Made available in DSpace on 2015-04-11T14:02:59Z (GMT). No. of bitstreams: 1 Patricia Silva Peres.pdf: 506475 bytes, checksum: 40dfa72e28b5cca338c104148bd4ef06 (MD5) Previous issue date: 2006-02-24 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The simultaneous alignment of many DNA or protein sequences is one of the commonest tasks in computational molecular biology. Multiple alignments are important in many applications, such as, predicting the structure of new sequences, demonstrating the relationship between new sequences and existing families of sequences, inferring the evolutionary history of a family of sequences,finding the characteristic motifs (core blocks) between biological sequences, assembling fragments in DNA sequencing, and many others. Currently, the most popular strategy used for solving the multiple sequence alignment problem is the progressive alignment. Each step of this strategy might generate an error which is expected to be low for closely related sequences but increases as sequences diverge. Therefore, determining the order in which the sequences will be aligned is a key step in the progressive alignment strategy. Traditional approaches take into account, in each iteration of the progressive alignment, only the closest pair or groups of sequences to be aligned. Such strategy minimizes the error introduced in each step, but may not be the best option to minimize the final error. Based on that hypothesis, this work aims the study and the application of a global clustering technique to perform a previous analysis of all sequences in order to separate them into groups according to their similarities. These groups, then, guide the traditional progressive alignment, as an attempt to minimize the overall error introduced by the steps of the progressive alignment and improve the final result. To assess the reliability of this new strategy, three well-known methods were modified for the purpose of introducing the new sequence clustering stage. The accuracy of new versions of the methods was tested using three diferent reference collections. Besides, the modified methods were compared with their original versions. Results of the conducted experiments depict that the new versions of the methods with the global clustering stage really obtained better alignments than their original versions in the three reference collections and achieving improvement over the main methods found in literature, with an increase of only 3% on average in the running time. / O alinhamento simultâneo entre várias seqüências de DNA ou proteína é um dos principais problemas em biologia molecular computacional. Alinhamentos múltiplos são importantes em muitas aplicações, tais como, predição da estrutura de novas seqüências, demonstração do relacionamento entre novas seqüências e famílias de seqüências já existentes, inferência da história evolutiva de uma família de seqüências, descobrimento de padrões que sejam compartilhados entre seqüências, montagem de fragmentos de DNA, entre outras. Atualmente, a estratégia mais popular utilizada na resolução do problema do alinhamento múltiplo é o alinhamento progressivo. Cada etapa desta estratégia pode gerar uma taxa de erro que tenderá a ser baixa no caso de seqüências muito similares entre si, porêm tenderá a ser alta na medida em que as seqüências divergirem. Portanto, a determinação da ordem de alinhamento das seqüências constitui-se em um passo fundamental na estratégia de alinhamento progressivo. Estratégias tradicionais levam em consideração, a cada iteração do alinhamento progressivo, apenas o par ou grupo de seqüências mais próximo a ser alinhado. Tal estratégia minimiza a taxa de erro introduzida em cada etapa, porém pode não ser a melhor forma para minimizar a taxa de erro final. Baseado nesta hipótese, este trabalho tem por objetivo o estudo e aplicação de uma técnica de agrupamento global para executar uma análise prévia de todas as seqüências de forma a separálas em grupos de acordo com suas similaridades. Estes grupos, então, guiarão o alinhamento progressivo tradicional, numa tentativa de minimizar a taxa de erro global introduzida pelas etapas do alinhamento progressivo e melhorar o resultado final. Para avaliar a contabilidade desta nova estratégia, três métodos conhecidos foram modificados com o objetivo de agregar a nova etapa de agrupamento de seqüências. A acurácia das novas versões dos métodos foi testada utilizando três diferentes coleções de referências. Além disso, os métodos modificados foram comparadas com suas respectivas versões originais. Os resultados dos experimentos mostram que as novas versões dos métodos com a etapa de agrupamento global realmente obtiveram alinhamentos melhores do que suas versões originais nas três coleções de referência e alcançando melhorias sobre os principais métodos encontrados na literatura, com um aumento de apenas 3% em média no tempo de execução.

This thesis explores the potential to unify three emerging disciplines: enterprise engineering, enterprise architecture and enterprise ontology. The current fragmentation that exists in literature on enterprise alignment and design constrains the development and growth of the emerging disciplines. Enterprises need to use a multi-disciplinary approach when they continuously align, design and re-design the enterprise. Although enterprises need to be aligned internally (across various enterprise facets), as well as externally (with the environment), most alignment approaches still focus on business-IT alignment, i.e. aligning the business operations with the information and communication technologies and systems of the enterprise. This study focuses on a popular business-IT alignment approach,called the foundation for execution approach, and its associated artefact, called the operating model. The study acknowledges the theoretical contribution of the operating model to establish the required level of business process integration and standardisation at an enterprise in delivering goods and services to customers. Highlighting the practical problems in selecting an operating model for an enterprise, and more specifically the practical problems of identifying process reuse potential at an enterprise, a thesis statement is formulated: The operating model concept, as part of a business-IT alignment approach, can be enhanced with a process reuse identification framework, when a business-IT alignment contextualisation is used. The study is divided into two research questions. The first research question addresses the current fragmentation that exists in the literature, which impairs reuse of the existing business-IT alignment knowledge base. An inductive literature review develops the Business-IT Alignment Model to provide a common contextualisation for current business-IT alignment approaches. The second research question addresses the practical problems of the operating model regarding the identification of process reuse potential at an enterprise. Applying the newly developed Business-IT Alignment Model as a contextualisation instrument, the study demonstrates the use of design research in developing the Process Reuse Identification Framework. The conclusion after the investigation of the two research questions is that the thesis statement was confirmed, i.e. the operating model concept, as part of a business-IT alignment approach, can be enhanced with a process reuse identification framework, when a business-IT contextualisation is used. / Thesis (PhD)--University of Pretoria, 2013. / Industrial and Systems Engineering / Unrestricted

Heparan sulfate Proteoglycans (HSPG) are ubiquitous molecules with indispensable functions in various biological processes. Glypicans are a family of HSPG’s, characterized by a Gpi-anchor which directs them to the cell surface and/or extracellular matrix where they regulate growth factor signaling during development and disease. We report the identification and expression pattern of glypican genes from zebrafish. The zebrafish genome contains 10 glypican homologs, as opposed to six in mammals, which are highly conserved and are phylogenetically related to the mammalian genes. Some of the fish glypicans like Gpc1a, Gpc3, Gpc4, Gpc6a and Gpc6b show conserved synteny with their mammalian cognate genes. Many glypicans are expressed during the gastrulation stage, but their expression becomes more tissue specific and defined during somitogenesis stages, particularly in the developing central nervous system. Existence of multiple glypican orthologs in fish with diverse expression pattern suggests highly specialized and/or redundant function of these genes during embryonic development.

Master‘s thesis is created in a form of a study and deals with the level crossing of the railway line in Chropyně. Thesis solves modification of existing crossover in two variants in the road design cathegory marked as S7,5. This master‘s thesis verify a direction of road by underpass beneath the railway line number 300. Although mainly this study solves the option of overcoming the railway overpass in the displaced position. At the same time it deals with various possibilities of connecting the displaced option to the existing road network.

This thesis presents short DNA alignment tools optimization. These short DNA reads are products of next\nobreakdash-generation sequencing technologies. The results produced by existing align\-ment tools can be influenced by various parameters. For this purpose, an optimization framework to find the optimal values of selected parameters was developed. This framework is based on differencial evolution algorithm and its main goal is to maximize the alignment accuracy. The functionality of the framework was tested on both real and generated data sets of short DNA reads. An accurate alignment is crucial for correct prediction of various genetic characteristics.

The subject of the master´s thesis is designing a bypass of the village Ochoz u Brna. The bypass will by designed in four variations which will be compared to each other by several criterias. Then one variation will be chosen and designed in detail. The goal of the master´s thesis is reduction of the traffic intensity of the current road II/373 in Ochoz u Brna by redirecting transit traffic outside the village. This will lead to an increase of safety in the village.

The recent uprise of end-to-end speech translation models requires a new generation of parallel corpora, composed of a large amount of source language speech utterances aligned with their target language textual translations. We hereby show a pipeline and a set of methods to collect hundreds of hours of English audio-book recordings and align them with their Italian textual translations, using exclusively public domain resources gathered semi-automatically from the web. The pipeline consists in three main areas: text collection, bilingual text alignment, and forced alignment. For the text collection task, we show how to automatically find e-book titles in a target language by using machine translation, web information retrieval, and named entity recognition and translation techniques. For the bilingual text alignment task, we investigated three methods: the Gale–Church algorithm in conjunction with a small-size hand-crafted bilingual dictionary, the Gale–Church algorithm in conjunction with a bigger bilingual dictionary automatically inferred through statistical machine translation, and bilingual text alignment by computing the vector similarity of multilingual embeddings of concatenation of consecutive sentences. Our findings seem to indicate that the consecutive-sentence-embeddings similarity computation approach manages to improve the alignment of difficult sentences by indirectly performing sentence re-segmentation. For the forced alignment task, we give a theoretical overview of the preferred method depending on the properties of the text to be aligned with the audio, suggesting and using a TTS-DTW (text-to-speech and dynamic time warping) based approach in our pipeline. The result of our experiments is a publicly available multi-modal corpus composed of about 130 hours of English speech aligned with its Italian textual translation and split in 60561 triplets of English audio, English transcript, and Italian textual translation. We also post-processed the corpus so as to extract 40-MFCCs features from the audio segments and released them as a data-set.

Dieser Beitrag möchte mit der Weiterentwicklung von Assessment Literacy für zukunftsfähige Lern- und Prüfungsumgebungen an Hochschulen (Advanced Learning and Examination Spaces) einen Beitrag zur Qualitätssicherung von Studium und Lehre leisten. Dazu wird die Entwicklung von Assessment Literacy bei Hochschullehrenden auf zwei Stufen dargelegt: Zunächst werden exemplarische Problemfelder aus verschiedenen Prüfungsformaten beschrieben und Lösungsvorschläge angeboten, um Ansatzpunkte für die Reflexion der eigenen Prüfungspraxis zu liefern (Kap. 2.1). Auf einer zweiten Stufe werden Assessments als Teil von kompetenzorientierten Lern- und Prüfungsumgebungen gesehen. Dazu wird das Konstrukt Kompetenz, dessen Bedeutung im Hochschulkontext sowie das Constructive Alignment als hochschuldidaktisches Planungsmodell für eine kompetenzorientierte Hochschullehre und als Steuerungsinstrument für die Qualitätssicherung von Prüfungen skizziert. Vor diesem Hintergrund werden Ansatzpunkte für das Konzept einer Assessment Literacy in Higher Education abgeleitet, die Funktionsweisen, Rahmenbedingungen und Formate des Prüfens in einen systematischen Zusammenhang bringen sollen (Abb. 1). Diese Wissenssammlung beansprucht nicht dem Leser Unbekanntes zu entdecken. Vielmehr soll Vorhandenes gesammelt, gesichtet, geordnet und bewertet werden und so als Ausgangsbasis für künftige Forschungen im Bereich des Lehrens und Lernens an Hochschulen dienen.

To test nanosize surface patterning for application as implant material, a suitable titanium composition has to be found first. Therefore we investigated the effect of surface chemistry on attachment and differentiation of osteoblast-like cells on pure titanium prepared by pulsed laser deposition (TiPLD) and different Ti alloys (Ti6Al4V, TiNb30 and TiNb13Zr13). Early attachment (30 min) and alkaline phosphatase (ALP) activity (day 5) was found to be fastest and highest, respectively, in cells grown on TiPLD and Ti6Al4V. Osteoblasts seeded on TiPLD produced most osteopontin (day 10), whereas expression of this extracellular matrix protein was an order of magnitude lower on the TiNb30 surface. In contrast, expression of the corresponding receptor, CD44, was not influenced by surface chemistry. Thus, TiPLD was used for further experiments to explore the influence of surface nanostructures on osteoblast adhesion, differentiation and orientation. By laser-induced oxidation, we produced patterns of parallel Ti oxide lines with different widths (0.2–10 μm) and distances (2–20 and 1,000 μm), but a common height of only 12 nm. These structures did not influence ALP activity (days 5–9), but had a positive effect on cell alignment. Two days after plating, the majority of the focal contacts were placed on the oxide lines. The portion of larger focal adhesions bridging two lines was inversely related to the line distance (2–20 μm). In contrast, the portion of aligned cells did not depend on the line distance. On average, 43% of the cells orientated parallel towards the lines, whereas 34% orientated vertically. In the control pattern (1,000 μm line distance), cell distribution was completely at random. Because a significant surplus of the cells preferred a parallel alignment, the nanosize difference in height between Ti surface and oxide lines may be sufficient to orientate the cells by contact guiding. However, gradients in electrostatic potential and surface charge density at the Ti/Ti oxide interface may additionally influence focal contact formation and cell guidance. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

With rising complexity of high performance computing systems and their parallel software, performance analysis and optimization has become essential in the development of efficient applications. The comparison of performance data is a key operation required in performance analysis. An analyst may conduct different types of comparisons in order to understand the performance properties of an application. One use case is comparing performance data from multiple measurements. Typical examples for such comparisons are before/after comparisons when applying optimizations or changing code versions. Besides comparing performance between multiple runs, also comparing performance characteristics across the parallel execution streams of an application is essential to detect performance problems. This is typically useful to detect imbalances, outliers, or changing runtime behavior during the execution of an application. While such comparisons are straightforward for the aggregated data in performance profiles, only limited solutions exist for comparing event traces. Trace-based analysis, i.e., the collection of fine-grained information on individual application events with timestamps and application context, has proven to be a powerful technique. The detailed performance information included in event traces make them very suitable for performance analysis. However, this level of detail also presents a challenge because it implies a large and overwhelming amount of data. Currently, users need to perform manual comparison of event traces, which is extremely challenging and time consuming because of the large volume of detailed data and the need to correctly line up trace events. To fill the gap of missing solutions for automatic comparison of event traces, this work proposes a set of techniques that automatically align traces. The alignment allows their structural comparison and the highlighting of differences between them. A set of novel metrics provide the user with an objective measure of the differences between traces, both in terms of differences in the event stream and timing differences across events. An additional important aspect of trace-based analysis is the visualization of performance data in event timelines. This has proven to be a powerful approach for the detection of various types of performance problems. However, visualization of large numbers of event timelines quickly hits the limits of available display resolution. Likewise, identifying performance problems is challenging in the large amount of visualized performance data. To alleviate these problems this work proposes two new approaches for event timeline visualization. First, novel folding strategies for event timelines facilitate visual scalability and provide powerful overviews of performance data at the same time. Second, this work presents an effective approach that automatically identifies and highlights several types of performance critical sections in an application run. This approach identifies time dominant functions of an application and subsequently uses them to analyze runtime imbalances throughout the application run. Intuitive visualizations present the resulting runtime variations and guide the analyst to performance hot spots. Evaluations with benchmarks and real-world applications assess all introduced techniques. The effectiveness of the comparison approaches is demonstrated by showing automatically detected performance issues and structural differences between different versions of applications and across parallel execution streams. Case studies showcase the capabilities of the event timeline visualization techniques by demonstrating scalable performance data visualizations and detecting performance problems and code inefficiencies in real-world applications.