluxes of the Guarani Aquifer System, Brazil

The groundwater recharge and water fluxes of the Guarani Aquifer System in the state of Sao Paulo in Brazil were assessed through a numeric model. The study area (6,748 km(2)) comprises Jacar,-Gua double dagger A(0) and Jacar,-Pepira River watersheds, tributaries of the Tiet River in the central region of the state. GIS based tools were used in the storage, processing and analysis of data. Main hydrologic phenomena were selected, leading to a groundwater conceptual model, taking into account the significant outcrops occurring in the study area. Six recharge zones were related to the geologic formation and structures of the semi-confined and phreatic aquifer. The model was calibrated against the baseflows and static water levels of the wells. The results emphasize the strong interaction of groundwater flows between watersheds and the groundwater inflow into the rivers. It has been concluded that lateral groundwater exchanges between basins, the deep discharges to the regional system, and well exploitation were not significant aquifer outflows when compared to the aquifer recharge. The results have shown that the inflows from the river into the aquifer are significant and have the utmost importance since the aquifer is potentially more vulnerable in these places.

Heterogeneous modeling of an anaerobic sequencing batch biofilm reactor (ASBBR)

The objective of this study was to estimate the first-order intrinsic kinetic constant (k(1)) and the liquid-phase mass transfer coefficient (k(c)) in a bench-scale anaerobic sequencing batch biofilm reactor (ASBBR) fed with glucose. A dynamic heterogeneous mathematical model, considering two phases (liquid and solid), was developed through mass balances in the liquid and solid phases. The model was adjusted to experimental data obtained from the ASBBR applied for the treatment of glucose-based synthetic wastewater with approximately 500 mg L-1 of glucose, operating in 8 h batch cycles, at 30 degrees C and 300 rpm. The values of the parameters obtained were 0.8911 min(-1) for k(1) and 0.7644 cm min(-1) for kc. The model was validated utilizing the estimated parameters with data obtained from the ASBBR operating in 3 h batch cycles, with a good representation of the experimental behavior. The solid-phase mass transfer flux was found to be the limiting step of the overall glucose conversion rate.

Solution of a heterogeneous modeling of a horizontal-flow anaerobic immobilized biomass (HAIB) reactor by the sequencing method

A modeling study was completed to develop a methodology that combines the sequencing and finite difference methods for the simulation of a heterogeneous model of a tubular reactor applied in the treatment of wastewater. The system included a liquid phase (convection diffusion transport) and a solid phase (diffusion reaction) that was obtained by completing a mass balance in the reactor and in the particle, respectively. The model was solved using a pilot-scale horizontal-flow anaerobic immobilized biomass (HAIB) reactor to treat domestic sewage, with the concentration results compared with the experimental data. A comparison of the behavior of the liquid phase concentration profile and the experimental results indicated that both the numerical methods offer a good description of the behavior of the concentration along the reactor. The advantage of the sequencing method over the finite difference method is that it is easier to apply and requires less computational time to model the dynamic simulation of outlet response of HAIB.

Digital versus Conventional Radiography for Imaging Fatigue Cracks in Riveted Lap Joints of Hybrid Glass Reinforced Fiber/Metal Laminate

A round robin program zoos conducted to assess the ability of three different X-radiographic systems for imaging internal fatigue cracks in riveted lap joints of composite glass reinforced fiber/metal laminate. From an engineering perspective, conventional film radiography and direct radiography have produced the best results, identifying and characterizing in detail internal damage on metallic faying surfaces of fastened glass reinforced fiber/metal laminate joints. On the other hand, computed radiographic images presented large projected geometric distortions and feature shifts due to the angular incident radiation beam, disclosing only partial internal cracking patterns.

Modeling and Analysis of Piezoelectric Energy Harvesting From Aeroelastic Vibrations Using the Doublet-Lattice Method

Multifunctional structures are pointed out as an important technology for the design of aircraft with volume, mass, and energy source limitations such as unmanned air vehicles (UAVs) and micro air vehicles (MAVs). In addition to its primary function of bearing aerodynamic loads, the wing/spar structure of an UAV or a MAV with embedded piezoceramics can provide an extra electrical energy source based on the concept of vibration energy harvesting to power small and wireless electronic components. Aeroelastic vibrations of a lifting surface can be converted into electricity using piezoelectric transduction. In this paper, frequency-domain piezoaeroelastic modeling and analysis of a canti-levered platelike wing with embedded piezoceramics is presented for energy harvesting. The electromechanical finite-element plate model is based on the thin-plate (Kirchhoff) assumptions while the unsteady aerodynamic model uses the doublet-lattice method. The electromechanical and aerodynamic models are combined to obtain the piezoaeroelastic equations, which are solved using a p-k scheme that accounts for the electromechanical coupling. The evolution of the aerodynamic damping and the frequency of each mode are obtained with changing airflow speed for a given electrical circuit. Expressions for piezoaeroelastically coupled frequency response functions (voltage, current, and electrical power as well the vibratory motion) are also defined by combining flow excitation with harmonic base excitation. Hence, piezoaeroelastic evolution can be investigated in frequency domain for different airflow speeds and electrical boundary conditions. [DOI:10.1115/1.4002785]