O presente trabalho possui como objetivo o estudo das propriedades dos filmes finos amorfos para aplicações em dispositivos fotônicos. Foram produzidos, por meio da técnica sputtering, filmes finos de telureto BWT, a partir de alvos cerâmicos com composição em peso de 54,6 TeO2 - 22,6 WO3 - 22,8 Bi2O3. A escolha dos vidros BWT se deve às qualidades elétricas e ópticas dos teluretos. Filmes com nanopartículas de ouro foram produzidos e a nucleação das nanopartículas se deu por tratamento térmico. Os filmes produzidos foram caracterizados pelas técnicas de elipsometria, perfilometria, espectrometria de fluorescência de raios-X por energia dispersiva, difração de raios-X, transmissão, absorção e microscopia eletrônica de transmissão e de varredura. Como etapa, final foram produzidos guias de onda do tipo rib por meio de procedimentos de corrosão e litografia, a fim de que fossem testados guiamentos de luz em 632,8 nm e em 1050 nm. Foram usados diferentes fluxos de SF6 para corrosão dos filmes, resultando em guias de diferentes valores de h_core. Os guias com h_core de 63 e 82 nm apresentaram perda de no máximo 3,5 dB/cm para guiamento em 632,8 e 1050 nm em guias com larguras que variaram de 6 a 10 m. As simulações realizadas mostraram guiamento multímodo para todos os casos. O material BWT é, portanto, promissor para aplicações em dispositivos fotônicos. / The objective of this present work is study the properties of amorphous thin films for applications in photonic devices. Thin films of tellurite BWT were produced by sputtering technique using targets whose compositions in weight are 54.6 TeO2 - 22.6 WO3 - 22.8 Bi2O3. BWT was chosen due to the electrical and optical properties of tellurite. Films with gold nanoparticles were produced and the nucleation of the nanoparticles was obtained by heat treatment. Films were characterized by the techniques of elipsometry, perfilometry, energy dispersive X-ray spectroscopy, X-ray diffraction, absorption, transmission, scanning electronic and transmission electronic microscopies. The final step was production of BWT rib waveguides using lithography and reactive-ion etching in order to test light guiding at 632.8 nm and 1050 nm. BWT rib waveguides were produced, using different flux of SF6 for the etching, resulting in waveguides with different values of h_core. Waveguides with 63 and 82 nm of h_core presented maximum loss of 3,5 dB/cm at 632.8 nm and 1050 nm wavelengths in guides with widths ranging from 6 to 10 m. All simulations showed multimode guiding. The BWT material is a potential candidate for applications in photonic devices.

O presente trabalho possui como objetivo o estudo das propriedades dos filmes finos amorfos para aplicações em dispositivos fotônicos. Foram produzidos, por meio da técnica sputtering, filmes finos de telureto BWT, a partir de alvos cerâmicos com composição em peso de 54,6 TeO2 - 22,6 WO3 - 22,8 Bi2O3. A escolha dos vidros BWT se deve às qualidades elétricas e ópticas dos teluretos. Filmes com nanopartículas de ouro foram produzidos e a nucleação das nanopartículas se deu por tratamento térmico. Os filmes produzidos foram caracterizados pelas técnicas de elipsometria, perfilometria, espectrometria de fluorescência de raios-X por energia dispersiva, difração de raios-X, transmissão, absorção e microscopia eletrônica de transmissão e de varredura. Como etapa, final foram produzidos guias de onda do tipo rib por meio de procedimentos de corrosão e litografia, a fim de que fossem testados guiamentos de luz em 632,8 nm e em 1050 nm. Foram usados diferentes fluxos de SF6 para corrosão dos filmes, resultando em guias de diferentes valores de h_core. Os guias com h_core de 63 e 82 nm apresentaram perda de no máximo 3,5 dB/cm para guiamento em 632,8 e 1050 nm em guias com larguras que variaram de 6 a 10 m. As simulações realizadas mostraram guiamento multímodo para todos os casos. O material BWT é, portanto, promissor para aplicações em dispositivos fotônicos. / The objective of this present work is study the properties of amorphous thin films for applications in photonic devices. Thin films of tellurite BWT were produced by sputtering technique using targets whose compositions in weight are 54.6 TeO2 - 22.6 WO3 - 22.8 Bi2O3. BWT was chosen due to the electrical and optical properties of tellurite. Films with gold nanoparticles were produced and the nucleation of the nanoparticles was obtained by heat treatment. Films were characterized by the techniques of elipsometry, perfilometry, energy dispersive X-ray spectroscopy, X-ray diffraction, absorption, transmission, scanning electronic and transmission electronic microscopies. The final step was production of BWT rib waveguides using lithography and reactive-ion etching in order to test light guiding at 632.8 nm and 1050 nm. BWT rib waveguides were produced, using different flux of SF6 for the etching, resulting in waveguides with different values of h_core. Waveguides with 63 and 82 nm of h_core presented maximum loss of 3,5 dB/cm at 632.8 nm and 1050 nm wavelengths in guides with widths ranging from 6 to 10 m. All simulations showed multimode guiding. The BWT material is a potential candidate for applications in photonic devices.

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The Devils Lake defection of 2005 demands a re-evaluation of the venerable Boundary Waters Treaty (BWT) between Canada and the United States. Why was the long-successful water agreement unable to solve this relatively minor dispute? More importantly, given irregularities between theoretical assertions and institutional history, what theory of international relations best explains a cooperative agreement that spans a near-century? Due to the complexities of shared river systems, any theory that seeks to explain international cooperation must adequately encompass three separate sources of state motivation. First, it must explain the technical, basin-position-driven realities that affect state attitudes towards negotiations. Second, it must explain the longer-term strategic factors that can inspire states to accept immediate losses for subsequent gains. Finally, it must acknowledge domestic sources of influence and understand how these forces constrain the state vis-à-vis others. This paper argues that liberalism, as defined by Andrew Moravcsik, is the best theoretical candidate. This is proven by comparing interpretations of the BWT history through realist, neoliberal, constructivist, and liberal lenses. After identifying and examining each theory's strengths and weaknesses, liberalism emerges as the most holistic view and should be favoured as a primary explanatory theory. Liberalism's theoretical underpinnings – interest group politics – best handles the technical, strategic, and domestic influences that affect Canada-US water relations. Whether examining what prompted efforts to initiate a water-sharing agreement, explaining the agreement's final structure, determining the impetus for continued cooperation, or identifying the incentives to finally break from treaty obligations, liberalism provides the most satisfying solutions. Though derived from the Canada-US border relationship, liberalism's superiority is not limited to the North American watershed. Because the factors examined are common to all shared international river systems and the paper's results are scalable, this suggests that liberalism will continue to be the appropriate primary IR theory to employ when examining state decision-making regarding water-sharing agreements.

The Devils Lake defection of 2005 demands a re-evaluation of the venerable Boundary Waters Treaty (BWT) between Canada and the United States. Why was the long-successful water agreement unable to solve this relatively minor dispute? More importantly, given irregularities between theoretical assertions and institutional history, what theory of international relations best explains a cooperative agreement that spans a near-century? Due to the complexities of shared river systems, any theory that seeks to explain international cooperation must adequately encompass three separate sources of state motivation. First, it must explain the technical, basin-position-driven realities that affect state attitudes towards negotiations. Second, it must explain the longer-term strategic factors that can inspire states to accept immediate losses for subsequent gains. Finally, it must acknowledge domestic sources of influence and understand how these forces constrain the state vis-à-vis others. This paper argues that liberalism, as defined by Andrew Moravcsik, is the best theoretical candidate. This is proven by comparing interpretations of the BWT history through realist, neoliberal, constructivist, and liberal lenses. After identifying and examining each theory's strengths and weaknesses, liberalism emerges as the most holistic view and should be favoured as a primary explanatory theory. Liberalism's theoretical underpinnings – interest group politics – best handles the technical, strategic, and domestic influences that affect Canada-US water relations. Whether examining what prompted efforts to initiate a water-sharing agreement, explaining the agreement's final structure, determining the impetus for continued cooperation, or identifying the incentives to finally break from treaty obligations, liberalism provides the most satisfying solutions. Though derived from the Canada-US border relationship, liberalism's superiority is not limited to the North American watershed. Because the factors examined are common to all shared international river systems and the paper's results are scalable, this suggests that liberalism will continue to be the appropriate primary IR theory to employ when examining state decision-making regarding water-sharing agreements.

Common image compression standards are usually based on frequency transform such as Discrete Cosine Transform or Wavelets. We present a different approach for loss-less image compression, it is based on combinatorial transform. The main transform is Burrows Wheeler Transform (BWT) which tends to reorder symbols according to their following context. It becomes a promising compression approach based on contextmodelling. BWT was initially applied for text compression software such as BZIP2 ; nevertheless it has been recently applied to the image compression field. Compression scheme based on Burrows Wheeler Transform is usually lossless ; therefore we imple-ment this algorithm in medical imaging in order to reconstruct every bit. Many vari-ants of the three stages which form the original BWT-based compression scheme can be found in the literature. We propose an analysis of the more recent methods and the impact of their association. Then, we present several compression schemes based on this transform which significantly improve the current standards such as JPEG2000and JPEG-LS. In the final part, we present some open problems which are also further research directions

The Devils Lake defection of 2005 demands a re-evaluation of the venerable Boundary Waters Treaty (BWT) between Canada and the United States. Why was the long-successful water agreement unable to solve this relatively minor dispute? More importantly, given irregularities between theoretical assertions and institutional history, what theory of international relations best explains a cooperative agreement that spans a near-century? Due to the complexities of shared river systems, any theory that seeks to explain international cooperation must adequately encompass three separate sources of state motivation. First, it must explain the technical, basin-position-driven realities that affect state attitudes towards negotiations. Second, it must explain the longer-term strategic factors that can inspire states to accept immediate losses for subsequent gains. Finally, it must acknowledge domestic sources of influence and understand how these forces constrain the state vis-à-vis others. This paper argues that liberalism, as defined by Andrew Moravcsik, is the best theoretical candidate. This is proven by comparing interpretations of the BWT history through realist, neoliberal, constructivist, and liberal lenses. After identifying and examining each theory's strengths and weaknesses, liberalism emerges as the most holistic view and should be favoured as a primary explanatory theory. Liberalism's theoretical underpinnings – interest group politics – best handles the technical, strategic, and domestic influences that affect Canada-US water relations. Whether examining what prompted efforts to initiate a water-sharing agreement, explaining the agreement's final structure, determining the impetus for continued cooperation, or identifying the incentives to finally break from treaty obligations, liberalism provides the most satisfying solutions. Though derived from the Canada-US border relationship, liberalism's superiority is not limited to the North American watershed. Because the factors examined are common to all shared international river systems and the paper's results are scalable, this suggests that liberalism will continue to be the appropriate primary IR theory to employ when examining state decision-making regarding water-sharing agreements. / Arts, Faculty of / Political Science, Department of / Graduate

La bioinformática es la aplicación de las ciencias computacionales a la gestión y análisis de datos biológicos. A partir de 2005, con la aparición de los secuenciadores de ADN de nueva generación surge lo que se conoce como Next Generation Sequencing o NGS. Un único experimento biológico puesto en marcha en una máquina de secuenciación NGS puede producir fácilmente cientos de gigabytes o incluso terabytes de datos. Dependiendo de la técnica elegida este proceso puede realizarse en unas pocas horas o días. La disponibilidad de recursos locales asequibles, tales como los procesadores multinúcleo o las nuevas tarjetas gráfi cas preparadas para el cálculo de propósito general GPGPU (General Purpose Graphic Processing Unit ), constituye una gran oportunidad para hacer frente a estos problemas. En la actualidad, un tema abordado con frecuencia es el alineamiento de secuencias de ADN. En bioinformática, el alineamiento permite comparar dos o más secuencias de ADN, ARN, o estructuras primarias proteicas, resaltando sus zonas de similitud. Dichas similitudes podrían indicar relaciones funcionales o evolutivas entre los genes o proteínas consultados. Además, la existencia de similitudes entre las secuencias de un individuo paciente y de otro individuo con una enfermedad genética detectada podría utilizarse de manera efectiva en el campo de la medicina diagnóstica. El problema en torno al que gira el desarrollo de la tesis doctoral consiste en la localización de fragmentos de secuencia cortos dentro del ADN. Esto se conoce bajo el sobrenombre de mapeo de secuencia o sequence mapping. Dicho mapeo debe permitir errores, pudiendo mapear secuencias incluso existiendo variabilidad genética o errores de lectura en el mapeo. Existen diversas técnicas para abordar el mapeo, pero desde la aparición de la NGS destaca la búsqueda por pre jos indexados y agrupados mediante la transformada de Burrows-Wheeler [28] (o BWT en lo sucesivo). Dicha transformada se empleó originalmente en técnicas de compresión de datos, como es el caso del algoritmo bzip2. Su utilización como herramienta para la indización y búsqueda posterior de información es más reciente [22]. La ventaja es que su complejidad computacional depende únicamente de la longitud de la secuencia a mapear. Por otra parte, una gran cantidad de técnicas de alineamiento se basan en algoritmos de programación dinámica, ya sea Smith-Watterman o modelos ocultos de Markov. Estos proporcionan mayor sensibilidad, permitiendo mayor cantidad de errores, pero su coste computacional es mayor y depende del tamaño de la secuencia multiplicado por el de la cadena de referencia. Muchas herramientas combinan una primera fase de búsqueda con la BWT de regiones candidatas al alineamiento y una segunda fase de alineamiento local en la que se mapean cadenas con Smith-Watterman o HMM. Cuando estamos mapeando permitiendo pocos errores, una segunda fase con un algoritmo de programación dinámica resulta demasiado costosa, por lo que una búsqueda inexacta basada en BWT puede resultar más e ficiente. La principal motivación de la tesis doctoral es la implementación de un algoritmo de búsqueda inexacta basado únicamente en la BWT, adaptándolo a las arquitecturas paralelas modernas, tanto en CPU como en GPGPU. El algoritmo constituirá un método nuevo de rami cación y poda adaptado a la información genómica. Durante el periodo de estancia se estudiarán los Modelos ocultos de Markov y se realizará una implementación sobre modelos de computación funcional GTA (Aggregate o Test o Generate), así como la paralelización en memoria compartida y distribuida de dicha plataforma de programación funcional. / Salavert Torres, J. (2014). Inexact Mapping of Short Biological Sequences in High Performance Computational Environments [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/43721

Les méthodes classiques de compression d’image sont communément basées sur des transformées fréquentielles telles que la transformée en Cosinus Discret (DCT) ou encore la transformée discrète en ondelettes. Nous présentons dans ce document une méthode originale basée sur une transformée combinatoire celle de Burrows-Wheeler(BWT). Cette transformée est à la base d’un réagencement des données du fichier servant d’entrée au codeur à proprement parler. Ainsi après utilisation de cette méthode sur l’image originale, les probabilités pour que des caractères identiques initialement éloignés les uns des autres se retrouvent côte à côte sont alors augmentées. Cette technique est utilisée pour la compression de texte, comme le format BZIP2 qui est actuellement l’un des formats offrant un des meilleurs taux de compression. La chaîne originale de compression basée sur la transformée de Burrows-Wheeler est composée de 3 étapes. La première étape est la transformée de Burrows-Wheeler elle même qui réorganise les données de façon à regrouper certains échantillons de valeurs identiques. Burrows et Wheeler conseillent d’utiliser un codage Move-To-Front (MTF) qui va maximiser le nombre de caractères identiques et donc permettre un codage entropique (EC) (principalement Huffman ou un codeur arithmétique). Ces deux codages représentent les deux dernières étapes de la chaîne de compression. Nous avons étudié l’état de l’art et fait des études empiriques de chaînes de compression basées sur la transformée BWT pour la compression d’images sans perte. Les données empiriques et les analyses approfondies se rapportant aux plusieurs variantes de MTF et EC. En plus, contrairement à son utilisation pour la compression de texte,et en raison de la nature 2D de l’image, la lecture des données apparaît importante. Ainsi un prétraitement est utilisé lors de la lecture des données et améliore le taux de compression. Nous avons comparé nos résultats avec les méthodes de compression standards et en particulier JPEG 2000 et JPEG-LS. En moyenne le taux de com-pression obtenu avec la méthode proposée est supérieur à celui obtenu avec la norme JPEG 2000 ou JPEG-LS / Common image compression standards are usually based on frequency transform such as Discrete Cosine Transform or Wavelets. We present a different approach for loss-less image compression, it is based on combinatorial transform. The main transform is Burrows Wheeler Transform (BWT) which tends to reorder symbols according to their following context. It becomes a promising compression approach based on contextmodelling. BWT was initially applied for text compression software such as BZIP2 ; nevertheless it has been recently applied to the image compression field. Compression scheme based on Burrows Wheeler Transform is usually lossless ; therefore we imple-ment this algorithm in medical imaging in order to reconstruct every bit. Many vari-ants of the three stages which form the original BWT-based compression scheme can be found in the literature. We propose an analysis of the more recent methods and the impact of their association. Then, we present several compression schemes based on this transform which significantly improve the current standards such as JPEG2000and JPEG-LS. In the final part, we present some open problems which are also further research directions

This thesis deals with Burrows-Wheeler transform (BWT) and possibilities of acceleration of this transform on graphics processing unit (GPU). Methods of compression based on BWT are introduced, as well as software libraries CUDA and OpenCL for writing programs for GPU. Parallel variants of BWT are implemented, as well as following steps necessary for compression, using CUDA library. Amount of compression of used approaches are tested and parallel versions are compared to their sequential counterparts.