Stressful Life Events and their Trajectories among Midlife Women: Observations from the Seattle Midlife Women's Health Study

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

A study of computational methods to analyze gene expression data

The recent advent of new technologies has led to huge amounts of genomic data. With these data come new opportunities to understand biological cellular processes underlying hidden regulation mechanisms and to identify disease related biomarkers for informative diagnostics. However, extracting biological insights from the immense amounts of genomic data is a challenging task. Therefore, effective and efficient computational techniques are needed to analyze and interpret genomic data. In this thesis, novel computational methods are proposed to address such challenges: a Bayesian mixture model, an extended Bayesian mixture model, and an Eigen-brain approach. The Bayesian mixture framework involves integration of the Bayesian network and the Gaussian mixture model. Based on the proposed framework and its conjunction with K-means clustering and principal component analysis (PCA), biological insights are derived such as context specific/dependent relationships and nested structures within microarray where biological replicates are encapsulated. The Bayesian mixture framework is then extended to explore posterior distributions of network space by incorporating a Markov chain Monte Carlo (MCMC) model. The extended Bayesian mixture model summarizes the sampled network structures by extracting biologically meaningful features. Finally, an Eigen-brain approach is proposed to analyze in situ hybridization data for the identification of the cell-type specific genes, which can be useful for informative blood diagnostics. Computational results with region-based clustering reveals the critical evidence for the consistency with brain anatomical structure.

Biodiesel a partir de óleos de alta acidez: desenvolvimento de um processo catalítico homogêneo

O presente trabalho visa o desenvolvimento de um processo para a produção de biodiesel partindo de óleos de alta acidez, aplicando um processo em duas etapas de catálise homogênea. A primeira é a reação de esterificação etílica dos ácidos graxos livres, catalisada por H2SO4, ocorrendo no meio de triglicerídeos e a segunda é a transesterificação dos triglicerídeos remanescentes, ocorrendo no meio dos ésteres alquílicos da primeira etapa e catalisada com álcali (NaOH) e álcool etílico ou metílico. A reação de esterificação foi estudada com uma mistura modelo consistindo de óleo de soja neutro acidificado artificialmente com 15%p de ácido oleico PA. Este valor foi adotado, como referência, devido a certas gorduras regionais (óleo de mamona advinda de agricultura familiar, sebos de matadouro e óleo de farelo de arroz, etc.) apresentarem teores entre 10-20%p de ácidos graxos livres. Nas duas etapas o etanol é reagente e também solvente, sendo a razão molar mistura:álcool um dos parâmetros pesquisados nas relações 1:3, 1:6 e 1:9. Outros foram a temperatura 60 e 80ºC e a concentração percentual do catalisador, 0,5, 1,0 e 1,5%p, (em relação à massa de óleo). A combinatória destes parâmetros resultou em 18 reações. Dentre as condições reacionais estudadas, oito atingiram acidez aceitável inferior a 1,5%p possibilitando a definição das condições para aplicação ótima da segunda etapa. A melhor condição nesta etapa ocorreu quando a reação foi conduzida a 60°C com 1%p de H2SO4 e razão molar 1:6. No final da primeira etapa foram realizados tratamentos pertinentes como a retirada do catalisador e estudada sua influência sobre a acidez final, utilizando-se de lavagens com e sem adição de hexano, seguidas de evaporação ou adição de agente secante. Na segunda etapa estudaram-se as razões molares de óleo:álcool de 1:6 e 1:9 com álcool metílico e etílico, com 0,5 e 1%p de NaOH assim como o tratamento da reação (lavagem ou neutralização do catalisador) a 60°C, resultando em 16 experimentos. A melhor condição nesta segunda etapa ocorreu com 0,5%p de NaOH, razão molar óleo:etanol de 1:6 e somente as reações em que se aplicaram lavagens apresentaram índices de acidez adequados (<1,0%p) coerentes com os parâmetros da ANP.

Heat transfer performance investigation of nanofluids flow in pipe

Different types of base fluids, such as water, engine oil, kerosene, ethanol, methanol, ethylene glycol etc. are usually used to increase the heat transfer performance in many engineering applications. But these conventional heat transfer fluids have often several limitations. One of those major limitations is that the thermal conductivity of each of these base fluids is very low and this results a lower heat transfer rate in thermal engineering systems. Such limitation also affects the performance of different equipments used in different heat transfer process industries. To overcome such an important drawback, researchers over the years have considered a new generation heat transfer fluid, simply known as nanofluid with higher thermal conductivity. This new generation heat transfer fluid is a mixture of nanometre-size particles and different base fluids. Different researchers suggest that adding spherical or cylindrical shape of uniform/non-uniform nanoparticles into a base fluid can remarkably increase the thermal conductivity of nanofluid. Such augmentation of thermal conductivity could play a more significant role in enhancing the heat transfer rate than that of the base fluid. Nanoparticles diameters used in nanofluid are usually considered to be less than or equal to 100 nm and the nanoparticles concentration usually varies from 5% to 10%. Different researchers mentioned that the smaller nanoparticles concentration with size diameter of 100 nm could enhance the heat transfer rate more significantly compared to that of base fluids. But it is not obvious what effect it will have on the heat transfer performance when nanofluids contain small size nanoparticles of less than 100 nm with different concentrations. Besides, the effect of static and moving nanoparticles on the heat transfer of nanofluid is not known too. The idea of moving nanoparticles brings the effect of Brownian motion of nanoparticles on the heat transfer. The aim of this work is, therefore, to investigate the heat transfer performance of nanofluid using a combination of smaller size of nanoparticles with different concentrations considering the Brownian motion of nanoparticles. A horizontal pipe has been considered as a physical system within which the above mentioned nanofluid performances are investigated under transition to turbulent flow conditions. Three different types of numerical models, such as single phase model, Eulerian-Eulerian multi-phase mixture model and Eulerian-Lagrangian discrete phase model have been used while investigating the performance of nanofluids. The most commonly used model is single phase model which is based on the assumption that nanofluids behave like a conventional fluid. The other two models are used when the interaction between solid and fluid particles is considered. However, two different phases, such as fluid and solid phases is also considered in the Eulerian-Eulerian multi-phase mixture model. Thus, these phases create a fluid-solid mixture. But, two phases in the Eulerian-Lagrangian discrete phase model are independent. One of them is a solid phase and the other one is a fluid phase. In addition, RANS (Reynolds Average Navier Stokes) based Standard κ-ω and SST κ-ω transitional models have been used for the simulation of transitional flow. While the RANS based Standard κ-ϵ, Realizable κ-ϵ and RNG κ-ϵ turbulent models are used for the simulation of turbulent flow. Hydrodynamic as well as temperature behaviour of transition to turbulent flows of nanofluids through the horizontal pipe is studied under a uniform heat flux boundary condition applied to the wall with temperature dependent thermo-physical properties for both water and nanofluids. Numerical results characterising the performances of velocity and temperature fields are presented in terms of velocity and temperature contours, turbulent kinetic energy contours, surface temperature, local and average Nusselt numbers, Darcy friction factor, thermal performance factor and total entropy generation. New correlations are also proposed for the calculation of average Nusselt number for both the single and multi-phase models. Result reveals that the combination of small size of nanoparticles and higher nanoparticles concentrations with the Brownian motion of nanoparticles shows higher heat transfer enhancement and thermal performance factor than those of water. Literature suggests that the use of nanofluids flow in an inclined pipe at transition to turbulent regimes has been ignored despite its significance in real-life applications. Therefore, a particular investigation has been carried out in this thesis with a view to understand the heat transfer behaviour and performance of an inclined pipe under transition flow condition. It is found that the heat transfer rate decreases with the increase of a pipe inclination angle. Also, a higher heat transfer rate is found for a horizontal pipe under forced convection than that of an inclined pipe under mixed convection.

High spatial resolution land use and land cover mapping of the Brazilian Legal Amazon in 2008 using Landsat-5/TM and MODIS data.

Understanding spatial patterns of land use and land cover is essential for studies addressing biodiversity, climate change and environmental modeling as well as for the design and monitoring of land use policies. The aim of this study was to create a detailed map of land use land cover of the deforested areas of the Brazilian Legal Amazon up to 2008. Deforestation data from and uses were mapped with Landsat-5/TM images analysed with techniques, such as linear spectral mixture model, threshold slicing and visual interpretation, aided by temporal information extracted from NDVI MODIS time series. The result is a high spatial resolution of land use and land cover map of the entire Brazilian Legal Amazon for the year 2008 and corresponding calculation of area occupied by different land use classes. The results showed that the four classes of Pasture covered 62% of the deforested areas of the Brazilian Legal Amazon, followed by Secondary Vegetation with 21%. The area occupied by Annual Agriculture covered less than 5% of deforested areas; the remaining areas were distributed among six other land use classes. The maps generated from this project ? called TerraClass - are available at INPE?s web site (http://www.inpe.br/cra/projetos_pesquisas/terraclass2008.php)

Simple approximate MAP inference for Dirichlet processes mixtures

The Dirichlet process mixture model (DPMM) is a ubiquitous, flexible Bayesian nonparametric statistical model. However, full probabilistic inference in this model is analytically intractable, so that computationally intensive techniques such as Gibbs sampling are required. As a result, DPMM-based methods, which have considerable potential, are restricted to applications in which computational resources and time for inference is plentiful. For example, they would not be practical for digital signal processing on embedded hardware, where computational resources are at a serious premium. Here, we develop a simplified yet statistically rigorous approximate maximum a-posteriori (MAP) inference algorithm for DPMMs. This algorithm is as simple as DP-means clustering, solves the MAP problem as well as Gibbs sampling, while requiring only a fraction of the computational effort. (For freely available code that implements the MAP-DP algorithm for Gaussian mixtures see http://www.maxlittle.net/.) Unlike related small variance asymptotics (SVA), our method is non-degenerate and so inherits the “rich get richer” property of the Dirichlet process. It also retains a non-degenerate closed-form likelihood which enables out-of-sample calculations and the use of standard tools such as cross-validation. We illustrate the benefits of our algorithm on a range of examples and contrast it to variational, SVA and sampling approaches from both a computational complexity perspective as well as in terms of clustering performance. We demonstrate the wide applicabiity of our approach by presenting an approximate MAP inference method for the infinite hidden Markov model whose performance contrasts favorably with a recently proposed hybrid SVA approach. Similarly, we show how our algorithm can applied to a semiparametric mixed-effects regression model where the random effects distribution is modelled using an infinite mixture model, as used in longitudinal progression modelling in population health science. Finally, we propose directions for future research on approximate MAP inference in Bayesian nonparametrics.

Dynamic Bayesian network for semantic place classification in mobile robotics

In this paper, the problem of semantic place categorization in mobile robotics is addressed by considering a time-based probabilistic approach called dynamic Bayesian mixture model (DBMM), which is an improved variation of the dynamic Bayesian network. More specifically, multi-class semantic classification is performed by a DBMM composed of a mixture of heterogeneous base classifiers, using geometrical features computed from 2D laserscanner data, where the sensor is mounted on-board a moving robot operating indoors. Besides its capability to combine different probabilistic classifiers, the DBMM approach also incorporates time-based (dynamic) inferences in the form of previous class-conditional probabilities and priors. Extensive experiments were carried out on publicly available benchmark datasets, highlighting the influence of the number of time-slices and the effect of additive smoothing on the classification performance of the proposed approach. Reported results, under different scenarios and conditions, show the effectiveness and competitive performance of the DBMM.

Advanced statistical models for the segregation, identification and measurement of coexisting sound sources

Long-term monitoring of acoustical environments is gaining popularity thanks to the relevant amount of scientific and engineering insights that it provides. The increasing interest is due to the constant growth of storage capacity and computational power to process large amounts of data. In this perspective, machine learning (ML) provides a broad family of data-driven statistical techniques to deal with large databases. Nowadays, the conventional praxis of sound level meter measurements limits the global description of a sound scene to an energetic point of view. The equivalent continuous level Leq represents the main metric to define an acoustic environment, indeed. Finer analyses involve the use of statistical levels. However, acoustic percentiles are based on temporal assumptions, which are not always reliable. A statistical approach, based on the study of the occurrences of sound pressure levels, would bring a different perspective to the analysis of long-term monitoring. Depicting a sound scene through the most probable sound pressure level, rather than portions of energy, brought more specific information about the activity carried out during the measurements. The statistical mode of the occurrences can capture typical behaviors of specific kinds of sound sources. The present work aims to propose an ML-based method to identify, separate and measure coexisting sound sources in real-world scenarios. It is based on long-term monitoring and is addressed to acousticians focused on the analysis of environmental noise in manifold contexts. The presented method is based on clustering analysis. Two algorithms, Gaussian Mixture Model and K-means clustering, represent the main core of a process to investigate different active spaces monitored through sound level meters. The procedure has been applied in two different contexts: university lecture halls and offices. The proposed method shows robust and reliable results in describing the acoustic scenario and it could represent an important analytical tool for acousticians.

Proprieta chemo-dinamiche delle sottostrutture nell'alone retrogrado della nostra galassia

Le stelle nate nelle galassie satelliti accresciute dalla MW durante il suo processo evolutivo, sono oggi mescolate nell'Alone Retrogrado della nostra Galassia, ma mantengono una coerenza chimica e dinamica che ci consente di identificarle e di ricostruirne l'origine. Tuttavia, investigare la chimica o la dinamica in maniera indipendente non è sufficiente per fare ciò. L'associazione di stelle a specifici eventi di merging basata esclusivamente sulla loro posizione nello spazio degli IoM può non essere univoca e portare quindi ad identificazioni errate o ambigue. Allo stesso tempo, la composizione chimica delle stelle riflette la composizone del gas della galassia in cui le stelle si sono formate, ma galassie evolutesi in maniera simile sono difficilmente distinguibili nei soli piani chimici. Combinare l'informazione chimica a quella dinamica è quindi necessario per ricostruire in maniera accurata la storia di formazione ed evoluzione della MW. In questa tesi è stato analizzato un campione di 66 stelle dell'Alone Retrogrado della MW (localizzate nei dintorni solari) combinando i dati fotometrici di Gaia e quelli spettroscopici ottenuti con PEPSI@LBT. L'obiettivo principale di questo lavoro è di associare univocamente le stelle di questo campione alle rispettive galassie progenitrici tramite l'utilizzo coniugato delle informazioni chimiche e cinematiche. Per fare questo, è stata prima di tutto ricostruita l'orbita di ognuna delle stelle. In seguito, l'analisi degli spettri dei targets ha permesso di ottenere le abbondanze chimiche. L'identificazione delle sottostrutture è stata effettuata attraverso un'analisi chemo-dinamica statisticamente robusta, ottenuta tramite l'applicazione di un metodo di Gaussian Mixture Model, e l'associazione finale ai relativi progenitori, nonchè la loro interpretazione in termini di strutture indipendenti, è stata eseguita accoppiando questa informazione con la composizione chimica dettagliata di ogni stella.

Phase diagram of a model for a binary mixture of nematic molecules on a Bethe lattice

We investigate the phase diagram of a discrete version of the Maier-Saupe model with the inclusion of additional degrees of freedom to mimic a distribution of rodlike and disklike molecules. Solutions of this problem on a Bethe lattice come from the analysis of the fixed points of a set of nonlinear recursion relations. Besides the fixed points associated with isotropic and uniaxial nematic structures, there is also a fixed point associated with a biaxial nematic structure. Due to the existence of large overlaps of the stability regions, we resorted to a scheme to calculate the free energy of these structures deep in the interior of a large Cayley tree. Both thermodynamic and dynamic-stability analyses rule out the presence of a biaxial phase, in qualitative agreement with previous mean-field results.

Pattern formation during mesophase growth in a homologous series

Remarkable differences in the shape of the nematic-smectic-B interface in a quasi-two-dimensional geometry have been experimentally observed in three liquid crystals of very similar molecular structure, i.e., neighboring members of a homologous series. In the thermal equilibrium of the two mesophases a faceted rectanglelike shape was observed with considerably different shape anisotropies for the three homologs. Various morphologies such as dendritic, dendriticlike, and faceted shapes of the rapidly growing smectic-B germ were also observed for the three substances. Experimental results were compared with computer simulations based on the phase field model. The pattern forming behavior of a binary mixture of two homologs was also studied.