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.

Modeling and analysis of laminate composite plates with embedded active-passive piezoelectric networks

The objective of this work is to present the finite element modeling of laminate composite plates with embedded piezoelectric patches or layers that are then connected to active-passive resonant shunt circuits, composed of resistance, inductance and voltage source. Applications to passive vibration control and active control authority enhancement are also presented and discussed. The finite element model is based on an equivalent single layer theory combined with a third-order shear deformation theory. A stress-voltage electromechanical model is considered for the piezoelectric materials fully coupled to the electrical circuits. To this end, the electrical circuit equations are also included in the variational formulation. Hence, conservation of charge and full electromechanical coupling are guaranteed. The formulation results in a coupled finite element model with mechanical (displacements) and electrical (charges at electrodes) degrees of freedom. For a Graphite-Epoxy (Carbon-Fibre Reinforced) laminate composite plate, a parametric analysis is performed to evaluate optimal locations along the plate plane (xy) and thickness (z) that maximize the effective modal electromechanical coupling coefficient. Then, the passive vibration control performance is evaluated for a network of optimally located shunted piezoelectric patches embedded in the plate, through the design of resistance and inductance values of each circuit, to reduce the vibration amplitude of the first four vibration modes. A vibration amplitude reduction of at least 10 dB for all vibration modes was observed. Then, an analysis of the control authority enhancement due to the resonant shunt circuit, when the piezoelectric patches are used as actuators, is performed. It is shown that the control authority can indeed be improved near a selected resonance even with multiple pairs of piezoelectric patches and active-passive circuits acting simultaneously. (C) 2010 Elsevier Ltd. All rights reserved.

Hybrid modeling of convective laminar flow in a permeable tube associated with the cross-flow process

The confined flows in tubes with permeable surfaces arc associated to tangential filtration processes (microfiltration or ultrafiltration). The complexity of the phenomena do not allow for the development of exact analytical solutions, however, approximate solutions are of great interest for the calculation of the transmembrane outflow and estimate of the concentration, polarization phenomenon. In the present work, the generalized integral transform technique (GITT) was employed in solving the laminar and permanent flow in permeable tubes of Newtonian and incompressible fluid. The mathematical formulation employed the parabolic differential equation of chemical species conservation (convective-diffusive equation). The velocity profiles for the entrance region flow, which are found in the connective terms of the equation, were assessed by solutions obtained from literature. The velocity at the permeable wall was considered uniform, with the concentration at the tube wall regarded as variable with an axial position. A computational methodology using global error control was applied to determine the concentration in the wall and concentration boundary layer thickness. The results obtained for the local transmembrane flux and the concentration boundary layer thickness were compared against others in literature. (C) 2007 Elsevier B.V. All rights reserved.

Experimental Analysis of Structural Change and Rheological Behavior of Macromolecular Solutions with Guar and Xanthan Gums in Crossflow Microfiltration Processing

The present paper reports on the structural change and rheological behavior of mixtures of macromolecular suspensions (guar and xanthan gums) in crossflow microfiltration processing. Mixtures in suspension of guar and xanthan gums at low concentrations (1,000 ppm) and different proportions were processed by microfiltration with membrane of nominal pore size of 0.4 mu m. The rheological behavior of the mixtures was investigated in rotational viscometers at two different temperatures, 25 and 40 C, at the beginning and at the end of each experiment. The shear stress (t) in function of the shear rate (gamma) was fitted and analyzed with the power-law model. All the mixtures showed flow behavior index values (n) lower than 1, characterizing non-Newtonian fluids (pseudoplastic). The samples of both mixtures and permeates were also analyzed by absorbency spectroscopy in infrared radiation. The absorbency analysis showed that there is good synergism between xanthan and guar gums without structure modifications or gel formation in the concentration process by microfiltration.

The influence of crystallographic orientation on the generation of multiple structural phases generation in Silicon by cyclic microindentation

A Raman scattering study on multiple phase generation in silicon submitted to successive Vickers microindentation cycles, in different crystallographic orientations, was performed. The microindentations were perfon-ned in a virgin single crystal (100)-oriented surface, in the [001] and [011] directions. The results indicated that the formation of multiple phases by cyclic microindentation may depend on the crystallographic direction and number of successive cycles: the onset of several different structural phases was detected after the third cycle for the [001] direction and only after 15 cycles for the [011] direction, indicating that there is a crystallographic orientation dependence for multiple phase generation. (C) 2007 Elsevier B.V. All rights reserved.

On the compressive strength prediction for concrete masonry prisms

The results of a combined experimental program and numerical modeling program to evaluate the behavior of ungrouted hollow concrete blocks prisms under uniaxial compression are addressed. In the numerical program, three distinct approaches have been considered using a continuum model with a smeared approach, namely plane-stress, plane-strain and three-dimensional conditions. The response of the numerical simulations is compared with experimental data of masonry prisms using concrete blocks specifically designed for this purpose. The elastic and inelastic parameters were acquired from laboratory tests on concrete and mortar samples that constitute the blocks and the bed joint of the prisms. The results from the numerical simulations are discussed with respect to the ability to reproduce the global response of the experimental tests, and with respect to the failure behavior obtained. Good agreement between experimental and numerical results was found for the peak load and for the failure mode using the three-dimensional model, on four different sets of block/mortar types. Less good agreement was found for plain stress and plain strain models.

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

An improved continuous medium technique for structural frame analysis

This paper presents an improved constitutive equation of frame in the context of continuous medium technique. This improved constitutive equation, which is a consistent formulation of column global bending, is applicable to a complete class of frameworks including the ideal shear frame panel, for which the beams are assumed to be rigid, and the associated column system, for which the rigidity of beams is negligible. Global buckling and second-order effects of the frame structure are discussed. The main results can be extended to other types of lateral stiffening elements as built-up columns. A worked example is presented in order to compare the main results with those obtained by the classic matrix method. Copyright (C) 2007 John Wiley & Sons, Ltd.

Structural behaviour of three-pile caps subjected to axial compressive loading

This work presents a comparative analysis about the behaviour of pile caps supported by 3 piles subjected to axial loading. Piles with 20 cm and 30 cm diameters were analysed. The main reinforcement was maintained in all the specimens, however, the arrangement of the secondary reinforcement varied. The main reinforcement consisted of steel bars connecting the piles. The secondary reinforcement was made up of: (a) bars going through the piles and through the projection of the column, (b) bars forming a network, and (c) vertical and horizontal stirrups. The main objective was the observation of the pile cap behaviour regarding the cracks and the modes of rupture. The real scale specimens were subjected to experimental tests until failure by rupture. Instruments were placed with the aim to obtain the displacement of the bases, the strains in the main and secondary reinforcement bars, in the compression struts, in the lower and upper nodal zones and in the sides of the caps. None of the caps reached failure by rupture with a load less than 1.12 times the theoretical load. The specimens ruptured due to the cracking of the compression strut and/or the yielding of the reinforcement bars in one direction.

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.

Dimension stone for building facades: methodology for structural design

The importance of a careful selection of rocks used in building facade cladding is highlighted. A simple and viable methodology for the structural detailing of dimension stones and the verification of the global performance is presented based on a Strap software simulation. The results obtained proved the applicability of the proposed structural dimensioning methodology which represents an excellent simple tool for dimensioning rock slabs used for building facade cladding. The Strap software satisfactorily simulated the structural conditions of the stone slabs under the studied conditions, allowing the determination of alternative slab dimensions and the verification of the cladding strength at the support.

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.

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]