In recent years the amount of biological data has increased exponentially. Most of these data can be represented as matrices relating two different entity types, such as drug-target interactions (relating drugs to protein targets), gene expression profiles (relating drugs or cell lines to genes), and drug sensitivity values (relating drugs to cell lines). Not only the size of these datasets is increasing, but also the number of different entity types that they relate. Furthermore, not all values in these datasets are typically observed, and some are very sparse. Matrix factorisation is a popular group of methods that can be used to analyse these matrices. The idea is that each matrix can be decomposed into two or more smaller matrices, such that their product approximates the original one. This factorisation of the data reveals patterns in the matrix, and gives us a lower-dimensional representation. Not only can we use this technique to identify clusters and other biological signals, we can also predict the unobserved entries, allowing us to prune biological experiments. In this thesis we introduce and explore several Bayesian matrix factorisation models, focusing on how to best use them for predicting these missing values in biological datasets. Our main hypothesis is that matrix factorisation methods, and in particular Bayesian variants, are an extremely powerful paradigm for predicting values in biological datasets, as well as other applications, and especially for sparse and noisy data. We demonstrate the competitiveness of these approaches compared to other state-of-the-art methods, and explore the conditions under which they perform the best. We consider several aspects of the Bayesian approach to matrix factorisation. Firstly, the effect of inference approaches that are used to find the factorisation on predictive performance. Secondly, we identify different likelihood and Bayesian prior choices that we can use for these models, and explore when they are most appropriate. Finally, we introduce a Bayesian matrix factorisation model that can be used to integrate multiple biological datasets, and hence improve predictions. This model hybridly combines different matrix factorisation models and Bayesian priors. Through these models and experiments we support our hypothesis and provide novel insights into the best ways to use Bayesian matrix factorisation methods for predictive purposes.

We give a formula for the Chern character on the DG category of global matrix factorizations on a smooth scheme $X$ with superpotential $w\in \Gamma(\O_X)$. Our formula takes values in a Cech model for Hochschild homology. Our methods may also be adapted to get an explicit formula for the Chern character for perfect complexes of sheaves on $X$ taking values in right derived global sections of the De-Rham algebra. Along the way we prove that the DG version of the Chern Character coincides with the classical one for perfect complexes.

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O objetivo do presente estudo foi avaliar os níveis das metaloproteinases da matriz MMP-9, MMP-3 e MMP-13, e das quimiocinas MCP-1, MIP-1β e RANTES, no fluido gengival de dentes sob força ortodôntica. Foram recrutados 14 pacientes (3 homens e 11 mulheres) que foram submetidos à movimentação ortodôntica dos caninos superiores. Amostras do fluido gengival foram coletadas com tiras de Periopaper em diferentes tempos. O volume do FG foi determinado com o uso do Periotron e os niveis das MMPs e das quimiocinas quantificados usando-se uma multianálise imunoenzimática com microesferas. Os resultados mostraram que existe um aumento significativo no volume do FG na área de pressão em quase todos os tempos analisados, quando comparados às áreas de tensão. Os níveis da MMP-9 foram muito superiores aos das MMP-13 e MMP-3. Na análise da evolução do tempo pode ser observada uma alteração significativa nos níveis da quantidade total de MMP-9, MMP-13 e MMP-3 e na concentração de MMP-13 e MMP-3 durante o período de movimentação dentária no lado de pressão. A elevação dos níveis de expressão destas MMPs 1 hora após a aplicação da força ortodôntica sugere que estas enzimas estejam envolvidas na remodelação periodontal induzida. As quimiocinas MCP-1, MIP-1β e RANTES foram detectadas no sulco gengival em todos os diferentes intervalos de tempo analisados, nas áreas de tensão e de pressão. Porém, diversas amostras estavam abaixo do nível de detecção do ensaio e, os níveis dessas quimiocinas no fluido gengival não parecem ser alterados pelas forças ortodônticas. / The goal of the present study was to evaluate the levels of the matrix metalloproteinases MMP-9, MMP-3 and MMP-13 and of the chemokines MCP-1, MIP-1β and RANTES in the gingival crevicular fluid of teeth under orthodontic forces. Fourteen subjects (3 males and 11 females) were enrolled and subjected to orthodontic tooth movement of their maxillary canines. Samples of gingival crevicular fluid were collected from both tension and pressure sides using Periopaper strips at different time points. The volume of GCF was determined using a Periotron and the levels of MMPs and chemokines quantified using a multiplex microbead immunoassay. The results demonstrated that the levels of MMP-9 were higher than the levels of MMP-13 and MMP-3. Statistically significant fluctuations during the orthodontic tooth movement could be detected for the total amount of MMP-9, MMP-13 and MMP-3 and for the concentration of MMP-13 and MMP-3 at the pressure side. The elevation in the levels of these MMPs, 1 hour after the application of the orthodontic force, suggests that these enzymes are involved in the induced periodontal remodeling. The chemokines MCP-1, MIP-1β and RANTES were detected in the GCF in both tension and pressure sides at different time points. However, several samples were below the level of detection of the assay and the levels of theses mediators in GCF did not seem to be altered by the orthodontic forces.

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Made available in DSpace on 2014-06-11T19:28:03Z (GMT). No. of bitstreams: 0 Previous issue date: 2002-02-26Bitstream added on 2014-06-13T20:57:40Z : No. of bitstreams: 1 oliveira_ca_me_arafo.pdf: 227077 bytes, checksum: bd756a932166596c8abaefd6455879f6 (MD5) / O propósito deste estudo foi analisar histologicamente a utilização da matriz dérmica acelular (AlloDermâ) associada ou não à proteína derivada da matriz do esmalte (Emdogainâ) em recessões gengivais criadas cirurgicamente em cães. Foram criados defeitos periodontais na superfície vestibular dos caninos superiores de seis cães. Estes foram submetidos à indução do acúmulo de placa por oito semanas, e após este período foram divididos e tratados em dois grupos: grupo I: matriz dérmica acelular; grupo II: matriz dérmica acelular associada à proteína derivada da matriz do esmalte, ambos com reposição coronária do retalho. Após três meses os animais foram sacrificados, os dentes retirados em bloco e processados histologicamente. Realizou-se análise histológica descritiva e histométrica, medindo-se a extensão do tecido epitelial, neoformação óssea e cementária, nível gengival, inserção conjuntiva e tamanho do defeito para os grupos I e II. Os resultados demonstraram valores estatisticamente iguais para as médias dos valores de cemento: 0.06 mm e 0.32 mm; osso: -0,75 mm e -0,86 mm; nível gengival: -2,15 mm e -3,11 mm; tamanho do defeito: 4,90 mm e 5,51 mm, respectivamente para os grupos I e II. Foi encontrada diferença estatisticamente significante em relação tecido epitelial, com médias de 2,88 mm e 2,15 mm, respectivamente para os grupos I e II. Não foi encontrada inserção conjuntiva. Com isso, pudemos concluir que o Emdogainâ não trouxe efeitos adicionais quando associado ao AlloDermâ. / The purpose of the present study was to histologically evaluate the healing of acellular dermal matrix (AlloDermâ), associated or not, a enamel matrix proteins (Emdogainâ) in gingival recessions defects created in dogs. Recessions defects were surgically created (5X7 mm) on the buccal aspect of the uppercuspids in contralateral jaw quadrants, in 6 mongrel dogs. The defects were exposed to plaque accumulation for 2 months. After they were divided into 2 groups, according to the treatment applied: Group I- acellular dermal matrix and coronally positioned flap; Group II: acellular dermal matrix, enamel matrix proteins and coronally positioned flap. After 3 months, the animals were sacrificed, and the blocks obtained were processed. Histologic and histometric analysis were performed to examine: ephithelium formation, cementum and bone regeneration, connective tissue adaptation, attachment level and defect measure. Results did not show a statistically significant difference in the cementum and bone regeneration, connective tissue adaptation, attachment level and defect measure parameters. The mean values were: 0,06 mm and 0,32 mm for cementum regeneration; -0,75 mm and -0,86 mm for bone regeneration; -2,15mm and -3,11 mm for attachment level; and 4,90 mm and 5,51 mm for defect measure, in the I and II groups, respectively. The ephithelium formation parameter was 2,88 mm and 2,15 mm, in the I and II groups, respectively, with a statistically significant difference. Within limits of this study, it can be concluded that Emdogainâ not brought additional effects when associated with AlloDermâ.

Made available in DSpace on 2014-06-11T19:24:03Z (GMT). No. of bitstreams: 0 Previous issue date: 2005Bitstream added on 2014-06-13T20:28:06Z : No. of bitstreams: 1 massagli_sr_me_bauru.pdf: 1536916 bytes, checksum: 1bba9694c744b08cd501ec8dab24ffc6 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O objetivo deste trabalho é mostrar como Matrix é o exemplo mais representativo do que se costuma chamar de filme de ficção cyberpunk e como o filme expõe e propõe como matéria conceitual básica o acesso a um novo topos, ou melhor, um u-topos, um não-espaço, também chamado de hiperespaço. No filme, um espaço para onde nossa subjetividade foi transportada e escravizada, enquanto nossos corpos jazem dóceis, subjugados e adormecidos em úteros mecânicos, sendo alimentados por cordões umbilicais metálicos. Trata-se de uma nova espacialidade, espelhada em nosso mundo contemporâneo, com a qual podemos nos relacionar através de alguma interface, em que fatos e coisas são-nos reapresentados a partir da simulação de um tempo real , que supõe um outro espaço-tempo social, de um novo tipo, espaço de auto-representação social imaterialmente fundada na existência de eventos gerados por técnicas digitais. Assim, partindo do pressuposto de que vivemos numa sociedade pós-moderna e da premissa de que, com o fim do Modernismo, a experiência do tempo e da subjetividade cedeu lugar à experiência pós-moderna do espaço, a preocupação que estará à frente de todas as outras neste trabalho será a de localizar no filme Matrix processos que reflitam as formas de apropriação espacial dessa mesma sociedade. A questão do espaço, enquanto conceito clássico, kantiano, de categoria universal dada a priori, que emoldura mesmo a experiência, será substituída por outra, que introduz a idéia de espaço enquanto diferentes formas de experimentar o real... / The goal of this work is to demonstrate how Matrix is the most representative example of what has been called cyberpunk fiction movie and how it reveals and propose as a basic conceptual issue the access to a new topos, or better saying, to a u-topos, a nonspace, also called cyberspace. In the movie, a space where our subjectivity was displaced to and enslaved, whereas our bodies rest docile, subjugated and sleeping in mechanical wombs, being fed through metallic umbilical lace. It s a new special dimension, mirrored on our contemporary world, with which we can relate by means of some interface and in which facts and objects are re-presented to us from the perspective of the simulation of a real time that elicits another social time-space, a dimension of self-representation socially and materially founded on the existence of technically generated events. Thus, from the premisse that we live in a postmodern society and that, once Modernism is over, the postmodern experience of time and subjectivity has yielded to the postmodern experience of space, the main concern during this work will be to locate in the film processes that reflect the appropriation of space within this society. The issue of space, as a classical, Kantian concept, of a universal category that frame the experience, will be replaced by another, which introduces the idea of space as different forms of experiencing the real. Space will be approached as a cultural concept that can be formulated in basis of forms of appropriation self-organized between two ends: power and resistance, which, in a reductionist way, can be understood in terms of virtual and real space, respectively... (Complete abstract, click electronic address below)