Programas sofrem diversas modificações ao longo das etapas de desenvolvimento, implantação e manutenção. A evolução de um software pode ter várias causas: correção de erros, inclusão de novas funcionalidades ou até mesmo, como é o caso de programas orientados a aspecto, transformações estruturais podem fazer parte da semântica do sistema. Apesar de modificações serem comuns, não é tarefa trivial prever como estas afetam o comportamento dos programas, já que os componentes de software normalmente interagem de forma complexa, o que faz com que mesmo pequenas alterações possam introduzir comportamentos indesejados. Transformação de grafos, também conhecida como reescrita de grafos, é um importante paradigma para modelagem e análise de sistemas. Modelos baseados em transformação de grafos, como gramáticas de grafos, permitem uma modelagem ao mesmo tempo intuitiva e com semântica precisa, permitindo a aplicação de técnicas de análise como verificação de modelos e análise de par crítico no estudo do comportamento de sistemas. A teoria por trás de transformação de grafos vem sendo desenvolvida a várias décadas, e atualmente está descrita de uma forma bastante abstrata. Contudo, ainda não possui uma definição natural de reescritas de alta ordem, que facilitaria a definição de evolução de especificações compostas por regras de reescrita de grafo, tais como gramáticas de grafos. Nesta tese são abordadas a modelagem e a análise de sistemas sob modificações programadas no contexto de gramáticas de grafos. A generalização da abordagem de pushout duplo para reescrita de grafos é utilizada como o princípio geral para descrever, simultaneamente, a semântica do sistema e modificações estruturais. Para tal, introduzimos uma noção de reescrita de segunda ordem para modificar a estrutura de regras de transformação de grafos, e usando isso, definimos modelos equipados simultaneamente de regras de primeira e segunda ordem, chamados gramáticas de grafos de segunda ordem. Através destes modelos podemos representar simultaneamente transformações estruturais e execução do sistema, e relacionar formalmente ambos tipos de reescrita. Também propomos novas técnicas para investigar o efeito da modificação de regras sobre a aplicação destas. Finalmente, como um exemplo de aplicação da teoria, caracterizamos construções de sistemas orientados a aspectos através de gramáticas de grafos de segunda ordem, e discutimos como utilizar as novas técnicas para estudar o efeito da combinação aspectual sobre o sistema inicial. / Software systems are not static entities: they usually undergo several changes along their development and maintenance cycles. Software evolution may be required for several reasons, such as the inclusion of new functionalities, the correction of errors or even as part of the system semantics, as it is the case of aspect-oriented systems. However, it is usually not trivial to foresee how structural changes can affect the system behaviour, since system components often interact in very complex ways, and even trivial modifications may introduce new problems. Graph transformation, also known as graph rewriting, has been used throughout the years as an important paradigm for system modelling and analysis. Models based on graph transformation, such as graph grammars, allow an intuitive but formal representation of the system behaviour, allowing the usage of analysis techniques such as model checking and static analysis of rule interaction. The theory behind graph transformation is quite general, and has been studied since the 1970s. However, it still lacks a general notion of higher-order rewriting that would allow a natural definition of model transformations for graph grammars. The lack of general second-order characterization presents difficulties for employing graph grammars as targets of model transformations, and studying how model transformations affect their natural behaviour. In this thesis we address the problem of modelling and analysing systems undergoing programmed modifications in the context of graph grammars. We use the generalization of the double-pushout approach for graph rewriting as a principle for defining simultaneously the system semantics and structural modifications. To achieve this, we introduce a notion of second-order graph rewriting that acts on graph transformation rules. Based on secondorder rewriting we are able to define second-order graph grammars, models equipped with a first-order layer, representing the original system execution, and a second-order layer, representing a model transformation. Using second-order graph grammar we can encode simultaneously model transformations and system execution, allowing us to formally relate them. Moreover, we propose new techniques to investigate the effect of rule modification over their effect on graphs. As an application example, we characterize aspect-oriented constructions for graph grammars, and discuss how to relate the aspect weaving layer with the base system semantics.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Neste trabalho, provamos novos resutados de rigidez para hipersuperfÃcies quase-Einsteins no espaÃo euclidiano, baseado-se nos resultados pinching do autovalor. EntÃo, nÃs deduzimos alguns resultados anÃlogos para hipersuperfÃcies quase-umbÃlicas e uma nova caracterizaÃÃo de esferas geodÃsicas / In this work, we prove new rigidity results for almost-Einstein hypersurfaces of the Euclidean space, based on previous eigenvalue pinching results. Then, we deduce some comparable result for almost-umbilic hypersurfaces and new characterizations of geodesic spheres.

Programas sofrem diversas modificações ao longo das etapas de desenvolvimento, implantação e manutenção. A evolução de um software pode ter várias causas: correção de erros, inclusão de novas funcionalidades ou até mesmo, como é o caso de programas orientados a aspecto, transformações estruturais podem fazer parte da semântica do sistema. Apesar de modificações serem comuns, não é tarefa trivial prever como estas afetam o comportamento dos programas, já que os componentes de software normalmente interagem de forma complexa, o que faz com que mesmo pequenas alterações possam introduzir comportamentos indesejados. Transformação de grafos, também conhecida como reescrita de grafos, é um importante paradigma para modelagem e análise de sistemas. Modelos baseados em transformação de grafos, como gramáticas de grafos, permitem uma modelagem ao mesmo tempo intuitiva e com semântica precisa, permitindo a aplicação de técnicas de análise como verificação de modelos e análise de par crítico no estudo do comportamento de sistemas. A teoria por trás de transformação de grafos vem sendo desenvolvida a várias décadas, e atualmente está descrita de uma forma bastante abstrata. Contudo, ainda não possui uma definição natural de reescritas de alta ordem, que facilitaria a definição de evolução de especificações compostas por regras de reescrita de grafo, tais como gramáticas de grafos. Nesta tese são abordadas a modelagem e a análise de sistemas sob modificações programadas no contexto de gramáticas de grafos. A generalização da abordagem de pushout duplo para reescrita de grafos é utilizada como o princípio geral para descrever, simultaneamente, a semântica do sistema e modificações estruturais. Para tal, introduzimos uma noção de reescrita de segunda ordem para modificar a estrutura de regras de transformação de grafos, e usando isso, definimos modelos equipados simultaneamente de regras de primeira e segunda ordem, chamados gramáticas de grafos de segunda ordem. Através destes modelos podemos representar simultaneamente transformações estruturais e execução do sistema, e relacionar formalmente ambos tipos de reescrita. Também propomos novas técnicas para investigar o efeito da modificação de regras sobre a aplicação destas. Finalmente, como um exemplo de aplicação da teoria, caracterizamos construções de sistemas orientados a aspectos através de gramáticas de grafos de segunda ordem, e discutimos como utilizar as novas técnicas para estudar o efeito da combinação aspectual sobre o sistema inicial. / Software systems are not static entities: they usually undergo several changes along their development and maintenance cycles. Software evolution may be required for several reasons, such as the inclusion of new functionalities, the correction of errors or even as part of the system semantics, as it is the case of aspect-oriented systems. However, it is usually not trivial to foresee how structural changes can affect the system behaviour, since system components often interact in very complex ways, and even trivial modifications may introduce new problems. Graph transformation, also known as graph rewriting, has been used throughout the years as an important paradigm for system modelling and analysis. Models based on graph transformation, such as graph grammars, allow an intuitive but formal representation of the system behaviour, allowing the usage of analysis techniques such as model checking and static analysis of rule interaction. The theory behind graph transformation is quite general, and has been studied since the 1970s. However, it still lacks a general notion of higher-order rewriting that would allow a natural definition of model transformations for graph grammars. The lack of general second-order characterization presents difficulties for employing graph grammars as targets of model transformations, and studying how model transformations affect their natural behaviour. In this thesis we address the problem of modelling and analysing systems undergoing programmed modifications in the context of graph grammars. We use the generalization of the double-pushout approach for graph rewriting as a principle for defining simultaneously the system semantics and structural modifications. To achieve this, we introduce a notion of second-order graph rewriting that acts on graph transformation rules. Based on secondorder rewriting we are able to define second-order graph grammars, models equipped with a first-order layer, representing the original system execution, and a second-order layer, representing a model transformation. Using second-order graph grammar we can encode simultaneously model transformations and system execution, allowing us to formally relate them. Moreover, we propose new techniques to investigate the effect of rule modification over their effect on graphs. As an application example, we characterize aspect-oriented constructions for graph grammars, and discuss how to relate the aspect weaving layer with the base system semantics.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-04-26T13:23:08Z No. of bitstreams: 1 marianagenymoreira.pdf: 8374988 bytes, checksum: 38a7b2c61f3df104e6c9f034df1386ae (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-04-26T13:53:43Z (GMT) No. of bitstreams: 1 marianagenymoreira.pdf: 8374988 bytes, checksum: 38a7b2c61f3df104e6c9f034df1386ae (MD5) / Made available in DSpace on 2017-04-26T13:53:43Z (GMT). No. of bitstreams: 1 marianagenymoreira.pdf: 8374988 bytes, checksum: 38a7b2c61f3df104e6c9f034df1386ae (MD5) Previous issue date: 2016-05-31 / Nas últimas décadas a qualidade da energia elétrica disponibilizada na rede elétrica tornou-se foco. Este fato é justificado pela combinação dos aumentos da poluição dos sinais na rede e do número de dispositivos eletrônicos sensíveis às variações do sinal de alimentação, especialmente tendo em vista o novo cenário de redes inteligentes. Um dos desafios das redes inteligentes é a redução de eventos ou falhas devido à baixa qualidade de energia elétrica, principalmente envolvendo distúrbios harmônicos e inter-harmônicos, provocados pela utilização de cargas e sistemas eletrônicos. Os impactos e prejuízos causados por distúrbios harmônicos e inter-harmônicos são importantes o suficiente para torná-los foco de inúmeros estudos, posto que não há, até a presente data, um método de análise desses componentes eficiente o bastante para atuar no controle e proteção de sistemas de potência. Este trabalho busca contribuir para a melhoria da análise desses componentes de frequência e, nesse sentido, propõe um sistema de detecção, classificação e identificação de distúrbios de qualidade de energia, especialmente, harmônicos, sub-harmônicos e inter harmônicos, baseado em estatística de ordem superior. São contemplados ainda distúrbios de amplitude de curta duração: sags e swells. A estrutura proposta contempla ainda um contador de componentes inter-harmônicos e sub-harmônicos, capaz de apontar a existência e quantificar esses componentes mesmo quando combinados a outros distúrbios harmônicos. As metodologias propostas pelo trabalho exibem resultados bastante expressivos tanto em relação à eficiência das aplicações em qualidade de energia quanto em relação ao desempenho computacional. / The power quality available on the electrical power system became focus in the last decades. This fact is explained by the combination of signal pollutions increasing and the number of electronic devices sensitive to power signal variations, especially in the smart grids scenario. One of the challenges of smart grids is the reduction of events or failures due to the low power quality, mainly involving harmonics and inter-harmonics disturbances, caused by the use of fillers and electronic systems. Impacts and losses caused by these disturbances are of great concern in numerous studies, since there is not an efficient analysis method capable of dealing with this kind of disturbances. This thesis seeks to contribute in the sense of harmonics and inter-harmonics analysis by proposing a power quality disturbances detection, classification and identification system, based on higher order statistics. The proposed structure also includes a inter-harmonics and sub-harmonics components counter, able to point out the existence and to quantify these components even when they are combined with other harmonic disturbances. The proposed methodologies show suitable results both in terms of efficiency of investments in power quality as compared to the computational performance.

[pt] O tema da presente dissertação é o problema da demarcação entre os termos lógicos e extralógicos no âmbito das ciências formais, anunciado primeiramente por Alfred Tarski em seu artigo de 1936, On the Concept of Logical Consequence. Depois de expor e discutir o problema em questão, mostrando seu surgimento a partir da necessidade de uma definição materialmente adequada do conceito de conseqüência lógica, analisamos a solução formulada por Tarski em um artigo publicado postumamente, intitulado What Are Logical Notions? Algumas discussões subsidiárias, igualmente importantes para o trabalho como um todo, dizem respeito à concepção dos conceitos de modelo e interpretação que se podem depreender dos artigos supracitados, e de como ela difere da assim chamada concepção standard em teoria de modelos. Nosso objetivo principal é mostrar o lugar ocupado pelo conceito de forma lógica na obra de Tarski, e de como sua concepção acerca deste conceito implica uma visão ampliada do conceito de conseqüência lógica, cuja caracterização correta torna necessária a estratificação das formas lógicas numa hierarquia de tipos. / [en] The subject of this paper is the problem of demarcation between logical and extra-logical terms of formal languages, as formulated for the first time by Tarski in his 1936 paper On the Concept of Logical Consequence. After presenting and discussing the demarcation problem, pointing out how it arises from the need for a materially adequate definition of the concept of logical consequence, we analyze the solution presented by Tarski in his posthumously published paper, entitled What Are Logical Notions? Some subsidiary issues, that are also important for the work as a whole, concern the conception of model and interpretation that springs from the two papers mentioned, and how this conception differs from the standard conception in model theory. Our main goal is to show the place occupied by the concept of logical form in Tarski`s work, and how his conception of this concept implies a broader view about the related concept of logical consequence whose correct characterization makes necessary the stratification of logical forms into a hierarchy of types.

Repetitive verbal patterns of speech are a trait associated with high-functioning autism (HFA). For some, this higher-order restricted, repetitive behavior impedes learning, social opportunities, and access to work environments. Despite emerging motivation for establishing social relationships, some individuals with HFA lack the behavioral prerequisites to establish meaningful relationships. The purpose of this study is to demonstrate the effectiveness of teaching interaction to decrease higher-order verbal restricted and repetitive behaviors (RRBs) for four adults with HFA. Through a multiple baseline design across participants, individuals were exposed to a function-based intervention (i.e., teaching interaction) that systematically taught and reinforced alternative communicative behaviors while interrupting repetitive speech with specific feedback. Teaching interaction effectively reduced RRBs and increased alternative conversation for all four participants. Three of the four participants elected to participate in post-intervention maintenance sessions that occurred in individualized naturalistic settings. Their conversation behaviors maintained with one participant receiving one booster session.

This master‘s thesis deals with the use of higher order cumulants for classification of cardiac cycles. Second-, third-, and fourth-order cumulants were calculated from ECG recorded in isolated rabbit hearts during experiments with repeated ischemia. Cumulants properties useful for the subsequent classification were verified on ECG segments from control and ischemic group. The results were statistically analyzed. Cumulants are then used as feature vectors for classification of ECG segments by means of artificial neural network.

A large aspect ratio leads to higher ion capacity in miniaturized ion trap mass spectrometers. The aspect ratio (AR) of an ion trap represents the ratio between an extended trapping dimension and the characteristic trapping dimension. In contrast to linear and rectilinear traps, changing the AR of a toroidal ion trap (TorIT) results in changes to the degree of curvature and shape of the trapping potential, and hence, on performance as a mass analyzer. SIMION simulations show that higher-order terms in the trapping potential vary strongly for small and moderate AR values (below ~10), with the effects asymptotically flattening for larger AR values. Because of the asymmetry in electrode geometry, the trapping center does not coincide with the geometric center of the trap, and this displacement also varies with AR. For instance, in the asymmetric TorIT, the saddle point in the trapping potential and the geometric trap center differ from +0.6 to -0.4 mm depending on AR. Ion secular frequencies also change with the AR. Whereas ions in the simplified TorIT have stable trajectories for any value of AR, ions in the asymmetric TorIT become unstable at large AR values. Variations in high-order terms, the trapping center, and secular frequencies with AR are a unique feature of toroidal traps, and require significant changes in trap design and operation as the aspect ratio is changed.

Even after their discovery more than 60 years ago, little is known about how messenger RNAs (mRNAs) are packaged inside the cells. To ensure efficient and accurate delivery of the intended message to its proper destination, it is important to package the informational molecule in a way that protects it from premature degradation but also proper decoding at the destination. However, very little is known about the this fundamentally important step of mRNA packaging inside eukaryotic cells. To this end, we developed a novel approach, RIPPLiT (RNA ImmunoPrecipitation and Proximity Ligation in Tandem), to capture the 3D architecture of the ribonucleoprotein particles (RNPs) of interest transcriptome-wide. To begin with, we applied RIPPLiT to the exon-junction complex (EJC), a set of proteins stably bound to a spliced RNA. EJCs have been shown to interact with other proteins like SR- and SR-like to form megadalton sized complexes and help protect large regions of mRNAs. Thus, we hypothesized that these RNPs would provide an ideal system to elucidate the higher order organization of mRNPs. Preliminary analysis of data obtained from RIPPLiT consisted of “chimeric reads”, reads with multiple RNA fragments ligated together, which could not be analyzed with any of the existing bioinformatics tools. Thus, we developed a new bioinformatics suite, ChimeraTie, to map, analyze and visualize chimeric reads. Performing polymer analysis on chimeric reads obtained for hundreds of mRNAs, we were able to predict that mRNPs are linearly and densely packed into flexible rod-like structures before they undergo translation. In this thesis, along with the detailed biological conclusion, I have also provided a step-wise manual to perform RIPPLiT experiment and analyze the ensuing data using ChimeraTie.

A subset of eukaryotic heterochromatin is located around the nucleoli, and this localization is correlated with gene silencing. Although there is some evidence for trans-acting factors organizing genomic loci around the nucleolus, the characterization of proteins and /or RNAs involved in perinculeolar heterochromatin localization and maintenance is incomplete. Notably, the mammalian female inactive X chromosome, a well-studied model of facultative heterochromatin, frequently resides in the perinucleolar regions during mid to late S phase. The disruption of the Xi–nucleolus association results in the erosion of heterochromatin compartment and silencing, which renders it a good model to investigate the mechanism and biological relevance of heterochromatin organization around the nucleolus. This dissertation will present evidence showing that Ki-67 regulates inactive X (Xi) chromosome association with nucleoli, maintains Xi heterochromatic structures, and regulates cell cycle progression, in cell-type-specific manner dependent on checkpoint proficiency. Ki-67 protein plays roles in heterochromatin organization during interphase. Upon Ki-67 depletion, a subset of Xi in human female hTERT-RPE1 moved away from nucleolus and displayed several features of compromised heterochromatin maintenance. These chromatin alterations were limited to Xi chromosomes localized away from the nuclear lamina and were not observed in virally transformed 293T cells upon Ki-67 depletion. Furthermore, I demonstrated that the different Xi heterochromatin alteration responses result from cell-type-specific reduced proportion of cells in S phase upon Ki-67 depletion. In human hTERT-RPE1, WI-38, IMR90, hTERT-BJ cell lines, depletion of Ki-67 slowed entry into S phase and coordinately downregulated genes related to DNA replication. These cell lines are able to induce p21 expression upon Ki-67 depletion. On the contrary, alteration of transcription and cell cycle progression were not observed in tumor-derived HeLa, U2OS and 293T cell lines. These cell lines do not induce p21 expression either. I additionally examined the Ki-67 function in mouse cell cultures. Depletion of Ki-67 neither redistributes inactive X chromosome nor regulates S phase progression in primary female mouse embryonic cells.