Thesis (Ph.D. (Environment and Resource Studies))--Mahidol University, 2009.

Diss.--Katholisch-theologische Fakultät--Ludwig-Maximilians-Universität München, 1990.

Genetic and protein interactions are essential to regulate cellular machinery. Their identification has become an important aim of systems biology research. In recent years, a variety of computational network inference algorithms have been employed to reconstruct gene regulatory networks from post-genomic data. However, precisely predicting these regulatory networks remains a challenge. We began our study by assessing the ability of various network inference algorithms to accurately predict gene regulatory interactions using benchmark simulated datasets. It was observed from our analysis that different algorithms have strengths and weaknesses when identifying regulatory networks, with a gene-pair interaction (edge) predicted by one algorithm not always necessarily consistent with the other. An edge not predicted by most inference algorithms may be an important one, and should not be missed. The naïve consensus (intersection) method is perhaps the most conservative approach and can be used to address this concern by extracting the edges consistently predicted across all inference algorithms; however, it lacks credibility as it does not provide a quantifiable measure for edge weights. Existing quantitative consensus approaches, such as the inverse-variance weighted method (IVWM) and the Borda count election method (BCEM), have been previously implemented to derive consensus networks from diverse datasets. However, the former method was biased towards finding local solutions in the whole network, and the latter considered species diversity to build the consensus network. In this thesis we proposed a novel consensus approach, in which we used Fishers Combined Probability Test (FCPT) to combine the statistical significance values assigned to each network edge by a number of different networking algorithms to produce a consensus network. We tested our method by applying it to a variety of in silico benchmark expression datasets of different dimensions and evaluated its performance against individual inference methods, Bayesian models and also existing qualitative and quantitative consensus techniques. We also applied our approach to real experimental data from the yeast (S. cerevisiae) network as this network has been comprehensively elucidated previously. Our results demonstrated that the FCPT-based consensus method outperforms single algorithms in terms of robustness and accuracy. In developing the consensus approach, we also proposed a scoring technique that quantifies biologically meaningful hierarchical modular networks.

Acetylation was previously thought to occur exclusively on histones, but recent high-throughput screens have identified thousands of non-histone substrates. Despite the identification of these sites, little is known about how these acetyltransferase enzymes target their substrates. Gcn5 is the catalytic acetyltransferase found within the highly conserved SAGA complex. Recently, a member of this complex, Ada2, was found to impact Gcn5 substrate selection. In the yeast model organism Saccharomyces cerevisiae, a synthetic substrate developed from a proposed Gcn5-specific consensus sequence is used to identify regulators of Gcn5 substrate selection. This work is the first to demonstrate that addition of a consensus sequence is enough to confer acetylation of a non-substrate. With this method, Ada3 was identified as a key regulator, and acetylome profiling identified novel targets for Gcn5 dependent acetylation specifically regulated by Ada3. This system could be adapted for other acetyltransferases to identify regulators of substrate selection.

During the last four decades, precisely from the early 1970s, U.S. foreign policy has played a dominant role in the U.S. political landscape. The current political discourse is predominantly marked by divided government, polarized politics and gridlock. Such a contentious political environment has proved to be detrimental for efficient and effective policy-making in foreign policy. There are significant factors that profoundly complicate the process of decision making and congressional-presidential relations. Partisan and ideological differences under the conditions of divided government are dominant in the current political process and in turn affect the prospects of legislative-executive consensus and dissension. Other factors such as media salience, public opinion, and electoral imperatives also complicate the dynamics of legislative-executive relations. In an era in which heightened political brinkmanship has enveloped Washington politics, continuum of consensus and dissension between Congress and the president on strategic foreign policy issues has virtually become a norm. This dissertation examines the dynamics of legislative-executive relations in two high politics U.S. foreign policy issue areas of treaty process and war powers. It appears that in contemporary U.S. foreign policymaking the trajectory of a continuum of legislative-executive consensus and dissension is a new normal and potentially irreversible, as Congress and the president try ardently to preserve their respective constitutional prerogatives. Empirical investigation across these two issue areas demonstrates a new era of a resurgent Congress marked by its greater assertive role and acting as a consequential player in the foreign policy domain. The passage of the War Powers Resolution in 1973 by Congress, overriding a presidential veto, has profound implications in the modern political landscape. It was a pivotal moment that permanently transformed the future road map of congressional-presidential relations. Since then the U.S. political system has been relentlessly experiencing an institutional power struggle in the foreign policy domain. Findings suggest that when Congress determines to confront the president and exercise its constitutional responsibilities it becomes very difficult for the president to overcome such congressional resistance. Interbranch competition has virtually created a consistent trajectory of a continuum of legislative-executive consensus and dissension in the foreign policy decision-making process.

O objetivo deste trabalho é desvelar as contradições inerentes às políticas ou ações que preconizam o artesanato enquanto meio de sobrevivência nas comunidades indígenas Mbyá-Guarani no estado do Rio Grande do Sul (RS). A atividade artesanal integra programas de inclusão social na condição de solução para a geração de renda e preservação identitária dessas comunidades. Entretanto, oculta uma estratégia que procrastina o enfrentamento do problema da concessão e demarcação das terras indígenas. O consenso social formado em torno dessa política fragiliza a luta pela terra por parte dos povos originários, e o incentivo ao artesanato acaba por desviar as atenções dessa questão crítica. Ainda assim, o artesanato indígena é uma alternativa legítima para a preservação de modos de fazer e formas de organização autóctones que definem padrões de interação social autônomos. É, portanto, uma atividade capaz de manter vivos os sistemas societais específicos de cada etnia indígena. Mas, em contraponto a esse consenso, formula-se a hipótese de que tal política impede o fortalecimento de uma agenda pública realmente efetiva no que diz respeito ao cumprimento da legislação que determina a demarcação e registro das terras indígenas. Para viver em acordo com seus modos tradicionais, as comunidades indígenas precisam dispor de amplos espaços naturais preservados. E isso não é contemplado quando ocorrem assentamentos em áreas de tamanho diminuto e pobres em recursos naturais. Trata-se, pois, da defesa de um posicionamento que confronta tanto a política indigenista quanto a pesquisa em administração no Brasil, que têm se pautado por doutrinas que não oferecem respostas a questões como essas. A filosofia positivista, que propunha a conversão do indígena tido como selvagem em cidadão civilizado, integrado à sociedade, foi dominante em praticamente toda a história da política indigenista brasileira, e seus resquícios ainda se fazem presentes. O paradigma sistêmico-estrutural funcionalista, por outro lado, tem constituído a ortodoxia nos estudos em administração no Brasil e tanto o questionamento de seus pressupostos quanto a busca por outras formas organizativas têm sido feitos de modo fragmentado. Por fim, compreende-se que a questão indígena, pela carga de interesses, preconceitos e toda sorte de equívocos que a cercam, torna-se um meio privilegiado para que se explore a crítica nos estudos organizacionais. Uma crítica que se propõe a desvelar a aparência de que se estaria diante de políticas transformadoras quando, de fato, permanecem incontestes os mecanismos fundamentais da exploração capitalista. Ainda que imersos no discurso positivo do respeito e da valorização da diversidade. / The goal of this Thesis is to address the contradictions contained in the policies, and the actions that uses handicrafts as a means of survival in indigenous communities Mbyá-Guarani in the State of Rio Grande do Sul (Brazil). Handicraft activities are part of social inclusion programs as a solution for generating income and preserving the identity of these communities. However, it cloaks a strategy which defers addressing the problem of the allocation and demarcation of indigenous lands. The social consensus formed around this policy weakens the struggle for land of the indigenous peoples. It is argued that incentives to engage in handicrafts serve to deflect attention from this critical issue. Nonetheless, handicrafts represent a legitimate alternative for preserving indigenous ways of operating and forms of organization that define independent patterns of social interaction. It is, therefore, an activity capable of maintaining the specific societal systems of each indigenous ethnic group. However, in opposition to this consensus, it is defended the hypothesis that this policy prevents the strengthening of a truly effective public agenda with regard to the enforcement of legislation which determines the demarcation and registration of indigenous lands. To live according to their traditional ways, indigenous communities need to have preserved natural areas. And this is not taken into account when settlements occur in small areas that are poor in natural resources. This position challenges both the indigenous policy and management research in Brazil, which have been based on doctrines that do not provide answers to these questions. The positivist philosophy, which proposed the conversion of the Indians, held as savages, into civilized citizens, integrated into society, has predominated virtually the entire history of Brazil's indigenous policy and its remnants are still present today. The systemic-structural functionalist paradigm, on the other hand, has constituted the orthodoxy of management studies in Brazil and both the questioning of its assumptions as well as the search for other organizational forms have been conducted in piecemeal fashion. Lastly, it is understood that the indigenous issue, given the weight of interests, prejudices and all the misconceptions surrounding it, has become a prime means to critically explore these organizational studies. A criticism which, in this Thesis, endeavors to lay bare the appearance that we are dealing with transformational policies, when, in fact, the underlying mechanisms of capitalist exploitation remain unchallenged. Though immersed in positive discourse about respect and valuing diversity.

O objetivo deste trabalho é desvelar as contradições inerentes às políticas ou ações que preconizam o artesanato enquanto meio de sobrevivência nas comunidades indígenas Mbyá-Guarani no estado do Rio Grande do Sul (RS). A atividade artesanal integra programas de inclusão social na condição de solução para a geração de renda e preservação identitária dessas comunidades. Entretanto, oculta uma estratégia que procrastina o enfrentamento do problema da concessão e demarcação das terras indígenas. O consenso social formado em torno dessa política fragiliza a luta pela terra por parte dos povos originários, e o incentivo ao artesanato acaba por desviar as atenções dessa questão crítica. Ainda assim, o artesanato indígena é uma alternativa legítima para a preservação de modos de fazer e formas de organização autóctones que definem padrões de interação social autônomos. É, portanto, uma atividade capaz de manter vivos os sistemas societais específicos de cada etnia indígena. Mas, em contraponto a esse consenso, formula-se a hipótese de que tal política impede o fortalecimento de uma agenda pública realmente efetiva no que diz respeito ao cumprimento da legislação que determina a demarcação e registro das terras indígenas. Para viver em acordo com seus modos tradicionais, as comunidades indígenas precisam dispor de amplos espaços naturais preservados. E isso não é contemplado quando ocorrem assentamentos em áreas de tamanho diminuto e pobres em recursos naturais. Trata-se, pois, da defesa de um posicionamento que confronta tanto a política indigenista quanto a pesquisa em administração no Brasil, que têm se pautado por doutrinas que não oferecem respostas a questões como essas. A filosofia positivista, que propunha a conversão do indígena tido como selvagem em cidadão civilizado, integrado à sociedade, foi dominante em praticamente toda a história da política indigenista brasileira, e seus resquícios ainda se fazem presentes. O paradigma sistêmico-estrutural funcionalista, por outro lado, tem constituído a ortodoxia nos estudos em administração no Brasil e tanto o questionamento de seus pressupostos quanto a busca por outras formas organizativas têm sido feitos de modo fragmentado. Por fim, compreende-se que a questão indígena, pela carga de interesses, preconceitos e toda sorte de equívocos que a cercam, torna-se um meio privilegiado para que se explore a crítica nos estudos organizacionais. Uma crítica que se propõe a desvelar a aparência de que se estaria diante de políticas transformadoras quando, de fato, permanecem incontestes os mecanismos fundamentais da exploração capitalista. Ainda que imersos no discurso positivo do respeito e da valorização da diversidade. / The goal of this Thesis is to address the contradictions contained in the policies, and the actions that uses handicrafts as a means of survival in indigenous communities Mbyá-Guarani in the State of Rio Grande do Sul (Brazil). Handicraft activities are part of social inclusion programs as a solution for generating income and preserving the identity of these communities. However, it cloaks a strategy which defers addressing the problem of the allocation and demarcation of indigenous lands. The social consensus formed around this policy weakens the struggle for land of the indigenous peoples. It is argued that incentives to engage in handicrafts serve to deflect attention from this critical issue. Nonetheless, handicrafts represent a legitimate alternative for preserving indigenous ways of operating and forms of organization that define independent patterns of social interaction. It is, therefore, an activity capable of maintaining the specific societal systems of each indigenous ethnic group. However, in opposition to this consensus, it is defended the hypothesis that this policy prevents the strengthening of a truly effective public agenda with regard to the enforcement of legislation which determines the demarcation and registration of indigenous lands. To live according to their traditional ways, indigenous communities need to have preserved natural areas. And this is not taken into account when settlements occur in small areas that are poor in natural resources. This position challenges both the indigenous policy and management research in Brazil, which have been based on doctrines that do not provide answers to these questions. The positivist philosophy, which proposed the conversion of the Indians, held as savages, into civilized citizens, integrated into society, has predominated virtually the entire history of Brazil's indigenous policy and its remnants are still present today. The systemic-structural functionalist paradigm, on the other hand, has constituted the orthodoxy of management studies in Brazil and both the questioning of its assumptions as well as the search for other organizational forms have been conducted in piecemeal fashion. Lastly, it is understood that the indigenous issue, given the weight of interests, prejudices and all the misconceptions surrounding it, has become a prime means to critically explore these organizational studies. A criticism which, in this Thesis, endeavors to lay bare the appearance that we are dealing with transformational policies, when, in fact, the underlying mechanisms of capitalist exploitation remain unchallenged. Though immersed in positive discourse about respect and valuing diversity.

abstract: ABTRACT For decades the United States has tried to increase the number of students pursuing science, technology, engineering, and mathematics (STEM) education and careers. Educators and policy makers continue to seek strategies to increase the number of students in the STEM education pipeline. Public institutions of higher education are involved in this effort through education and public outreach (EPO) initiatives. Arizona State University opened its largest research facility, the new Interdisciplinary Science and Technology Building IV (ISTB4) in September, 2012. As the new home of the School of Earth & Space Exploration (SESE), ISTB4 was designed to serve the school's dedication to K-12 education and public outreach. This dissertation presents a menu of ideas for revamping the EPO program for SESE. Utilizing the Delphi method, I was able to clarify which ideas would be most supported, and those that would not, by a variety of important SESE stakeholders. The study revealed that consensus exists in areas related to staffing and expansion of free programming, whereas less consensus exist in the areas of fee-based programs. The following most promising ideas for improving the SESE's EPO effort were identified and will be presented to SESE's incoming director in July, 2013: (a) hire a full-time director, theater manager, and program coordinator; (b) establish a service-learning requirement obligating undergraduate SESE majors to serve as docent support for outreach programs; (c) obligate all EPO operations to advise, assist, and contribute to the development of curricula, activities, and exhibits; (d) perform a market and cost analysis of other informational education venues offering similar programming; (3) establish a schedule of fee-based planetarium and film offerings; and (f) create an ISTB4 centric, fee-based package of programs specifically correlated to K12 education standards that can be delivered as a fieldtrip experience. / Dissertation/Thesis / Ed.D. Higher and Postsecondary Education 2013

O objetivo deste trabalho é desvelar as contradições inerentes às políticas ou ações que preconizam o artesanato enquanto meio de sobrevivência nas comunidades indígenas Mbyá-Guarani no estado do Rio Grande do Sul (RS). A atividade artesanal integra programas de inclusão social na condição de solução para a geração de renda e preservação identitária dessas comunidades. Entretanto, oculta uma estratégia que procrastina o enfrentamento do problema da concessão e demarcação das terras indígenas. O consenso social formado em torno dessa política fragiliza a luta pela terra por parte dos povos originários, e o incentivo ao artesanato acaba por desviar as atenções dessa questão crítica. Ainda assim, o artesanato indígena é uma alternativa legítima para a preservação de modos de fazer e formas de organização autóctones que definem padrões de interação social autônomos. É, portanto, uma atividade capaz de manter vivos os sistemas societais específicos de cada etnia indígena. Mas, em contraponto a esse consenso, formula-se a hipótese de que tal política impede o fortalecimento de uma agenda pública realmente efetiva no que diz respeito ao cumprimento da legislação que determina a demarcação e registro das terras indígenas. Para viver em acordo com seus modos tradicionais, as comunidades indígenas precisam dispor de amplos espaços naturais preservados. E isso não é contemplado quando ocorrem assentamentos em áreas de tamanho diminuto e pobres em recursos naturais. Trata-se, pois, da defesa de um posicionamento que confronta tanto a política indigenista quanto a pesquisa em administração no Brasil, que têm se pautado por doutrinas que não oferecem respostas a questões como essas. A filosofia positivista, que propunha a conversão do indígena tido como selvagem em cidadão civilizado, integrado à sociedade, foi dominante em praticamente toda a história da política indigenista brasileira, e seus resquícios ainda se fazem presentes. O paradigma sistêmico-estrutural funcionalista, por outro lado, tem constituído a ortodoxia nos estudos em administração no Brasil e tanto o questionamento de seus pressupostos quanto a busca por outras formas organizativas têm sido feitos de modo fragmentado. Por fim, compreende-se que a questão indígena, pela carga de interesses, preconceitos e toda sorte de equívocos que a cercam, torna-se um meio privilegiado para que se explore a crítica nos estudos organizacionais. Uma crítica que se propõe a desvelar a aparência de que se estaria diante de políticas transformadoras quando, de fato, permanecem incontestes os mecanismos fundamentais da exploração capitalista. Ainda que imersos no discurso positivo do respeito e da valorização da diversidade. / The goal of this Thesis is to address the contradictions contained in the policies, and the actions that uses handicrafts as a means of survival in indigenous communities Mbyá-Guarani in the State of Rio Grande do Sul (Brazil). Handicraft activities are part of social inclusion programs as a solution for generating income and preserving the identity of these communities. However, it cloaks a strategy which defers addressing the problem of the allocation and demarcation of indigenous lands. The social consensus formed around this policy weakens the struggle for land of the indigenous peoples. It is argued that incentives to engage in handicrafts serve to deflect attention from this critical issue. Nonetheless, handicrafts represent a legitimate alternative for preserving indigenous ways of operating and forms of organization that define independent patterns of social interaction. It is, therefore, an activity capable of maintaining the specific societal systems of each indigenous ethnic group. However, in opposition to this consensus, it is defended the hypothesis that this policy prevents the strengthening of a truly effective public agenda with regard to the enforcement of legislation which determines the demarcation and registration of indigenous lands. To live according to their traditional ways, indigenous communities need to have preserved natural areas. And this is not taken into account when settlements occur in small areas that are poor in natural resources. This position challenges both the indigenous policy and management research in Brazil, which have been based on doctrines that do not provide answers to these questions. The positivist philosophy, which proposed the conversion of the Indians, held as savages, into civilized citizens, integrated into society, has predominated virtually the entire history of Brazil's indigenous policy and its remnants are still present today. The systemic-structural functionalist paradigm, on the other hand, has constituted the orthodoxy of management studies in Brazil and both the questioning of its assumptions as well as the search for other organizational forms have been conducted in piecemeal fashion. Lastly, it is understood that the indigenous issue, given the weight of interests, prejudices and all the misconceptions surrounding it, has become a prime means to critically explore these organizational studies. A criticism which, in this Thesis, endeavors to lay bare the appearance that we are dealing with transformational policies, when, in fact, the underlying mechanisms of capitalist exploitation remain unchallenged. Though immersed in positive discourse about respect and valuing diversity.

Made available in DSpace on 2014-06-12T15:59:34Z (GMT). No. of bitstreams: 2 arquivo5182_1.pdf: 7099391 bytes, checksum: 9ae548e6659db775935f03eac2fa2f35 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2006 / Um dos principais objetivos da biologia molecular é descobrir o funcionamento de redes complexas de interação entre elementos celulares. Nas últimas décadas um grande volume de dados biológicos vem sendo produzido assim como modelos computacionais que fazem uso destes dados. Os métodos computacionais para Reconstrução de Redes de Genes apresentam-se como uma ferramenta importante para auxiliar no estudo e entendimento desta complexidade. Este trabalho apresenta uma proposta para Reconstrução de Redes de Genes que utiliza-se de diferentes fontes de dados e incorpora conhecimento biológico com o objetivo de melhorar a qualidade da inferência. Comparou-se a abordagem proposta com um trabalho anterior. Foram realizados experimentos com dados artificiais e dados reais de S. cerevisiae. O modelo proposto apresentou melhores resultados que o anterior em todos os critérios de avaliação para experimentos com dados artificiais. Na avaliação com dados reais a nova abordagem apresentou uma pequena melhora em apenas uma das configurações testadas