The field of epigenetics is gaining popularity and speed, due in part to its capability to answer lingering questions about the root cause of certain diseases. Epigenetics plays a crucial role in regulation of the cell and cell survival, particularly by cytosine methylation. It remains controversial if DNMT’s which facilitate methylation are present in mammalian mitochondria and what the functional significance they may have on modification of mitochondrial DNA. CRISPR-Cas9 technology enabled genome editing to remove the MTS (mitochondrial targeting sequence) from DNMT1 of HCT116 cells, purposefully minimizing effects on nuclear cytosine methylation, while exclusively impacting mitochondrial modification. Removal of the DNMT1 MTS did not completely prevent the localization of this enzyme to the mitochondria according to immunoblot analysis. As well, deletion of the MTS in DNMT1 revealed only a small decline in transcription; not until removal of DNMT3B did we see a two-fold decrease in transcription from mitochondrial protein coding genes. No significant decline in transcription occurred when a DNMT3B knockout also lost the MTS of DNMT1; this study is evidencing that DNMT3B is possibly the more significant methyltransferase in the mitochondria. Our aim from this study and future research is to clearly characterize which enzymes in the mitochondria are controlling cytosine modifications and to understand the mechanistic complexities that accompany cause and consequence of epigenetic modifications.

We present Depfix, a system for automatic post-editing of phrase-based English-to-Czech machine trans- lation outputs, based on linguistic knowledge. First, we analyzed the types of errors that a typical machine translation system makes. Then, we created a set of rules and a statistical component that correct errors that are common or serious and can have a potential to be corrected by our approach. We use a range of natural language processing tools to provide us with analyses of the input sentences. Moreover, we reimple- mented the dependency parser and adapted it in several ways to parsing of statistical machine translation outputs. We performed both automatic and manual evaluations which confirmed that our system improves the quality of the translations.

This practice based PhD project investigates the language ideologies which surround the specific multilingual context of rural primary education in Zambia. The project comprises of a creative documentary film and a complementary written submission. The fieldwork and filming of the project took place over 12 months between September 2011 and August 2012 in the community of Lwimba, in Chongwe District, Zambia. The project focuses on the experiences of a single grade one class, their teacher, and the surrounding community of Lwimba. The majority of the school children speak the community language of Soli. The regional lingua franca, and language of the teacher, however, is Nyanja, and the students must also learn Zambia’s only official language, English. At the centre of the project is a research inquiry focusing on the language ideologies which surround each of these languages, both within the classroom and the wider rural community. The project also simultaneously aims to investigate and reflect on the capacity of creative documentary film to engage with linguistic anthropological research. The film at the centre of the project presents a portrait of Annie, a young, urban teacher of the community’s grade one class, as well as three students and their families. Through the narrativised experiences of the teacher and children, it aims to highlight the linguistic ideologies present within the language events and practices in and around the classroom, as well as calling attention to their intersection with themes of linguistic modernity, multilingualism, and language capital. The project’s written submission is separated into three major chapters separated into the themes of narrative, value and text respectively. Each chapter will focus on subjects related to both the research inquiry and the project’s documentary film methodology. Chapter one outlines the intersection of political-historical narratives of nationhood and language that surround the project, and reflects on the practice of internal narrative construction within documentary film. Chapter two firstly focuses on the language valuations within the institutional setting of the classroom and the wider community, and secondly proposes a two-phase perspective of evaluation and value creation as a means to examine the practice of editing within documentary film making. Chapter three addresses the theme of text through discussing the role of literacy acquisition and use in the classroom and community, as well as analysing and reflecting on the practice of translation and subtitle creation within the project.

In this paper, I will detail the film making techniques that my crew and I employed while making AM800, my thesis film at the University of New Orleans. I will detail the creative and technical steps we took, from the earliest stages of idea conceptualization to the final phases of post-production and screening. During my recounting of this process, I will discuss our creative goals, the challenges that we faced while achieving these goals, and the resulting product's effectiveness as a narrative short film. The quality of the final product will be gauged through the results of test screenings and direct audience feedback.

A montagem cinematográfica foi um advento que mudou os rumos da história do audiovisual. O processo de edição e montagem possui uma importância ímpar na constituição da linguagem audiovisual. Modificada desde Méliès e aperfeiçoada ao longo do tempo, a montagem cinematográfica se tornou um dos pilares sobre os quais se sustentam os estudos de diversos autores dentro da história do Audiovisual, especificamente na história e teoria do cinema. Através da leitura de inúmeras dessas obras, em conjunto com a análise fílmica, podemos constatar que a manipulação do tempo e do espaço durante o processo de montagem de uma obra audiovisual permite a construção de múltiplos sentidos discursivos. Considerando essa relevância da montagem na construção da narrativa fílmica, esse projeto visa refletir sua importância discursiva por meio da análise de um recurso empregado constantemente na montagem: o faux raccord. A evidência do aparato e a adição de sentidos na etapa da pós-produção através da utilização do faux raccord faz com que esse elemento seja fulcral na análise da importância da montagem discursiva. Assim, essa pesquisa busca postular uma precisa definição para o termo, bem como situá-lo na produção teórica e audiovisual ao longo da história. Compreendendo seus usos e aplicações e averiguando de que modo esse elemento gesta nos filmes sentidos discursivos e propicia ao espectador a percepção dessa construção de sentido através da evidência do corte. / Film editing was a invention that changed the course of audiovisual\'s history. The process of editing has a unique importance in the creation of audiovisual language. Modified since Méliès and improved over time, film editing became one of the pillars in film studies, specifically in history and film theory. By reading many theoretical works, combined with film analysis, we note that the manipulation of time and space during the film editing process of an audiovisual work allows the construction of multiple discursive meanings. Considering the importance of editing in the construction of film narrative, this project is a reflection of discursive importance through the analysis of a resource constantly used in film editing: faux raccord. Therefore, this research seeks to postulate a precise definition for the term, and place it in the theoretical and audiovisual production throughout history. Understanding its uses and applications, and reflecting how this element generates discursive meanings in films and provides the spectator the perception of meaning construction through the evidence of the cut.

Tendo atuado no meio artístico e intelectual brasileiro do segundo pós-guerra até o fim da década seguinte, o veneziano Ruggero Jacobbi (1920-1981) foi um destacado crítico, tradutor e difusor da literatura brasileira, especialmente do drama e da lírica. A pesquisa procura, na perspectiva dos Estudos Descritivos da Tradução, recorrer ao instrumental da crítica genética aplicado à grandiosa tradução Invenzione di Orfeo, trabalho que lhe teria tomado décadas de dedicação, a partir da obra maior do poeta nordestino Jorge de Lima. O levantamento de documentos em acervos na Itália permitiu a consolidação de um dossiê genético a partir do qual se discute o processo tradutório no bojo da atuação brasilianista de Jacobbi. Os nomes do poeta Murilo Mendes e da filóloga Luciana Stegagno Picchio surgem no estudo como frequentes coadjuvantes deste que talvez tenha sido o empreendimento mais ambicioso do amigo. Antes da reconstituição crítico-genética, no entanto, apresenta-se a fulgurante presença da obra lírica do poeta alagoano no distante país peninsular, desde a primeira figuração por obra de Giuseppe Ungaretti até as investidas exegéticas fundamentais de Stegagno Picchio. Para tanto, por sua vez, apresenta-se e se discute a trajetória geral, brasileira e, depois, brasilianista de Ruggero Jacobbi, com atenção ao legado relativo à lírica nacional, que culmina no objeto maior desta dissertação. Entre a teatralização engajada da Litania dos Pobres de Cruz e Sousa para uma montagem brechtiana apresentada no Teatro Brasileiro de Comédia (TBC) em 1950 e a publicação póstuma do grande exemplo de transcriação, guia-nos o espírito crítico marxista-gramsciano e impuro de um intelectual marcado pelo ecletismo e pela contundência inconformista, formado em meio aos herméticos florentinos da era fascista e movido a refratar sua expressão insone em poesia, em teatro, no cinema, no diário, no ensaio, na crítica, na historiografia literária, na antologia e na tradução. / Since the Venetian Ruggero Jacobbi (1920-1981) acted in the Brazilian artistic and intellectual world from the second postwar until the end of the next decade, he was an important literary critic, translator and diffuser of the Brazilian literature, especially of the drama and lyric poetry. This research aims, in the Descriptive Translation Studies perspective, to use tools from the genetic editing (critique génétique) and apply them to the magnificent translation Invenzione di Orfeo, which work supposedly took some decades of dedication, of the most important work of the Brazilian northeastern poet Jorge de Lima. The process of gathering documents in documentary archives in Italy allowed the make of a genetic dossier, with which it was possible to discuss the translation process, in the Brazilianist works of Jacobbi. The names of the poet Murilo Mendes and of the philologist Luciana Stegagno Picchio appeared in this research because they have shared with Jacobbi the experience of carrying out the most ambitious project of his professional life. Before of the critical-genetic reconstitution, however, there was the brightening glow: the reception of the poetic work of the Alagoan poet in the peninsular country, which includes since the first manifestation made by Giuseppe Ungaretti until the fundamental exegetical attempts of Stegagno Picchio. Before this phase, there was the presentation of the Brazilian and Brazilianist trajectory of Ruggero Jacobbi, and then the discussion on this subject, with special attention to his legacy to the national lyric poetry, which culminated on what, is the main object of this work. In the journey from the political dramatization of Litania dos Pobres (from the poem by Cruz e Sousa) into a Brechtian play presented in the Brazilian Comedy Theater (Teatro Brasileiro de Comédia TBC) in 1950, to the posthumous publication of the great example of transcreation, the guide to us is this impure and marxist-gramscian critic spirit of an intellectual marked by the eclecticism and by the nonconformist force, shaped between the hermetic Florentines of the fascist era, a spirit which was moved to reflect his insomniac expression in the poetry, in the drama, in the filmmaking, in the diaries, in the essays, in the literary criticism, in the literary historiography, in the anthology and in the translation.

L'édition collaborative en temps réel permet à plusieurs utilisateurs d'éditer un même document simultanément grâce à des outils informatiques. Les applications d'édition collaborative en temps réel répliquent les données éditées chez chaque utilisateur, pour garantir une édition des données réactive et possible à chaque instant. Les conflits d'édition sont fréquents, et doivent être gérés automatiquement par l'application. L'application doit faire converger toutes les répliques vers un document commun, qui contient toutes les modifications exprimées par tous les utilisateurs. Les algorithmes actuels fonctionnent de manière satisfaisante pour des types de données simples et des possibilités d'édition minimes. Lorsque le document est plus complexe (document XML, texte structuré), ou qu'il peut être édité avec un ensemble élargi d'opérations (déplacement de texte, styliser du texte), lors de la résolution de conflits d'édition, les algorithmes échouent à proposer un contenu qui convienne aux utilisateurs. Les intentions des utilisateurs ne sont pas respectées. L'objectif de cette thèse est de proposer des algorithmes d'édition collaborative en temps réel qui respectent mieux les intentions des utilisateurs que les algorithmes actuels.Pour cela, nous étudions deux approches de la littérature nommées transformées opérationnelles et modèles de données répliquées commutatives, et montrons comment il est possible d'attribuer plus de sémantique aux opérations de base des algorithmes d'édition collaborative, ce qui permet aux utilisateurs d'exprimer avec plus de moyens leurs intentions, et aux algorithmes de résoudre plus efficacement les conflits d'édition / Real-time collaborative editors, like GoogleDocs or Etherpad, allow the simultaneous edition of a document by several users. These applications need to replicate the edited document, for the so called real-time purpose of permitting a fast and reactive editing by any user at any time. Editing conflicts frequently occur, and must be automatically handled by the application, in order to provide every users with the same copy of the document, containing every modifications issued. Most of current real-time collaborative editing algorithms were designed for simple data structures, like linear text, and simple editing ways, like inserting or removing a character only. These algorithms fail to offer an appropriate editing conflict resolution when used with a complex data structure, like XML, or with complex operations, like moving some text or adding some style. Copies are the sames but users' intentions are not preserved. The goal of this thesis is to design new real-time collaborative editing algorithms that ensure a better preservation of users' intentions. The first contribution of this thesis is an algorithm based on the Operational Transformation approach (OT). Our contribution is designed to handle rich text document (with stylized text and paragraphs) and to preserve the intentions of a set of high editing level operations (add style, merge paragraphs...). The second contribution uses the Commutative Replicated Data Types approach (CRDT), and offers an algorithm which preserves the update intention, while improving global performance of the approach when dealing with large blocs of data

What space does the mind occupy? A standard response to this question might be to locate the mind within the brain. However some argue that our mental processes also extend beyond the boundaries of the brain. Gallagher & Zahavi (2008) have termed these two views of the mind: internalism and externalism. In cinema, the role of editor as mediator between the cognitive activities of filmmakers, audiences and the editing equipment, makes their practice particularly suited for investigating these two seemingly incompatible views. When editors cut or join chunks of sound and image, they assemble externally what some would recognise internally as the mind’s fluctuations between one object of attention and the next. Their activities reveal a side of cinema, but also of the mind, which is usually hidden from view. The purpose of this thesis will therefore be to show how studying the process of editing contributes to our understanding of the relationship between mind and world. In order to address the question of where the editor’s mental processes are located, this study applies a phenomenographic methodology. Rather than attempt to understand cognition from a preconceived or objectively constituted position, phenomenography starts by examining variation in how a group of individuals view a particular process. This leads toward research findings that are presented from a ‘second-order perspective’ (Marton, 1981). In this thesis an understanding of how audiovisual material is selected and sequenced is revealed through fourteen interviews with British editors and directors. From the analysis of these interviews a framework emerged of five critical interrelated ways to approach the editing process. This evidence suggests that the cognitive process occurs in virtue of an editor’s physical activities, the editing equipment, plus a broader network of social and cultural relations that support the filmmaking environment. Refuting the belief that the mind is separate from the world, the editor’s mental processes are to be found distributed amongst a variety of internal and external features of their environment. The outcome of this thesis is a phenomenographic perspective on the editing process. This, I conclude, will help to inform cognitive scientists of the kinds of mental processes that editors are aware of. It also provides a wider audience of scholars with a framework for further research on variation in the process and practice of editing.

Condition based maintenance is becoming increasingly popular in many industrial contexts, offering substantial savings and minimising accidental damage. When applied to rotating machinery, its most common tool is vibration analysis, which relies on well-established mathematical models rooted in the theory of cyclo-non-stationary processes. However, the extraction of diagnostic information from the real world vibration signals is a delicate task requiring the application of sophisticated signal processing techniques, tailored for specific machines operating under restricted conditions. Such difficulty in the current state of the art of vibration analysis forces the industry to apply methods with reduced diagnostic capabilities but higher adaptability. However in doing so most of the potential of vibration analysis is lost and advanced techniques become of use only for academic endeavours. The aim of this document is to reduce the gap between industrial and academic applications of condition monitoring, offering ductile and automated tools which still show high detection capabilities. Three main lines of research are presented in this document. Firstly, the implementation of stochastic resonance in an electrical circuit to enhance directly the analog signal from an accelerometer, in order to lower the computational requirements in the next digital signal processing step. Secondly, the extension of already well-established digital signal processing techniques, cepstral prewhitening and spectral kurtosis, to a wider range of operating conditions, proving their effectiveness in the case of non-stationary speeds. Thirdly, the main contribution of the thesis: the introduction of two novel techniques capable of separating the vibrations of a defective component from the overall vibrations of the machine, by means of a threshold in the amplitude spectrum. After the separation, the cyclic content of the vibration signal is extracted and the thresholded signals provide an enhanced detection. The two proposed methods, phase editing and amplitude cyclic frequency decomposition, are both intuitive and of low computational complexity, but show the same capabilities as more sophisticated state of the art techniques. Furthermore, all these tools have been successfully tested on numerically simulated signals as well as on real vibration data from different machinery, lasting from laboratory test rigs to wind turbines drive-trains and aircraft engines. So in conclusion, the proposed techniques are a promising step toward the full exploitation of condition based maintenance in industrial contexts.

A produção de proteínas terapêuticas recombinantes compreende moléculas complexas e de alto valor agregado, incluindo a enzima glucocerebrosidase (GCase). Sua deficiência resulta na Doença de Gaucher, passível de tratamento por meio da terapia de reposição enzimática. A forma ativa da GCase recombinante usada na terapia apresenta resíduos terminais de manose expostos no seu perfil de glicosilação. Perfil este que espera-se ser reproduzido por meio da construção de uma linhagem de Pichia pastoris com um padrão de glicosilação humanizado, por meio da deleção de dois genes envolvidos no sistema de glicosilação da levedura: alg3 e och1, responsáveis pela posterior hiper-manosilação característica desse organismo. Assim, a expressão da GCase será usada como modelo no desenvolvimento desta linhagem de Pichia pastoris que permita a expressão de glicoproteínas com um perfil humanizado específico de glicosilação. Além da produção da linhagem mutante pela técnica de CRISPR/Cas9, propomos a construção de duas linhagens controle: uma expressando a proteína GCase para análise do seu padrão selvagem de glicosilação em P. pastoris e outra expressando a proteína Cas9 de Streptoccocus pyogenes (SpCas9). A linhagem P. pastoris/GCase foi construída testando-se duas sequências sinal de secreção diferentes: fosfatase alcalina (PHO1) e albumina humana (Alb). Resultados de western blot mostraram a GCase no lisado celular e baixos níveis de proteína secretada no sobrenadante de cultura, sendo mais expresso na linhagem contendo a sequência PHO1. A linhagem P. pastoris/SpCas9 foi construída e a enzima SpCas9 foi detectada via western blot no lisado celular após indução com metanol. Para a produção da linhagem com padrão de glicosilação humanizado propôs-se a deleção dos genes alg3 e och1 e a inserção, pela via de reparo por recombinação homóloga (HDR), de marcas de resistência aos antibióticos higromicina ou canamicina. Para tal, propusemos a construção de dois vetores finais de expressão do sistema CRISPR/Cas9 em P. pastoris, cada um contendo a enzima SpCas9 e os RNAs guia (gRNAs) para deleção do gene alg3 ou och1, e também a construção de dois fragmentos para HDR contendo o gene de resistência ao antibiótico flanqueado por regiões de 1Kb de homologia com a região de deleção do gene alg3 ou och1. A construção dos vetores e fragmentos para HDR foram inicialmente feitas por meio de técnicas de clonagem clássica. No entanto, apesar de inúmeras tentativas, resultados de PCR e sequenciamento mostraram o insucesso das construções. Partiu-se então para a técnica de Gibson Assembly®, através da qual os dois fragmentos para HDR foram construídos. Porém, os vetores de expressão contendo SpCas9 e os gRNAs ainda apresentam dificuldades na sua construção. Esforços ainda estão sendo feitos para a construção dos vetores e consequente tentativa de estabelecimento das linhagens mutantes. O sucesso no estabelecimento de um sistema de expressão de proteínas heterólogas com este padrão de glicosilação humano específico permitirá a obtenção e possível comercialização da GCase em sua forma terapêutica. Além disso, permitirá possíveis edições genômicas futuras para um padrão de maior complexidade de glicosilação humanizado, criando uma plataforma nacional para produção de outras glicoproteínas terapêuticas de interesse biotecnológico. / The production of therapeutic recombinant protein comprises complex and high valued molecules, including the glucocerebrosidase enzyme (GCase). Its deficiency results in Gaucher Disease, susceptible of treatment by enzymatic replacement therapy. The active form of recombinant GCase employed in therapy presents exposed terminal mannose residues in its glycosylation pattern. We hope to reproduce such pattern by constructing a Pichia pastoris strain with a specific human glycosylation pattern through the deletion of two genes involved in yeast glycosylation system, alg3 and och1, responsible for the final hyper-mannosylation characteristic of this organism. Therefore, the expression of GCase will be a case model for the development of the recombinant Pichia pastoris strain that could allow the expression of glycoproteins with a specific humanized glycosylation profile. Despite the establishment of the mutant strain using the CRISPR/Cas9 technique, we propose the construction of two control strains: one expressing the GCase protein for analysis of its wild type glycosylation pattern and another one expressing the Cas9 protein from Streptoccocus pyogenes (SpCas9). The P. pastoris/GCase strain was constructed testing two different secretion signal sequences: alkaline fosfatase (PHO1) and human albumin (Alb). Western blot results have shown GCase in cell lysate and in low expression levels in culture supernatant, being more expressed in the strain containing the PHO1 signal sequence. P. pastoris/SpCas9 strain was constructed and SpCas9 enzyme was detected via western blot in cell lysate after the induction with methanol. To produce the strain with the humanized glycosylation pattern, the deletion of alg3 and och1 genes was proposed along with the insertion, by homology directed repair pathway (HDR), of hygromycin and kanamycin antibiotics resistance marks. In order to do so, we have proposed the construction of two final expression vectors of the CRISPR/Cas9 system in P. pastoris, each one containing SpCas9 enzyme and the guide RNAs (gRNAs) for deletion of alg3 or och1, and also the construction of two fragments for HDR containing the antibiotics resistance gene flanked by 1Kb regions of homology with the deleted regions of alg3 or och1. Vectors and HDR fragments constructions were initially performed using classic cloning techniques. However, despite numerous tries, PCR and sequencing results have shown the failure of the constructions. Then, we moved on to the Gibson Assembly® technique, through which the two HDR fragments were built. Still, the expression vectors containing SpCas9 and the gRNAs presented difficulties in its assembly. Efforts continue to be made to successfully construct the remaining vectors and to establish the mutant lineage. Success in the establishment of a heterologous protein expression system with specific human glycosylation pattern will allow the obtainment and possible commercialization of the therapeutic form of GCase. Furthermore, it will also allow possible future genomic editing to a high complexity human glycosylation pattern, creating a national platform for the production of other therapeutic glycoproteins of biotechnological interest.