Ocular biometric investigation of anisometropia

The thesis aims to define further the biometric correlates in anisometropic eyes in order to provide a structural foundation for propositions concerning the development of ametropia.Biometric data are presented for 40 anisometropes and 40 isometropic controls drawn from Caucasian and Chinese populations.The principal finding was that the main structural correlate of myopia is an increase in axial rather than equatorial dimensions of the posterior globe. This finding has not been previously reported for in vivo work on humans. The computational method described in the thesis is a more accessible method for determination of eye shape than current imaging techniques such as magnetic resonance imaging or laser Doppler interferometry (LDI). Retinal contours derived from LDI and computation were shown to be closely matched. Corneal topography revealed no differences in corneal characteristics in anisometropic eyes, which supports the finding that anisometropia arises from differences in vitreous chamber depth.The corollary to axial expansion in myopia, that is retinal stretch in central regions of the posterior pole, was investigated by measurement of disc-to-fovea distances (DFD) using a scanning laser ophthalmoscope. DFD was found to increase with increased myopia, which demonstrates the primary contribution made by posterior central regions of the globe to axial expansion.The ocular pulse volume and choroidal blood flow, measured with the Ocular Blood Flow Tonograph, were found to be reduced in myopia; the reductions were found to be significantly correlated with vitreous chamber depth. The thesis includes preliminary data on whether the relationship arises from the influx of a blood bolus into eyes of different posterior volumes or represents actual differences in choroidal blood flow.The results presented in this thesis show the utility of computed retinal contour and demonstrate that the structural correlate of myopia is axial rather than equatorial expansion of the vitreous chamber. The technique is suitable for large population studies and its relative simplicity makes it feasible for longitudinal studies on the development of ametropia in, for example, children.

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

Background The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary relationships. Results Analysis based on the predicted networks suggests the following:: significantly stronger recombination signals (p = 0.003) for the inferred ancestors of the X4 strains, recombination events between different lineages and recombination events between putative reservoir virus and those from a later population, an early star-like topology observed for four of the patients who died of AIDS. A significantly higher number of recombinants were predicted at sampling points that corresponded to peaks in the viral load levels (p = 0.0042). Conclusion Our results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels.

Interações magnéticas e elétricas em GaMnAs

In this paper, we will address together the magnetic and electrical properties of a particular semiconductor, the GaMnAs. The treatment will be done analytically in the first part of the work, according to the computational method for simulation of physical systems through the implementation of the expressions obtained in the first part. All study of magnetic contribution will be made using an interaction Kondo type, using an approach by Green functions. The electrical part, which consists of the Coulomb interactions between carriers and Mn ions, will be treated within the approach of multiple scattering. The implementation of the proposed method will calculate the Green functions converged as multiple scattering solution and use them as a starting point for the calculation of the effective magnetic interactions between Mn ions mediated charge carriers. The concentration parameters were varied for Mn ions and carriers as well. The combination of these two parameters can lead to insulating, metal samples with carriers in Fermi level to low or high mobility. As a result a correlation between the obtained carrier mobility and the strength of magnetic interaction. The greater mobility, the greater the intensity of the interaction.

A Bayesian Dirichlet-Multinomial Test for Cross-Group Differences

Testing for differences within data sets is an important issue across various applications. Our work is primarily motivated by the analysis of microbiomial composition, which has been increasingly relevant and important with the rise of DNA sequencing. We first review classical frequentist tests that are commonly used in tackling such problems. We then propose a Bayesian Dirichlet-multinomial framework for modeling the metagenomic data and for testing underlying differences between the samples. A parametric Dirichlet-multinomial model uses an intuitive hierarchical structure that allows for flexibility in characterizing both the within-group variation and the cross-group difference and provides very interpretable parameters. A computational method for evaluating the marginal likelihoods under the null and alternative hypotheses is also given. Through simulations, we show that our Bayesian model performs competitively against frequentist counterparts. We illustrate the method through analyzing metagenomic applications using the Human Microbiome Project data.

Path Optimization in Free Energy Calculations

Free energy calculations are a computational method for determining thermodynamic quantities, such as free energies of binding, via simulation.

Currently, due to computational and algorithmic limitations, free energy calculations are limited in scope.

In this work, we propose two methods for improving the efficiency of free energy calculations.

First, we expand the state space of alchemical intermediates, and show that this expansion enables us to calculate free energies along lower variance paths.

We use Q-learning, a reinforcement learning technique, to discover and optimize paths at low computational cost.

Second, we reduce the cost of sampling along a given path by using sequential Monte Carlo samplers.

We develop a new free energy estimator, pCrooks (pairwise Crooks), a variant on the Crooks fluctuation theorem (CFT), which enables decomposition of the variance of the free energy estimate for discrete paths, while retaining beneficial characteristics of CFT.

Combining these two advancements, we show that for some test models, optimal expanded-space paths have a nearly 80% reduction in variance relative to the standard path.

Additionally, our free energy estimator converges at a more consistent rate and on average 1.8 times faster when we enable path searching, even when the cost of path discovery and refinement is considered.

Développement d'une méthode de prédiction de l'orientation et de l'insertion des protéines dans une membrane modèle

Les protéines membranaires intégrales jouent un rôle indispensable dans la survie des cellules et 20 à 30% des cadres de lectures ouverts codent pour cette classe de protéines. La majorité des protéines membranaires se trouvant sur la Protein Data Bank n’ont pas une orientation et une insertion connue. L’orientation, l’insertion et la conformation que les protéines membranaires ont lorsqu’elles interagissent avec une bicouche lipidique sont importantes pour la compréhension de leur fonction, mais ce sont des caractéristiques difficiles à obtenir par des méthodes expérimentales. Des méthodes computationnelles peuvent réduire le temps et le coût de l’identification des caractéristiques des protéines membranaires. Dans le cadre de ce projet de maîtrise, nous proposons une nouvelle méthode computationnelle qui prédit l’orientation et l’insertion d’une protéine dans une membrane. La méthode est basée sur les potentiels de force moyenne de l’insertion membranaire des chaînes latérales des acides aminés dans une membrane modèle composèe de dioléoylphosphatidylcholine.

Blade-wake interactions in cross-flow turbines

This paper presents analytical bounds for blade–wake interaction phenomenona occurring in rotating cross-flow turbines for wind and tidal energy generation (e.g. H rotors, Darrieus or vertical axis). Limiting cases are derived for one bladed turbines and extended to the more common three bladed configuration. Additionally, we present a classification of the blade–wake type of interactions in terms of limiting tip speed ratios. These bounds are validated using a high order h=p Discontinuous Galerkin solver with sliding meshes. This computational method enables highly accurate flow solutions and shows that the analytical bounds correspond to limiting blade-wake interactions in fully resolved flow simulations

Application of fuzzy logic for the evaluation of livestock slaughtering

A lógica fuzzy admite infinitos valores lógicos intermediários entre o falso e o verdadeiro. Com esse princípio, foi elaborado neste trabalho um sistema baseado em regras fuzzy, que indicam o índice de massa corporal de animais ruminantes com objetivo de obter o melhor momento para o abate. O sistema fuzzy desenvolvido teve como entradas as variáveis massa e altura, e a saída um novo índice de massa corporal, denominado Índice de Massa Corporal Fuzzy (IMC Fuzzy), que poderá servir como um sistema de detecção do momento de abate de bovinos, comparando-os entre si através das variáveis linguísticas )Muito BaixaM, ,BaixaB, ,MédiaM, ,AltaA e Muito AltaM. Para a demonstração e aplicação da utilização deste sistema fuzzy, foi feita uma análise de 147 vacas da raça Nelore, determinando os valores do IMC Fuzzy para cada animal e indicando a situação de massa corpórea de todo o rebanho. A validação realizada do sistema foi baseado em uma análise estatística, utilizando o coeficiente de correlação de Pearson 0,923, representando alta correlação positiva e indicando que o método proposto está adequado. Desta forma, o presente método possibilita a avaliação do rebanho, comparando cada animal do rebanho com seus pares do grupo, fornecendo desta forma um método quantitativo de tomada de decisão para o pecuarista. Também é possível concluir que o presente trabalho estabeleceu um método computacional baseado na lógica fuzzy capaz de imitar parte do raciocínio humano e interpretar o índice de massa corporal de qualquer tipo de espécie bovina e em qualquer região do País.

Inverse kinematics for upper limb compound movement estimation in exoskeleton-assisted rehabilitation

Robot-Assisted Rehabilitation (RAR) is relevant for treating patients affected by nervous system injuries (e.g., stroke and spinal cord injury) -- The accurate estimation of the joint angles of the patient limbs in RAR is critical to assess the patient improvement -- The economical prevalent method to estimate the patient posture in Exoskeleton-based RAR is to approximate the limb joint angles with the ones of the Exoskeleton -- This approximation is rough since their kinematic structures differ -- Motion capture systems (MOCAPs) can improve the estimations, at the expenses of a considerable overload of the therapy setup -- Alternatively, the Extended Inverse Kinematics Posture Estimation (EIKPE) computational method models the limb and Exoskeleton as differing parallel kinematic chains -- EIKPE has been tested with single DOFmovements of the wrist and elbow joints -- This paper presents the assessment of EIKPEwith elbow-shoulder compoundmovements (i.e., object prehension) -- Ground-truth for estimation assessment is obtained from an optical MOCAP (not intended for the treatment stage) -- The assessment shows EIKPE rendering a good numerical approximation of the actual posture during the compoundmovement execution, especially for the shoulder joint angles -- This work opens the horizon for clinical studies with patient groups, Exoskeleton models, and movements types --

Desenvolvimento de um sistema Inteligente para a análise de cartas dinamométricas no método de elevação por bombeio mecânico

The artificial lifting of oil is needed when the pressure of the reservoir is not high enough so that the fluid contained in it can reach the surface spontaneously. Thus the increase in energy supplies artificial or additional fluid integral to the well to come to the surface. The rod pump is the artificial lift method most used in the world and the dynamometer card (surface and down-hole) is the best tool for the analysis of a well equipped with such method. A computational method using Artificial Neural Networks MLP was and developed using pre-established patterns, based on its geometry, the downhole card are used for training the network and then the network provides the knowledge for classification of new cards, allows the fails diagnose in the system and operation conditions of the lifting system. These routines could be integrated to a supervisory system that collects the cards to be analyzed

Partial state bounding with a pre-specified time of non-linear discrete systems with time-varying delays

In this study, the authors address a new problem of finding, with a pre-specified time, bounds of partial states of non-linear discrete systems with a time-varying delay. A novel computational method for deriving the smallest bounds is presented. The method is based on a new comparison principle, a new algorithm for finding the infimum of a fractal function, and linear programming. The effectiveness of our obtained results is illustrated through a numerical example.

Idempotent weighted aggregation based on binary aggregation trees

We propose weighted aggregation algorithms for creating general idempotent weighted aggregators of n variables derived from related symmetric idempotent aggregators of two variables. This computational method, together with interpolative aggregation, can be used for the development of general idempotent logic aggregators that satisfy a variety of conditions necessary for building decision models in the area of weighted compensative logic.

A study of the speed and the accuracy of the Boundary Element Method as applied to the computational simulation of biological organs

In this work, first a Fortran code is developed for three dimensional linear elastostatics using constant boundary elements; the code is based on a MATLAB code developed by the author earlier. Next, the code is parallelized using BLACS, MPI, and ScaLAPACK. Later, the parallelized code is used to demonstrate the usefulness of the Boundary Element Method (BEM) as applied to the realtime computational simulation of biological organs, while focusing on the speed and accuracy offered by BEM. A computer cluster is used in this part of the work. The commercial software package ANSYS is used to obtain the `exact' solution against which the solution from BEM is compared; analytical solutions, wherever available, are also used to establish the accuracy of BEM. A pig liver is the biological organ considered. Next, instead of the computer cluster, a Graphics Processing Unit (GPU) is used as the parallel hardware. Results indicate that BEM is an interesting choice for the simulation of biological organs. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature. Also, a serial MATLAB code, and both serial and parallel versions of a Fortran code, which can solve three dimensional (3D) linear elastostatic problems using constant boundary elements, are provided as supplementary files that can be freely downloaded.

A study of the speed and the accuracy of the Boundary Element Method as applied to the computational simulation of biological organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated, with specific reference to the speed and the accuracy offered by BEM. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. A pig liver is the biological organ considered. Results indicate that BEM is an interesting choice for the simulation of biological organs. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.