Flexible strategies for association analysis with genomic phenotypes

Thesis (Ph.D.)--University of Washington, 2016-08

Imaging TC ed analisi tessiturale: caratterizzazione del parenchima polmonare di pazienti con broncopneumopatia cronica ostruttiva

La caratterizzazione del parenchima polmonare è un aspetto cruciale per l’identificazione dell’enfisema e dell’air trapping in pazienti affetti da broncopneumopatia cronica ostruttiva (BPCO). L’innovazione presente in questo lavoro di tesi è quella di utilizzare a questo scopo l’analisi tessiturale mediante il metodo delle matrici di co-occorrenza su immagini di tomografia computerizzata (TC) acquisite in inspirio ed espirio co-registrate. La co-registrazione che ha portato le immagini acquisite in espirio sullo stesso sistema di riferimento di quelle acquisite in inspirio è avvenuta utilizzando la trasformazione diffeomorfa B-Spline SyN, implementata nel software ANTs, ed è stata applicata sia alle immagini TC che alle features estratte da esse. Dalle matrici di co-occorrenza è stata calcolata la feature Energia, che misura l’uniformità dei livelli di grigio contenuti nell’immagine, e quindi la sua omogeneità. Partendo dal fatto che le aree parenchimali affette da enfisema e air trapping hanno alti livelli di omogeneità dovuti alla presenza dell’aria intrappolata al loro interno, l’idea alla base di questo lavoro è stata quella di identificare queste aree attraverso gli alti valori che l’Energia assume in loro corrispondenza. Sono state quindi stabilite sperimentalmente alcune soglie basate sui valori assunti dall’Energia in inspirio e in espirio. Sulla base di queste il parenchima polmonare è stato clusterizzato in diverse aree identificanti i tessuti sani, quelli affetti da enfisema e quelli affetti dall’air trapping. La clusterizzazione ottenuta è risultata coerente con la reale distribuzione dell’enfisema e dell’air trapping nei pazienti analizzati, dimostrando la validità della tecnica utilizzata e aprendo nuovi scenari futuri alla caratterizzazione del parenchima polmonare in questa patologia.

Développement et caractérisation de nouveaux nanocomposites polymères électriquement conductueurs pour plaques bipolaires de piles à combustible à membrane échangeuse de protons, PEMFC

Face à la diminution des ressources énergétiques et à l’augmentation de la pollution des énergies fossiles, de très nombreuses recherches sont actuellement menées pour produire de l’énergie propre et durable et pour réduire l’utilisation des sources d’énergies fossiles caractérisées par leur production intrinsèque des gaz à effet de serre. La pile à combustible à membrane échangeuse de protons (PEMFC) est une technologie qui prend de plus en plus d’ampleur pour produire l’énergie qui s’inscrit dans un contexte de développement durable. La PEMFC est un dispositif électrochimique qui fonctionne selon le principe inverse de l’électrolyse de l’eau. Elle convertit l’énergie de la réaction chimique entre l’hydrogène et l’oxygène (ou l’air) en puissance électrique, chaleur et eau; son seul rejet dans l’atmosphère est de la vapeur d’eau. Une pile de type PEMFC est constituée d’un empilement Électrode-Membrane-Électrode (EME) où la membrane consiste en un électrolyte polymère solide séparant les deux électrodes (l’anode et la cathode). Cet ensemble est intégré entre deux plaques bipolaires (BP) qui permettent de collecter le courant électrique et de distribuer les gaz grâce à des chemins de circulation gravés sur chacune de ses deux faces. La plupart des recherches focalisent sur la PEMFC afin d’améliorer ses performances électriques et sa durabilité et aussi de réduire son coût de production. Ces recherches portent sur le développement et la caractérisation des divers éléments de ce type de pile; y compris les éléments les plus coûteux et les plus massifs, tels que les plaques bipolaires. La conception de ces plaques doit tenir compte de plusieurs paramètres : elles doivent posséder une bonne perméabilité aux gaz et doivent combiner les propriétés de résistance mécanique, de stabilité chimique et thermique ainsi qu’une conductivité électrique élevée. Elles doivent aussi permettre d’évacuer adéquatement la chaleur générée dans le cœur de la cellule. Les plaques bipolaires métalliques sont pénalisées par leur faible résistance à la corrosion et celles en graphite sont fragiles et leur coût de fabrication est élevé (dû aux phases d’usinage des canaux de cheminement des gaz). C’est pourquoi de nombreuses recherches sont orientées vers le développement d’un nouveau concept de plaques bipolaires. La voie la plus prometteuse est de remplacer les matériaux métalliques et le graphite par des composites à matrice polymère. Les plaques bipolaires composites apparaissent attrayantes en raison de leur facilité de mise en œuvre et leur faible coût de production mais nécessitent une amélioration de leurs propriétés électriques et mécaniques, d’où l’objectif principal de cette thèse dans laquelle on propose: i) un matériau nanocomposite développé par extrusion bi-vis qui est à base de polymères chargés d’additifs solides conducteurs, incluant des nanotubes de carbone. ii) fabriquer un prototype de plaque bipolaire à partir de ces matériaux en utilisant le procédé de compression à chaud avec un refroidissement contrôlé. Dans ce projet, deux polymères thermoplastiques ont été utilisés, le polyfluorure de vinylidène (PVDF) et le polyéthylène téréphtalate (PET). Les charges électriquement conductrices sélectionnées sont: le noir de carbone, le graphite et les nanotubes de carbones. La combinaison de ces charges conductrices a été aussi étudiée visant à obtenir des formulations optimisées. La conductivité électrique à travers l’épaisseur des échantillons développés ainsi que leurs propriétés mécaniques ont été soigneusement caractérisées. Les résultats ont montré que non seulement la combinaison entre les charges conductrices influence les propriétés électriques et mécaniques des prototypes développés, mais aussi la distribution de ces charges (qui de son côté dépend de leur nature, leur taille et leurs propriétés de surface), avait aidé à améliorer les propriétés visées. Il a été observé que le traitement de surface des nanotubes de carbone avait aidé à l’amélioration de la conductivité électrique et la résistance mécanique des prototypes. Le taux de cristallinité généré durant le procédé de moulage par compression des prototypes de plaques bipolaires ainsi que la cinétique de cristallisation jouent un rôle important pour l’optimisation des propriétés électriques et mécaniques visées.

Coupled CFD Shape Optimization for aerodynamic profiles

The present document deals with the optimization of shape of aerodynamic profiles -- The objective is to reduce the drag coefficient on a given profile without penalising the lift coefficient -- A set of control points defining the geometry are passed and parameterized as a B-Spline curve -- These points are modified automatically by means of CFD analysis -- A given shape is defined by an user and a valid volumetric CFD domain is constructed from this planar data and a set of user-defined parameters -- The construction process involves the usage of 2D and 3D meshing algorithms that were coupled into own- code -- The volume of air surrounding the airfoil and mesh quality are also parametrically defined -- Some standard NACA profiles were used by obtaining first its control points in order to test the algorithm -- Navier-Stokes equations were solved for turbulent, steady-state ow of compressible uids using the k-epsilon model and SIMPLE algorithm -- In order to obtain data for the optimization process an utility to extract drag and lift data from the CFD simulation was added -- After a simulation is run drag and lift data are passed to the optimization process -- A gradient-based method using the steepest descent was implemented in order to define the magnitude and direction of the displacement of each control point -- The control points and other parameters defined as the design variables are iteratively modified in order to achieve an optimum -- Preliminary results on conceptual examples show a decrease in drag and a change in geometry that obeys to aerodynamic behavior principles

Integrated visual perception architecture for robotic clothes perception and manipulation

This thesis proposes a generic visual perception architecture for robotic clothes perception and manipulation. This proposed architecture is fully integrated with a stereo vision system and a dual-arm robot and is able to perform a number of autonomous laundering tasks. Clothes perception and manipulation is a novel research topic in robotics and has experienced rapid development in recent years. Compared to the task of perceiving and manipulating rigid objects, clothes perception and manipulation poses a greater challenge. This can be attributed to two reasons: firstly, deformable clothing requires precise (high-acuity) visual perception and dexterous manipulation; secondly, as clothing approximates a non-rigid 2-manifold in 3-space, that can adopt a quasi-infinite configuration space, the potential variability in the appearance of clothing items makes them difficult to understand, identify uniquely, and interact with by machine. From an applications perspective, and as part of EU CloPeMa project, the integrated visual perception architecture refines a pre-existing clothing manipulation pipeline by completing pre-wash clothes (category) sorting (using single-shot or interactive perception for garment categorisation and manipulation) and post-wash dual-arm flattening. To the best of the author’s knowledge, as investigated in this thesis, the autonomous clothing perception and manipulation solutions presented here were first proposed and reported by the author. All of the reported robot demonstrations in this work follow a perception-manipulation method- ology where visual and tactile feedback (in the form of surface wrinkledness captured by the high accuracy depth sensor i.e. CloPeMa stereo head or the predictive confidence modelled by Gaussian Processing) serve as the halting criteria in the flattening and sorting tasks, respectively. From scientific perspective, the proposed visual perception architecture addresses the above challenges by parsing and grouping 3D clothing configurations hierarchically from low-level curvatures, through mid-level surface shape representations (providing topological descriptions and 3D texture representations), to high-level semantic structures and statistical descriptions. A range of visual features such as Shape Index, Surface Topologies Analysis and Local Binary Patterns have been adapted within this work to parse clothing surfaces and textures and several novel features have been devised, including B-Spline Patches with Locality-Constrained Linear coding, and Topology Spatial Distance to describe and quantify generic landmarks (wrinkles and folds). The essence of this proposed architecture comprises 3D generic surface parsing and interpretation, which is critical to underpinning a number of laundering tasks and has the potential to be extended to other rigid and non-rigid object perception and manipulation tasks. The experimental results presented in this thesis demonstrate that: firstly, the proposed grasp- ing approach achieves on-average 84.7% accuracy; secondly, the proposed flattening approach is able to flatten towels, t-shirts and pants (shorts) within 9 iterations on-average; thirdly, the proposed clothes recognition pipeline can recognise clothes categories from highly wrinkled configurations and advances the state-of-the-art by 36% in terms of classification accuracy, achieving an 83.2% true-positive classification rate when discriminating between five categories of clothes; finally the Gaussian Process based interactive perception approach exhibits a substantial improvement over single-shot perception. Accordingly, this thesis has advanced the state-of-the-art of robot clothes perception and manipulation.

O impacto das medidas da Troika no desempenho económico-financeiro das empresas portuguesas

Os efeitos despoletados com a crise financeira de 2008 marcaram uma mudança radical de pensamentos e políticas entre as várias economias mundiais. Esta crise ficou marcada pelo enorme esforço que as economias tiveram que suportar, obrigando todos mercados a moldarem-se em função das contingências implementadas. Após análise e leitura de diversa literatura é consensual a referência ao início da crise financeira nos Estados Unidos da América (EUA) com o chamado subprime, percebendo-se também que muito rapidamente atingiria a Europa e todo o mundo. Desta forma, a Europa e inevitavelmente Portugal, acabaria por ser atingido e sofrer diversas consequências resultantes desta crise financeira. Na verdade, fruto da enorme turbulência dos mercados mundiais e da globalização, Portugal (incapaz de por si só sair da crise em que se viu envolvido) vê-se na necessidade de recorrer a ajuda externa por parte da Troika. Neste sentido, a presente dissertação tem como objetivo relatar resumidamente o início da crise financeira mundial, analisando o impacto das políticas de combate à crise implementadas em Portugal, no desempenho económico-financeiro das empresas portuguesas. Este estudo recaiu sobre a análise e perceção de comportamento de alguns indicadores económico financeiros entre os anos de 2010 a 2014, período durante o qual a Troika esteve presente em Portugal, implementando uma serie de reformas e políticas de combate à crise. Assim, debruçamo-nos sobre quatro setores de atividade (Construção Civil, Restauração, Hotelaria e Indústria do Calçado), observando os dados financeiros extraídos da base de dados SABI (Sistema de análise de Balanços Ibéricos) sobre empresas inseridas nos respetivos setores de atividade. Com base nos resultados do estudo realizado podemos concluir que o desempenho dos indicadores económico financeiros foram mais penalizados nos setores da Construção Civil e da Hotelaria.

Semiparametric modeling of the spatial distribution of occupational accident risk in the casual labor market, Piracicaba, southeast Brazil

The objective of this study was to estimate the spatial distribution of work accident risk in the informal work market in the urban zone of an industrialized city in southeast Brazil and to examine concomitant effects of age, gender, and type of occupation after controlling for spatial risk variation. The basic methodology adopted was that of a population-based case-control study with particular interest focused on the spatial location of work. Cases were all casual workers in the city suffering work accidents during a one-year period; controls were selected from the source population of casual laborers by systematic random sampling of urban homes. The spatial distribution of work accidents was estimated via a semiparametric generalized additive model with a nonparametric bidimensional spline of the geographical coordinates of cases and controls as the nonlinear spatial component, and including age, gender, and occupation as linear predictive variables in the parametric component. We analyzed 1,918 cases and 2,245 controls between 1/11/2003 and 31/10/2004 in Piracicaba, Brazil. Areas of significantly high and low accident risk were identified in relation to mean risk in the study region (p < 0.01). Work accident risk for informal workers varied significantly in the study area. Significant age, gender, and occupational group effects on accident risk were identified after correcting for this spatial variation. A good understanding of high-risk groups and high-risk regions underpins the formulation of hypotheses concerning accident causality and the development of effective public accident prevention policies.

Improving robustness of rolling stock circulations in rapid transit networks

The rolling stock circulation depends on two different problems: the rolling stock assignment and the train routing problems, which up to now have been solved sequentially. We propose a new approach to obtain better and more robust circulations of the rolling stock train units, solving the rolling stock assignment while accounting for the train routing problem. Here robustness means that difficult shunting operations are selectively penalized and propagated delays together with the need for human resources are minimized. This new integrated approach provides a huge model. Then, we solve the integrated model using Benders decomposition, where the main decision is the rolling stock assignment and the train routing is in the second level. For computational reasons we propose a heuristic based on Benders decomposition. Computational experiments show how the current solution operated by RENFE (the main Spanish train operator) can be improved: more robust and efficient solutions are obtained

Sintonia automática de controladores PID: uma abordagem neuro - genética

Dissertação de dout. em Electrónica e Computação, Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2004

Normative reference values for the 20-meter shuttlerun test in a population-based sample of schoolchildren in Bogota, Colombia: The FUPRECOL Study

Our aim was to determine the normative reference values of cardiorespiratory fitness (CRF) and to establish the proportion of subjects with low CRF suggestive of future cardio-metabolic risk.

Triceps and subscapular skinfold thicknesses percentiles and cut-offs for overweight and obesity in a population-based sample of schoolchildren in Bogota, Colombia

OBJECTIVES: The aims of this study were to establish a Colombian smoothed centile charts and LMS tables for tríceps, subscapular and sum tríceps+subscapular skinfolds; appropriate cut-offs were selected using receiver operating characteristic analysis based in a populationbased sample of schoolchildren in Bogota, Colombia and to compare them with international studies. METHODS: A total of 9 618 children and adolescents attending public schools in Bogota, Colombia (55.7% girls; age range of 9–17.9 years). Height, weight, body mass index (BMI), waist circumference, triceps and subscapular skinfold measurements were obtained using standardized methods. We have calculated tríceps+subscapular skinfold (T+SS) sum. Smoothed percentile curves for triceps and subscapular skinfold thickness were derived by the LMS method. Receiver operating characteristics curve (ROC) analyses were used to evaluate the optimal cut-off point of tríceps, subscapular and sum tríceps+subscapular skinfolds for overweight and obesity based on the International Obesity Task Force (IOTF) definitions. Data were compared with international studies. RESULTS: Subscapular, triceps skinfolds and T+SS were significantly higher in girls than in boys (P <0.001). The median values for triceps, subscapular as well as T+SS skinfold thickness increased in a sex-specific pattern with age. The ROC analysis showed that subscapular, triceps skinfolds and T+SS have a high discrimination power in the identification of overweight and obesity in the sample population in this study. Based on the raw non-adjusted data, we found that Colombian boys and girls had high triceps and subscapular skinfolds values than their counterparts from Spain, UK, German and US. CONCLUSIONS: Our results provide sex- and age-specific normative reference standards for the triceps and subscapular skinfold thickness values in a large, population-based sample of 3 schoolchildren and adolescents from an Latin-American population. By providing LMS tables for Latin-American people based on Colombian reference data, we hope to provide quantitative tools for the study of obesity and its complications.

Valores de referencia de la fuerza prensil en escolares colombianos. Estudio FUPRECOL

The primary aim of this study was to generate normative handgrip strength (HG) data for 10- to 17.9-year-olds. The secondary aim was to determine the relative proportion of Colombian children and adolescents that fall into established Health Benefit Zones (HBZ). This cross-sectional study is enrolling 7268 schoolchildren (boys n=3129 and girls n=4139, age 12.7 (2.4) years old. HG was measured using a hand dynamometer with an adjustable grip. Five HBZs (Needs Improvement, Fair, Good, Very Good, and Excellent) have been established that correspond to combined-HG. Centile smoothed curves, percentile and tables for the 3rd, 10th, 25th, 50th, 75th, 90th and 97th percentile were calculated using Cole’s LMS method. HG peaked in the sample at 22.2 (8.9) kg in boys and 18.5 (5.5) kg in girls. The increase in HG was greater for boys than for girls, but the peak HG was lower in girls than in boys. The HBZ data indicated that a higher overall percentage of boys than girls at each age group fell into the “Needs Improvement” zone, with differences particularly pronounced during adolescence. Our results provide, for the first time, sex- and age-specific HG reference standards for Colombian schoolchildren aged 9-17.9 years.

Normative reference of standing long jump for Colombian schoolchildren aged 9-17.9 years: The FUPRECOL study

El propósito del presente estudio era generar los valores normativos de salto largo para niños de 9-17.9 años, e investigar las diferencias de sexo y grupo de edad