The genus Gluconobacter consists of acetic acid bacteria which have the ability to generate acidic products from their substrates, particularly acetic acid from ethanol. For this reason, the gluconobacters live in acidic, sugary environments such as flowers, honey bees, fruits, cider, vinegar, wine and beer. The gluconobacters carry out a strictly respiratory type of metabolism using only oxygen as a terminal electron acceptor. They do not completely oxidize a substrate to carbon dioxide. Instead, they partially oxidize the substrate using membrane-bound dehydrogenases and excrete the product into the surrounding growth medium. It is these limited oxidations that make the gtuconobacters industrially useful. Although much is known about the physiology of the limited oxidations in the gluconobacters, little is known of their genetics, particularly, their plasmids. The overall purpose of this dissertation was to determine if Gluconobacter plasmids correlate with oxidative capability and/or antibiotic resistance. To achieve this goal, I first needed a way to screen strains of Gluconobacter for their ability to oxidize many different substrates. 'developed an assay that used an unusual artificial electron acceptor, tetranitroblue tetrazolium (TNBT) and then tested the ability of six strains to oxidize 13 chemical compounds. Although most strains were able to oxidize the 13 compounds tested, they accomplished this with varying extents of oxidation. These differences were noted even with strains representing the same species. / Ph. D.

Submitted by Erika Demachki (erikademachki@gmail.com) on 2015-05-22T15:58:29Z No. of bitstreams: 2 Dissertação - Gleiciele Mendes Viana Moscardo - 2012.pdf: 6640649 bytes, checksum: 88adb9875ad3fd59c33a460239672412 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Erika Demachki (erikademachki@gmail.com) on 2015-05-22T16:04:36Z (GMT) No. of bitstreams: 2 Dissertação - Gleiciele Mendes Viana Moscardo - 2012.pdf: 6640649 bytes, checksum: 88adb9875ad3fd59c33a460239672412 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2015-05-22T16:04:36Z (GMT). No. of bitstreams: 2 Dissertação - Gleiciele Mendes Viana Moscardo - 2012.pdf: 6640649 bytes, checksum: 88adb9875ad3fd59c33a460239672412 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2012-06-20 / This research addresses the musical comedy "Opera do Malandro" composed by Chico Buarque in 1978 and set during 40´s , at Rio de Janeiro, the final phase of the Estado Novo (1937-45). This investigation considers how Chico Buarque, using poetry and music, handled the censorship during the military dictatorship of the 70´s. It inserts "Opera do Malandro" in the context of the military dictatorship of the 70´s, considering the inclusion of multiple times in the preparation of the piece; the processes of hybridization that resulted in the "Opera do Malandro" and yet, the processes of identity representations, in particular those embodied in the figure of the rascal. Meaning to elucidate these questions, based on the concepts of phenomenological analysis and seeking support for the relationship between lyrics and music in musical rhetoric and Luiz Tatit´s studies, an analysis was made of the following poetic-musical songs that composes the piece: “O Malandro”, “Homenagem ao Malandro”, “Ópera” e “O Malandro nº2”. The analysis and interpretation of the query have confirmed the hypothesis presented that, from a language of "cracks" centered on the image of the rascal and the game of temporalities and hybridizations, Chico Buarque, using metaphores, presented the political, social and economic conditions of the country at those years, the 70´s. / A presente pesquisa aborda a comédia musical “Ópera do Malandro” composta por Chico Buarque em 1978 e ambientada no Rio de Janeiro dos anos de 1940, fase final do Estado Novo (1937-45). Constituem-se como eixos estruturantes desta investigação: a maneira como Chico Buarque lidou em termos poéticos e musicais com a censura durante a ditadura militar da década de 1970; a inserção da “Ópera do Malandro” no contexto da ditadura militar dos anos de 1970; a imbricação de tempos múltiplos na elaboração da peça; os processos de hibridação dos quais resultou a “Ópera do Malandro”, e ainda, os processos de representações identitárias, em especial, aquelas consubstanciadas na figura do malandro. Visando elucidar tais questões, baseando-se nos conceitos da análise fenomenológica e buscando respaldo para a relação letra e música na retórica musical e nos estudos de Luiz Tatit, foi realizada uma análise poético-musical das seguintes canções que compõe a peça: “O Malandro”, “Homenagem ao Malandro”, “Ópera” e “O Malandro nº2”. A análise e a interpretação dos questionamentos levantados confirmaram a hipótese apresentada de que, a partir de uma linguagem de “frestas” centrada na imagem do malandro e do jogo de temporalidades e hibridações, Chico Buarque metaforizou a situação política, social e econômica do país dos anos de 1970.

A pesquisa visa estabelecer que os campos definidos como ARTE, DESIGN e NARRATIVA têm limites muito mais fluidos, mutáveis e permeáveis do que, de fato, reconhecemos atualmente, e pretende fazer isso problematizando suas fronteiras. Parte-se da hipótese de que a categorização desses campos em áreas estanques, aparentemente estabelecidas e claras, é rasa, artificial, arbitrária, não dá conta de uma visão diagramática da produção contemporânea nos três campos referidos, em suas fronteiras e intersecções, nem alcança a profundidade de relações de origem e de influência cruzada entre os campos. Através de análise e revisão teórica, partindo da própria estrutura das narrativas formativas e das narrativas críticas nas três áreas e em áreas de fronteira, decorrem potenciais revisões internas dos campos e de suas intersecções, uma visão atualizada da complexidade das relações entre os três campos e novas possibilidades formativas, além de uma visão crítica dos discursos acessórios e de proposições metodológicas. Do ponto de vista metodológico, de fato, a investigação apoia-se em pesquisa bibliográfica, discussão de dispositivos de exemplo e análise teórica baseada em teorias-chave dos campos descritos, ARTE, DESIGN, NARRATIVA e suas hibridizações potenciais. Também através da apresentação de dispositivos próprios que expandem as questões centrais da investigação em outros suportes e interfaces, a discussão, que tem origem prática, poética e empírica, e toma uma forma teórica, linear, analítica, mas tem também conclusões, ou possibilidades, novamente práticas, poéticas e empíricas. O intuito é a tradução de um pensamento cuja origem é prática e poética, mas também bibliográfica, em uma análise teórica, transdisciplinar, com um possível desdobramento metodológico, a proposição de uma metodologia abdutiva. Apresentada por meio de dois discursos, teórico/analítico e criativo/artístico, a pesquisa trata das possibilidades formativas em campos próximos, ARTE, DESIGN e NARRATIVA, suas potenciais influências, cruzamentos, e de como é crítica para a atividade formativa e teórica nesses campos a diferença entre discursos prescritivos/propositivos e discursos descritivos/analíticos. Do ponto de vista teórico, a discussão baseia-se nos conceitos de Praxis e Poiesis de Agamben, na noção de estética de Pareyson e de arte contemporânea de C. Cauquelin, na semiótica Peirciana, partindo da leitura de L. Santaella, e de conceitos específicos de Danto, Pross e Belting sobre Arte; Cardoso, Dune, Raby e Coles sobre Design; e Caillois e Campos aplicados sobre Narrativa. / The research aims to establish that the fields defined as ART, DESIGN and NARRATIVE have limits that are much more fluid, changeable and permeable than we actually recognize today, and intends to do so by problematizing their borders. It is based on the hypothesis that the categorization of these fields into watertight areas, apparently established and clear, is shallow, artificial, arbitrary, does not account for a diagrammatic view of contemporary production in the three fields mentioned, in their borders and intersections, nor does it reach the depth of relations of origin and cross-influence between fields. Through theoretical analysis and revision, starting from the very structure of the formative narratives and the critical narratives in the three areas and in frontier areas, not only potential internal revisions of the fields and their intersections take place, but an updated view of the complexity of the relations between the three fields and new formative possibilities, as well as a critical view of the accessory discourses and methodological propositions. From a methodological point of view, the research is based on bibliographic research, discussion of example devices and theoretical analysis based on the key theories of the fields described, ART, DESIGN, NARRATIVE and their potential hybridizations. Also, through the presentation of original devices/artwork that expand the central questions of research in other supports and interfaces, the discussion, which has practical, poetic and empirical origins, and takes a theoretical, linear, analytical form, but also has conclusions, or possibilities, again practical, poetic and empirical. The intention is the translation of a thought whose origin is practical and poetic, but also bibliographical, in a theoretical and artistic transdisciplinary analysis, with a possible methodological unfolding, the proposition of an abductive methodology. Presented through two discourses, theoretical/analytical and creative/artistic, the research deals with the formative possibilities in nearby fields, ART, DESIGN and NARRATIVE, their potential influences, crossings, and how critical it is for the formative and theoretical activity in these fields the difference between prescriptive/propositional discourses and descriptive/analytical discourses. From a theoretical point of view, the discussion is based on the concepts of Agamben\'s Praxis and Poiesis, on the notion of Pareyson aesthetics and contemporary art by C. Cauquelin, on the Peircean Semiotics, based on the reading of L. Santaella, and specific concepts from Danto, Pross and Belting on ART; Cardoso, Dune, Raby and Coles on DESIGN; and Caillois and Campos applied on NARRATIVE.

A pesquisa visa estabelecer que os campos definidos como ARTE, DESIGN e NARRATIVA têm limites muito mais fluidos, mutáveis e permeáveis do que, de fato, reconhecemos atualmente, e pretende fazer isso problematizando suas fronteiras. Parte-se da hipótese de que a categorização desses campos em áreas estanques, aparentemente estabelecidas e claras, é rasa, artificial, arbitrária, não dá conta de uma visão diagramática da produção contemporânea nos três campos referidos, em suas fronteiras e intersecções, nem alcança a profundidade de relações de origem e de influência cruzada entre os campos. Através de análise e revisão teórica, partindo da própria estrutura das narrativas formativas e das narrativas críticas nas três áreas e em áreas de fronteira, decorrem potenciais revisões internas dos campos e de suas intersecções, uma visão atualizada da complexidade das relações entre os três campos e novas possibilidades formativas, além de uma visão crítica dos discursos acessórios e de proposições metodológicas. Do ponto de vista metodológico, de fato, a investigação apoia-se em pesquisa bibliográfica, discussão de dispositivos de exemplo e análise teórica baseada em teorias-chave dos campos descritos, ARTE, DESIGN, NARRATIVA e suas hibridizações potenciais. Também através da apresentação de dispositivos próprios que expandem as questões centrais da investigação em outros suportes e interfaces, a discussão, que tem origem prática, poética e empírica, e toma uma forma teórica, linear, analítica, mas tem também conclusões, ou possibilidades, novamente práticas, poéticas e empíricas. O intuito é a tradução de um pensamento cuja origem é prática e poética, mas também bibliográfica, em uma análise teórica, transdisciplinar, com um possível desdobramento metodológico, a proposição de uma metodologia abdutiva. Apresentada por meio de dois discursos, teórico/analítico e criativo/artístico, a pesquisa trata das possibilidades formativas em campos próximos, ARTE, DESIGN e NARRATIVA, suas potenciais influências, cruzamentos, e de como é crítica para a atividade formativa e teórica nesses campos a diferença entre discursos prescritivos/propositivos e discursos descritivos/analíticos. Do ponto de vista teórico, a discussão baseia-se nos conceitos de Praxis e Poiesis de Agamben, na noção de estética de Pareyson e de arte contemporânea de C. Cauquelin, na semiótica Peirciana, partindo da leitura de L. Santaella, e de conceitos específicos de Danto, Pross e Belting sobre Arte; Cardoso, Dune, Raby e Coles sobre Design; e Caillois e Campos aplicados sobre Narrativa. / The research aims to establish that the fields defined as ART, DESIGN and NARRATIVE have limits that are much more fluid, changeable and permeable than we actually recognize today, and intends to do so by problematizing their borders. It is based on the hypothesis that the categorization of these fields into watertight areas, apparently established and clear, is shallow, artificial, arbitrary, does not account for a diagrammatic view of contemporary production in the three fields mentioned, in their borders and intersections, nor does it reach the depth of relations of origin and cross-influence between fields. Through theoretical analysis and revision, starting from the very structure of the formative narratives and the critical narratives in the three areas and in frontier areas, not only potential internal revisions of the fields and their intersections take place, but an updated view of the complexity of the relations between the three fields and new formative possibilities, as well as a critical view of the accessory discourses and methodological propositions. From a methodological point of view, the research is based on bibliographic research, discussion of example devices and theoretical analysis based on the key theories of the fields described, ART, DESIGN, NARRATIVE and their potential hybridizations. Also, through the presentation of original devices/artwork that expand the central questions of research in other supports and interfaces, the discussion, which has practical, poetic and empirical origins, and takes a theoretical, linear, analytical form, but also has conclusions, or possibilities, again practical, poetic and empirical. The intention is the translation of a thought whose origin is practical and poetic, but also bibliographical, in a theoretical and artistic transdisciplinary analysis, with a possible methodological unfolding, the proposition of an abductive methodology. Presented through two discourses, theoretical/analytical and creative/artistic, the research deals with the formative possibilities in nearby fields, ART, DESIGN and NARRATIVE, their potential influences, crossings, and how critical it is for the formative and theoretical activity in these fields the difference between prescriptive/propositional discourses and descriptive/analytical discourses. From a theoretical point of view, the discussion is based on the concepts of Agamben\'s Praxis and Poiesis, on the notion of Pareyson aesthetics and contemporary art by C. Cauquelin, on the Peircean Semiotics, based on the reading of L. Santaella, and specific concepts from Danto, Pross and Belting on ART; Cardoso, Dune, Raby and Coles on DESIGN; and Caillois and Campos applied on NARRATIVE.

Made available in DSpace on 2014-08-20T13:25:36Z (GMT). No. of bitstreams: 1 Dissertacao_Henrique_Luche.pdf: 673254 bytes, checksum: 991fe8c33284715323691331edede6ba (MD5) Previous issue date: 2011-12-02 / The understanding of the physiological processes associated with yield and adaptation to stress conditions, as well as the application of this knowledge through breeding programs, have been appointed as key elements for the expansion of food production in the world. Among the physiological mechanisms widely discussed in the literature, the stay-green character has stood out for their carriers to give good performance as the yield, especially in restrictive environmental conditions such as drought, high temperatures occurring during the cycle and places with high incidence of certain plant pathogens. Therefore, this study aims to evaluate the consequences of delaying senescence, stay-green, in grain yield and phenotypic stability of this character in hexaploid wheat lines. The experiment was conducted in the winter season of the years 2003, 2004 and 2005 in the experimental field of the Plant Genomics and Breeding Center (FAEM / UFPel) located in the municipality of Capão do Leão. The experimental design was randomized blocks with three replicates with an observation unit of 1.8 m2. We evaluated 34 genotypes of wheat and 17 lines with them synchronized senescence, 15 the genetic constitutions bearing the stay-green character and two control elite cultivars (CD 177 and CEP 27). Observing the yield performance of stay-green and synchronized over the three years of evaluation, it is possible to establish an association among the presence of character with high yield, especially under conditions of abiotic stress factors, such as occurred in the year 2005. Analyzing the phenotypic stability parameters, the data corroborate the idea that the use of stay-green character contributes to reducing the environmental effect of the variation in the total phenotypic variation of the genotype for the traits of interest. Moreover, striking differences were seen in the degree and direction of association among the characters of genotype with normal and delayed senescence, suggesting that the choice of the selection criteria for conducting the segregating populations is very important. Therefeore, the use of character stay-green contributes positively to grain yield and phenotypic stability of this variable in hexaploid wheat lines. / O entendimento dos processos fisiológicos associados à produção e adaptação em condições de estresse, assim como a aplicação desse conhecimento via programas de melhoramento, têm sido apontado como elementos chaves para a expansão da produção de alimentos no mundo. Dentre os mecanismos fisiológicos amplamente discutidos na literatura, o caráter stay-green tem se destacado por atribuir à seus portadores bom desempenho quanto a rendimento de grãos, principalmente em condições de ambiente restritivas, como secas, ocorrência de elevadas temperaturas durante o ciclo e locais com elevada incidência de determinado fitopatógeno. Portanto, o presente estudo teve como objetivo avaliar os reflexos do retardamento da senescência, stay-green, no rendimento de grãos e na estabilidade fenotípica desse caráter em linhagens trigo hexaplóide. O experimento foi conduzido nos períodos de estação fria dos anos de 2003, 2004 e 2005, no campo experimental do Centro de Genômica e Fitomelhoramento (FAEM/UFPel), situado no município do Capão do Leão/RS, Brasil. O delineamento empregado foi de blocos ao acaso com três repetições, com uma unidade de observação de 1,8 m2. Foram avaliados 34 genótipos de trigo, sendo eles, 17 linhagens com senescência sincronizada, 15 constituições genéticas portadoras do caráter stay-green e duas cultivares elite testemunhas (CD 177 e CEP 27). Observando o comportamento do rendimento de grãos demonstrado pelas linhagens stay-green e sincronizadas ao longo dos três anos de avaliação, é possível estabelecer uma associação da presença do caráter com elevado rendimento de grãos, principalmente em condições de estresse abiótico, como ocorrido no ano de 2005. Analisando os parâmetros de estabilidade fenotípica, os dados corroboram a idéia de que o emprego do caráter stay-green colabora para a redução do efeito da variação de ambiente na variação fenotípica total do genótipo para os caracteres de interesse. Além disso, foram demonstradas diferenças bem marcantes quanto ao grau e direção de associação entre os caracteres de genótipo com senescência retardada e normal, devendo dar atenção na escolha dos critério para a seleção na condução de populações segregantes. Portanto, o emprego do caráter stay-green contribui positivamente para o rendimento de grãos e estabilidade fenotípica dessa variável em linhagens de trigo hexaplóide.

This work deals with particle swarm optimization. The theoretic part briefly describes the problem of optimization. The considerable part focuses on the overall description of particle swarm optimization (PSO). The principle, behavior, parameters, structure and modifications of PSO are described. The next part of the work is a recherché of variants of PSO, including hybridizations of PSO. In practical part the dynamic problems are analyzed and new designed algorithm for dynamic problems AHPSO is described (what it is based on, what was inspired, what elements are used and why). Algorithm is executed on the set of tasks (Moving peaks benchmark) and compared with the best publicly available variants of algorithm PSO on dynamic problems so far.

Στην παρούσα διδακτορική διατριβή προτείνονται μεθοδολογίες υπολογιστικής νοημοσύνης για την επεξεργασία και ανάλυση δεδομένων γονιδιακής έκφρασης μικροσυστοιχιών cDNA. Πιο συγκεκριμένα, στο πρώτο σκέλος αναπτύσσονται δύο νέες προσεγγίσεις για την εύρωστη εκτίμηση και διόρθωση του θορύβου υποβάθρου: η διόρθωση υποβάθρου βάσει εκατοστημορίων και η διόρθωση υποβάθρου βάσει παλινδρόμησης loess. Οι προσεγγίσεις αυτές καινοτομούν κυρίως στο ότι χρησιμοποιούν μία εύρωστη εκτίμηση του θορύβου υποβάθρου, γεγονός που τις καθιστά ιδανικές σε περιπτώσεις, όπου τα δεδομένα είναι θορυβώδη. Επιπροσθέτως, αναπτύσσεται ένα νέο, γενικής χρήσεως, πλαίσιο για τη συστηματική αξιολόγηση του βαθμού επίδρασης των μεθόδων διόρθωσης υποβάθρου. Μέσω του πλαισίου αυτού, οι δύο προτεινόμενες προσεγγίσεις, καθώς και άλλες ευρέως χρησιμοποιούμενες μέθοδοι, αξιολογούνται βάσει εφαρμογής τους σε διαφορετικά σύνολα δεδομένων αυτο-υβριδοποίησης, με τις πρώτες να εμφανίζουν ιδιαιτέρως καλή απόδοση. Το πλαίσιο αυτό καινοτομεί στο ότι ενσωματώνει νέα κριτήρια και τρόπους γραφικής απεικόνισης. Τόσο οι προτεινόμενες μέθοδοι εκτίμησης και διόρθωσης θορύβου υποβάθρου, όσο και το πλαίσιο συστηματικής αξιολόγησής τους, συνιστούν μία νέα, ενδελεχή μελέτη που προσανατολίζει στην εφαρμογή ή απόρριψη μίας συγκεκριμένης προσέγγισης, συνεισφέροντας εν τέλει στην κατάκτηση καλλίτερης ποιότητας δεδομένων μικροσυστοιχιών. Επίσης, στο δεύτερο σκέλος της διατριβής αναπτύσσεται ένα νέο, ολοκληρωμένο και γενικής χρήσεως πλαίσιο ανάλυσης δεδομένων μικροσυστοιχιών ούτως, ώστε να διερευνηθεί το ζήτημα εάν στην T-λευχαιμική κυτταρική σειρά CCRF-CEM επικρατούν εγγενείς ή επίκτητοι μηχανισμοί αντοχής στην πρεδνιζολόνη. Συγκεκριμένα, καταλλήλως επιλεχθέντα δεδομένα μικροσυστοιχιών cDNA – που διευκολύνουν την εξέταση τόσο της εξαρτώμενης από τη συγκέντρωση δράσης, όσο και της δυναμικής της ανταπόκρισης στην πρεδνιζολόνη (πρώιμη και όψιμη δράση) – γίνονται αντικείμενο επεξεργασίας και ενδελεχούς ανάλυσης, και βάσει συγκεκριμένων, προ-διατυπωμένων συλλογισμών, προσεγγίζεται το εν λόγω ερώτημα. Το πλαίσιο αυτό είναι καινοτόμο, εφόσον, πέραν του ότι ενσωματώνει μία πρωτότυπη ακολουθία μεθόδων, προσεγγίζει συστηματικά το πρόβλημα της εγγενούς ή επίκτητης αντοχής, συνεισφέροντας, έτσι, στην ευρύτερη προσπάθεια διερεύνησης των επακριβών μηχανισμών αντοχής των λευχαιμικών κυττάρων στα γλυκοκορτικοειδή. Τα αποτελέσματα από την εφαρμογή του στα δεδομένα της εν λόγω κυτταρικής σειράς συνηγορούν υπέρ της ύπαρξης μίας σύνθετης ανταπόκρισης του υπό μελέτη συστήματος στα γλυκοκορτικοειδή, η οποία όμως τείνει περισσότερο προς έναν εγγενή μηχανισμό αντοχής. / In the present Ph.D. thesis, computational intelligence methods for processing and analyzing cDNA microarray gene expression data are designed and developed. More specifically, in the first part of this thesis, the problem of background estimation and correction of two-channel microarray data is addressed and two novel algorithms are proposed, namely the percentiles-based and the loess-based background correction methods. Both approaches are based on the multiplicative model of background, while utilizing robust background noise estimators, thus making them ideal for noisy datasets. Furthermore, a new, generic framework for the systematic evaluation of the impact of the background estimating methodologies is suggested, whereupon the aforementioned methods as well as other approaches are evaluated by application to various publicly available self-self hybridization datasets. As suggested by this thorough, comparative evaluation our algorithms perform very well regarding noise reduction. The evaluation framework, which is based mainly on different and widely used statistical measures, incorporates new criteria and visualization methods. Moreover, it represents a novel, detailed contribution to the examination of the impact of background correction methods to the final interpretation of microarray experiments, conferring explicit guidance on the pros and cons of them and when they should be applied. Additionally, in the second part of this thesis, a new, generic, computational microarray data analysis framework is described, in order to examine the hypothesis of whether the resistant T-cell leukemia cell line CCRF-CEM posses an intrinsic or exert an acquired mechanism of resistance and to investigate the molecular imprint of this, upon prednisolone treatment. More analytically, using the above explained computational analysis workflow, microarray data that enable the examination of both the dose effect of prednisolone exposure and the dynamics (early and late) of the molecular response of the cells at the transcriptomic layer, are systematically analyzed based on specific, predefined formulations. The analysis of the results supports a complex mechanism of action for the cells which seems to favor though more the intrinsic mechanism of resistance.