Thesis (Ph.D.)--University of California, San Francisco, 2004. / Bibliography: leaves 92-101. Also available online.

Thesis (Ph. D.)--Ohio State University, 2005. / Title from first page of PDF file. Document formatted into pages; contains ix, 146 p.; also includes graphics (some col.) Includes bibliographical references (p. 145-146). Available online via OhioLINK's ETD Center

In my PhD polymer microarrays have been central in discovery of new materials for cardiovascular repair, cartilage tissue engineering and bacteria resistant medical devices. This has led to the work described in the following four chapters of my thesis. In the first part of my thesis polymers for the development of novel heart valve leaflets were identified. Diseased heart valves are currently replaced with the either synthetic or bioprosthetic (acellular xenografts) valve prostheses. While synthetic prosthesis have excellent durability, thromboembolic complications are frequent, requiring patients to undergo lifelong anti-coagulation therapy. On the other hand, the leaflets of bioprosthetic valves undergo structural deterioration, resulting in the patients having to undergo follow-up replacement surgeries. In order to overcome these shortcomings, the aim of this part of my PhD was to discover polymers that will enable the development of a ‘bio-synthetic’ heart valve, with the durability of synthetic valves and the biocompatibility of bioprosthetic vales. Polymers that bind valve interstitial cells (cells with a plastic fibroblast / myofibroblast phenotype that renew the extracellular matrix components of the valve leaflets) and also enable stable expression of key markers were identified. Immunohistochemistry and RNA expression analysis identified polymers for coating 3-D scaffolds, with the coated scaffolds showing excellent cell invasion, viability and maintenance of valve interstitial cell markers. To mimic the regions of the valve leaflets with differing stiffness, the response of valve interstitial cells to substrate stiffness was studied with various crosslinked gels. Thus, polymeric gels, prepared with the same chemical composition but with different Young’s modulus (covering 3 orders of magnitude) showed valve interstitial cell attachment with the cells showing differing behaviour based on the stiffness of the gels. In the second part of this thesis, polymers were identified for cartilage repair. Hyaline articular cartilage has very low potential for self-renewal, therefore cell-based therapies with autologous chondrocyte implantation are desired. Due to limited availability from biopsies, chondrocytes have to be expanded by in vitro culture; and fully defined synthetic culture substrates are essential for regulatory approvals. Using the high throughput approach I identified ‘hit’ polymers that allowed adhesion, proliferation and long-term culture of primary human chondrocytes and also chondrocytes derived from Mesenchymal stem cells. 2-D scale-up identified 2 lead polymers that supported long-term attachment and maintenance of chondrocyte markers. Since prolonged monolayer culture is known to induce loss of chondrocyte phenotype (dedifferentiation), 3D versions of the polymers were prepared and their potential for their long-term maintenance of chondrocytes via immunohistochemistry and RNA expression was demonstrated. The 3D gels were also used to encapsulate chondrocytes and their long-term maintenance of phenotype within these matrices, offers the exciting possibility of using these matrices for cartilage regeneration. The third part and fourth parts of the thesis focussed on reducing medical device associated infections. Thus polymers identified that prevented binding of a variety of bacteria including clinical isolates from infected medical devices, were used to coat two commercially available central venous catheters resulting in up to 96% reduction in bacterial binding. This non-binding was enhanced by the generation of polymeric nanocapsules containing the anti-bacterial eugenol (or its natural source clove oil). A coating consisting of eugenol nanocapsules entrapped within an interpenetrating network of the best bacteria repellent polymer, allowed slow-release of eugenol and further improved its performance.

Thesis (Ph. D.)--University of Hong Kong, 2010. / Includes bibliographical references (leaves 120-132). Also available in print.

Thesis (PhD) -- Auckland University of Technology, 2005. / Also held in print (267 leaves : col. ill. ; 30 cm.) in City Campus Theses Collection. (T 572.8636 GOH)

Neste trabalho é proposto um estudo comparativo de alguns métodos de Agrupamento (Hierárquico, K-médias e Self-Organizing Maps) e de Classificação (K-Vizinhos, Fisher, Máxima Verossimilhança, Aggregating e Regressão Local), os quais são apresentados teoricamente. Tais métodos são testados e comparados em conjuntos de dados reais, gerados com a técnica de Microarray. Esta técnica permite mensurar os níveis de expressão de milhares de genes simultaneamente, possibilitando comparações entre amostras de tecidos pelos perfis de expressão. É apresentada uma revisão de conceitos básicos relacionados ao processo de normalização, sendo este uma das primeiras etapas da análise deste tipo de conjunto de dados. Em particular, estivemos interessados em encontrar pequenos grupos de genes que fossem ?suficientes? para distinguir amostras em condições¸ biológicas diferentes. Por fim, é proposto um método de busca que, dado os resultados de um experimento envolvendo um grande número de genes, encontra de uma forma eficiente os melhores classificadores. / In this work we propose a comparative study of some clustering methods (Hierarchic, K -Means and Self-Organizing Maps) and some classification methods (K-Neighbours, Fisher, Maximum Likelihood, Aggregating and Local Regression), which are presented teoretically. The methods are tested and compared based on the analysis of some real data sets, generated from Microarray experiments. This technique allows for the measurement of expression levels from thousands of genes simultaneously, thus allowing the comparative analysis of sample of tissues in relation to their expression profile. We present a review of basic concepts regarding normalization of microarray data, one of the first steps in microarray analysis. In particular, we were interested in finding small groups of genes that were ?sufficient? to identify samples originating from different biological conditions. Finally, a search method is proposed, which will find efficiently the best classifiers from the results of an experiment involving a huge number of genes.

Thesis (Ph.D.) -- University of Texas at Arlington, 2008.

Neste trabalho é proposto um estudo comparativo de alguns métodos de Agrupamento (Hierárquico, K-médias e Self-Organizing Maps) e de Classificação (K-Vizinhos, Fisher, Máxima Verossimilhança, Aggregating e Regressão Local), os quais são apresentados teoricamente. Tais métodos são testados e comparados em conjuntos de dados reais, gerados com a técnica de Microarray. Esta técnica permite mensurar os níveis de expressão de milhares de genes simultaneamente, possibilitando comparações entre amostras de tecidos pelos perfis de expressão. É apresentada uma revisão de conceitos básicos relacionados ao processo de normalização, sendo este uma das primeiras etapas da análise deste tipo de conjunto de dados. Em particular, estivemos interessados em encontrar pequenos grupos de genes que fossem ?suficientes? para distinguir amostras em condições¸ biológicas diferentes. Por fim, é proposto um método de busca que, dado os resultados de um experimento envolvendo um grande número de genes, encontra de uma forma eficiente os melhores classificadores. / In this work we propose a comparative study of some clustering methods (Hierarchic, K -Means and Self-Organizing Maps) and some classification methods (K-Neighbours, Fisher, Maximum Likelihood, Aggregating and Local Regression), which are presented teoretically. The methods are tested and compared based on the analysis of some real data sets, generated from Microarray experiments. This technique allows for the measurement of expression levels from thousands of genes simultaneously, thus allowing the comparative analysis of sample of tissues in relation to their expression profile. We present a review of basic concepts regarding normalization of microarray data, one of the first steps in microarray analysis. In particular, we were interested in finding small groups of genes that were ?sufficient? to identify samples originating from different biological conditions. Finally, a search method is proposed, which will find efficiently the best classifiers from the results of an experiment involving a huge number of genes.

published_or_final_version / Electrical and Electronic Engineering / Doctoral / Doctor of Philosophy

Les tumeurs thyroïdiennes constituent les tumeurs endocrines les plus fréquentes. Parmi celles-ci, on distingue les adénomes, tumeurs bénignes et encapsulées, et les carcinomes, tumeurs malignes. Ceux-ci sont eux-mêmes subdivisés, principalement sur base histologique, en carcinomes papillaires ou folliculaires, qui conservent certaines caractéristiques de différenciation des cellules thyroïdiennes initiales dont ils dérivent, et qui peuvent évoluer en carcinomes anaplasiques, totalement dédifférenciés. Les carcinomes différenciés de la thyroïde sont généralement de bon pronostic, contrairement aux cancers anaplasiques qui sont nettement plus agressifs, avec un taux de survie à 5 ans inférieur à 5%. La technologie des microarrays permet d’analyser simultanément l’expression de milliers de gènes dans différentes cellules et différentes conditions physiologiques, pathologiques ou toxicologiques. Au cours de cette thèse de doctorat, nous avons déterminé le profil d’expression génique des carcinomes papillaires de la thyroïde à l’aide de la technique des microarrays en utilisant une plateforme contenant plus de 8000 gènes. Douze des 26 cancers papillaires étudiés étaient issus de patients habitant la région de Tchernobyl lors de l’explosion de la centrale nucléaire de 1986 et sont considérés comme des cancers radio-induits. Les 14 tumeurs restantes proviennent de patients habitant la France. Leur étiologie n’étant pas connue, ils sont considérés comme des cancers sporadiques. La réalisation de ces expériences nous a permis d’identifier des signatures moléculaires entre des sous-types de cancers papillaires. Premièrement, nous avons montré que malgré un profil d’expression génique global similaire entre les cancers papillaires sporadiques et radio-induits, une signature multigénique permet de les séparer, indiquant que des subtiles différences existent entre les deux types de tumeurs. Deux autres signatures indépendantes, l’une liée aux agents étiologiques présumés de ces tumeurs (radiation vs. H2O2), l’autre liée aux mécanismes de recombinaison homologue de l’ADN, permettent également de séparer les cancers post-Tchernobyl des cancers sporadiques. Nous avons interprété ces résultats comme une différence de susceptibilité à l’irradiation entre ces deux types de tumeurs. D’autre part, nous avons pu identifier une liste de gènes permettant de séparer les cancers papillaires à variante classique des autres sous-types de cancers papillaires. L’analyse de cette liste de gènes a permis de mettre en relation cette signature avec l’important remodelage de cette variante histologique par rapport aux autres. Ces expériences ont aussi abouti à l’obtention d’une liste de gènes différentiellement exprimés entre les cancers papillaires et leur tissu normal adjacent. Une analyse minutieuse de cette liste à l’aide d’outils statistiques a permis de mieux comprendre la physiopathologie de ces tumeurs et d’aboutir à différentes conclusions : (1) un changement de population cellulaire est observé, avec une surexpression de gènes liés à la réponse immune, reflétant l’infiltration lymphocytaire de ces tumeurs par rapport au tissu normal adjacent (2) la voie de signalisation JNK est activée par surexpression de ses composants (3) la voie de signalisation de l’EGF, également par une surexpression de ses composants, complémente les altérations génétiques des cancers papillaires pour l’activation constitutive de la voie ERK1/2 (4) une sousexpression des gènes de réponse précoce est observée (5) une surexpression de nombreuses protéases, d’inhibiteurs de protéases et de protéines de la matrice extracellulaire permet d’expliquer l’important remodelage des cancers papillaires (6) le profil d’expression génique des cancers papillaires peut être corrélé avec un mode de migration collectif de ces tumeurs. Finalement, dans la dernière partie de la thèse, nous avons déterminé le profil d’expression génique des cancers anaplasiques de la thyroïde et l’avons comparé à celui des cancers papillaires. Nous avons montré que les deux types de tumeurs présentent des profils moléculaires globaux distincts, reflétant leur comportement tumoral très différent.