Modernizing science&engineering software systems

As the demands for modernized legacy systems rise, so does the need for frameworks for information integration and tool interoperability. The Object Management Group (OMG) has adopted the Model Driven Architecture (MDA), which is an evolving conceptual architecture that aligns with this demand. MDA could help solve coupling problems of multidisciplinary character in science and engineering that consist of one or more applications, supported by one or more platforms. The objective of this paper is to describe rigorous techniques to control the evolution from science & engineering software legacy systems to MDA technologies. We propose a rigorous framework to reverse engineering code in the context of MDA. Considering that validation, verification and consistency are crucial activities in the modernization of systems that are critical to safety, security and economic profits, our approach emphasizes the integration of MDA with formal methods

Da tradução automática à tradução manual: estudo contrastivo da tradução automática e manual, através da tradução de dois artigos científicos

Trabalho de Projeto apresentado ao Instituto de Contabilidade e Administração do Porto para a obtenção do grau de Mestre em Tradução e Interpretação Especializadas, sob orientação do Mestre Alberto Couto.Nos dias de hoje a atividade de tradução exige uma pesquisa mais minuciosa por parte do tradutor pois, cada vez mais, é necessário fazer passar a mensagem exata do que se traduz e não apenas uma tradução literal que nem sempre traduz o original. Assim, são exigidas ao tradutor competências muito mais abrangentes, que ultrapassam as competências linguísticas. A par deste tradutor humano encontra-se o tradutor automático e a tradução automática, que nos últimos vinte anos têm vindo a assumir um papel relevante na área da tradução. Deste modo, este projeto pretende descrever a tradução automática para assim possuir bases para poder decidir se este tipo de tradução é credível e fidedigno. O corpus deste trabalho é constituído por dois artigos científicos em francês e pelas suas traduções em português. Estes textos são traduzidos de duas formas, pelo tradutor humano e pelo tradutor automático, utilizando como ferramenta o Google Tradutor. Portanto, após uma análise sintática e morfológica de ambos os textos são salientadas as diferenças, bem como as semelhanças, dos dois modos de tradução e levanta-se a problemática que este ato acarreta, bem como o perfil que um tradutor deve possuir.Nowadays the translation activity requires a more thorough search by the translator because it is increasingly necessary to convey the exact message from the source text and literal translation that does not always reflect the original. Thus, the translator needs to have many skills that go beyond language skills. Alongside this human translator is the automatic translator and machine translation, which, in the last twenty years, has assumed an important role in the translation area. Therefore, this project aims to describe the machine translation in order to have the bases to decide whether this type of translation is credible and trustworthy. The corpus of this work is the translation of two French papers into Portuguese. These texts are translated in two ways, by a human translator and by a machine translator, using the Google translator tool. Therefore, after a syntactic and morphological analysis of both texts, the differences and similarities of the two ways of translation are emphasized, as well as the issues raised by this type of translation, and the profile that a translator should have.De nos jours, l'activité de traduction nécessite d´ une recherche plus approfondie par le traducteur, car, de plus en plus, il est nécessaire de transmettre le message exact, pas seulement une traduction littérale qui ne reflète pas toujours l'original. Ainsi, le traducteur doit avoir des compétences beaucoup plus larges, allant au-delà des compétences linguistiques. A côté de ce traducteur humain on trouve la traduction automatique, qui pendant vingt ans a joué un rôle important dans le domaine de la traduction. Ainsi, ce projet vise à décrire la traduction automatique, pour essayer de juger objectivement si ce type de traduction est crédible et digne de confiance. Le corpus de ce travail est la traduction de deux articles scientifiques de français en portugais. Ces textes sont traduits de deux façons, par le traducteur humain et par le traducteur automatique, en utilisant comme outil le Google traducteur. Toutefois après une analyse de synthèse et morphologique de ces traductions, sont accentués les différences ainsi que les ressemblances des deux méthodes de traduction et on relève la problématique que cet acte apporte, tout comme le profil qu'un traducteur doit avoir

Migrating C/C++ Software to Mobile Platforms in the ADM Context

Software technology is constantly evolving and therefore the development of applications requires adapting software components and applications in order to be aligned to new paradigms such as Pervasive Computing, Cloud Computing and Internet of Things. In particular, many desktop software components need to be migrated to mobile technologies. This migration faces many challenges due to the proliferation of different mobile platforms. Developers usually make applications tailored for each type of device expending time and effort. As a result, new programming languages are emerging to integrate the native behaviors of the different platforms targeted in development projects. In this direction, the Haxe language allows writing mobile applications that target all major mobile platforms. Novel technical frameworks for information integration and tool interoperability such as Architecture-Driven Modernization (ADM) proposed by the Object Management Group (OMG) can help to manage a huge diversity of mobile technologies. The Architecture-Driven Modernization Task Force (ADMTF) was formed to create specifications and promote industry consensus on the modernization of existing applications. In this work, we propose a migration process from C/C++ software to different mobile platforms that integrates ADM standards with Haxe. We exemplify the different steps of the process with a simple case study, the migration of “the Set of Mandelbrot” C++ application. The proposal was validated in Eclipse Modeling Framework considering that some of its tools and run-time environments are aligned with ADM standards

Recovering Sequence Diagrams from Object-oriented Code

Software modernization is a current research area in the software industry intended to transform an existing software system to a new one satisfying new demands. The initiative Architecture-Driven Modernization (ADM) helps software developers in tackling reverse engineering, software evolution and, software modernization in general. To support modernization problems, the ADM Task Force has defined a set of metamodels such as KDM (Knowledge Discovery Metamodel), being the Eclipse-MDT MoDisco project the official support for software modernization. We propose the application of ADM principles to provide relevant model-based views on legacy systems. We describe a framework to reverse engineering models from object-oriented code. In this context, we show how to recover UML sequence diagrams from Java code. We validate our approach by using ADM standards and MoDisco platform. Our research can be considered a contribution to the MoDisco community; MoDisco does not support reverse engineering of sequence diagrams and, on the other hand, the MoDisco KDM Discover was used and enriched to obtain the required information for recovering interaction diagrams

Focusing on metabolomic dysregulation and modulation of retinal metabolism to develop novel therapeutic strategies for diabetic retinopathy

Tese de doutoramento, Medicina (Oftalmologia), Universidade de Lisboa, Faculdade de Medicina, 2015Diabetic retinopathy (DR) is a neurovascular complication of diabetes mellitus and a leading cause of blindness in adults below the age of 65, in industrialized nations. Currently there are 126.6 million people with DR worldwide (34.6% of the total diabetic population) and it is estimated that this number will increase to 191.0 million by 2030. Generally, DR is divided into two stages: non-proliferative diabetic retinopathy (NPDR), an earlier phase characterized by appearance of microaneurysms, dot and blot hemorrhages, capillary occlusions and nerve fiber layer infarcts and; and proliferative diabetic retinopathy (PDR), the late-stage disease, which is diagnosed when pathological neovascular changes are identified on the retinal surface and/or vitreous. Diabetic macular edema (DME) can develop at any stage and reflects a pathological increase in retinal vascular permeability. Despite its high prevalence, current availability of preventive and therapeutic strategies is far from ideal. In fact, there are no reliable biomarkers to predict risk of developing DR and no effective, targeted and early-acting therapies to sustainably and safely prevent disease progression into its vision threatening stages: PDR and DME. The two main therapeutic options currently available for DR are laser photocoagulation and intravitreal injections of anti-vascular endothelial growth factor (VEGF) agents; these constitute “non-selective” and destructive (especially for laser therapy) approaches that are not only unable to effectively and sustainably arrest retinal disease progression in every case, but can also potentially induce a myriad of undesired off-target effects at the retinal level and even systemically, in the case of VEGF antagonists. Moreover, they act late in the disease course. The lack of reliable rodent models - there is no diabetic mouse model that spontaneously recapitulates the late stages of DR - has greatly hindered research progress and development of novel and effective drugs for PDR, further contributing to the present therapeutic scenario. In this dissertation I will introduce and present my experimental work in the context of the following concepts, which can potentially lead to development of targeted, earlier acting, less destructive and more effective future therapies for DR: (1) DR has long been regarded as a vascular disease and present-day DR management guidelines are still based on this assumption. However, a growing body of evidence shows that retinal neuronal function becomes impaired before vascular changes can be detected; these findings along with those showing that adequate retinal functioning depends on stable intercellular interactions within neurovascular units, suggest that disrupting retinal neurovascular crosstalk may play a critical role in promoting disease development and progression. (2) Metabolomic studies have been surprisingly neglected in the investigation of DR’s pathophysiology, and this is clearly reflected by the fact that the metabolome of human DR remains unknown. Furthermore, the neuroretina is one of the most metabolically demanding tissues in the body per unit weight, and diabetes is triggered by a metabolic defect that profoundly impairs cellular energy production. These features constitute a potentially disastrous combination in regard to retinal functioning and suggest that studying retinal energy metabolism in DR is critical. (3) Metabolic cycles of photoreceptors, interneurons and glial cells are still under debate and, even though it is known that intercellular communications within the neurovascular unit (NVU) are mediated by metabolites whose production becomes dysregulated under pathological conditions, the precise mechanisms underlying retinal neurovascular coupling are not fully identified. Gaining further insight into these interactions is pivotal because retinal NVUs are responsible for regulating blood flow for functionally dynamic retinal neuronal networks and, thus, for their proper functioning. Besides the points stated above, additional clinical clues were considered to guide the research plan presented in this dissertation. One the strongest came from a subset of long-term diabetic patients who appear to be protected from developing late-stage DR, by an unknown mechanism. Studying these patients provides an excellent opportunity to identify protective factors and to further understand the mechanisms involved in progression of DR. In order to better understand how metabolic dysregulation impacts development of DR, how neurovascular interactions become compromised in the diabetic retina, and to develop strategies to potentially restore homeostasis within the NVU, we decided to use metabolomic analyses. A highly sensitive metabolomics mass-spectrometry based approach was used in ocular and serum samples to identify the most prominent metabolic perturbations, to acquire a global overview of the metabolomic landscape in late-stage DR and to identify potentially protective circulating factors. At the ocular level, late-stage diabetic retinopathy was associated with severe dysregulation in amino acid levels; this was especially prominent in those generated during arginine metabolism, suggesting a preferential activity in the arginase pathway over the alternative Nitric Oxide Synthase (NOS) pathway; Studies in the Oxygen-Induced-Retinopathy (OIR) mouse, a non-diabetic model that develops features of ischemic retinopathy, revealed a very similar metabolic landscape and, in vivo global isotope analysis confirmed the presence of asymmetrical arginine metabolism by showing: (1) over-activity in the arginase pathway leading to enhanced proline production; and (2) reduced activity in the alternative NOS pathway, with potentially reduced NO production. Even though NO’s role in DR and other retinopathies is not clearly understood, NO is known to be an important modulator of cellular interactions within the NVU and its lower availability in specific locations and/or time-points in pathological conditions may significantly contribute to the disruption of retinal neurovascular crosstalk. The work presented in this dissertation has also described novel functions for interneurons (amacrine and horizontal cells) and photoreceptors within the NVU, by showing that these cells play an active role in regulating their primary vasculature and thus, their blood supply. Furthermore, it has also shown that dysfunction of retinal neurons in this capacity can directly alter their own blood supply, therefore providing additional clues for disrupted retinal neurovascular crosstalk. Metabolomic analyses comparing serum samples from diabetic patients with or without PDR (long-term diabetic patients “protected” from late-stage DR versus those who were non-protected) revealed that “protected” patients had higher circulating levels of a purine metabolite, inosine. To assess its therapeutic potential in conditions of retinal ischemia, inosine was delivered to the eye of the OIR mouse where it enhanced effective revascularization of ischemic retinal areas, thus significantly reducing pathological neovascularization. These effects were associated with a favorable modulation of the local pro-inflammatory response that could result from an improved overall retinal metabolic status. These beneficial effects on retinal metabolism induced by inosine injections were observed as: (1) a reduction in basal mitochondrial respiration in vaso-obliterated areas (i.e., ischemic areas), which can potentially increase retinal neuronal tolerance to hypoxia by reducing the metabolic mismatch created by scarce metabolic supply and high neuronal demand; and (2) a reduction in proline production, suggesting antagonism of the arginase pathway (which is hyperactive in oxygen-induced-retinopathy and potentially in human PDR). In summary, the work presented in this dissertation employed a metabolomic-focused approach with a strong focus on neurovascular crosstalk to answer two intriguing questions regarding DR: (1) What is the characteristic ocular metabolic landscape of severe DR? (2) Is the “protection” against severe DR (observed in some long-term diabetic patients) associated with differences in circulating metabolic factors? The answers to these questions, presented below, could serve as the basis of future targeted, more effective and earlier acting therapeutics that would revolutionize DR patient management. Identification of the most prominently affected metabolic pathways in eyes with severe DR has identified specific pathways of amino acid metabolism as potential targets for development of new drugs for DR. We have also identified a circulating protective factor, inosine, in “protected” patients and further investigated its ability to (1) prevent development of retinal ischemia and pathological neovascularization; (2) adjust retinal metabolism to the limited energy supplies in ischemic areas; and (3) counteract development of prominent metabolic dysregulation by potentially inhibiting the pathology-promoting arginase pathway. We believe that inosine can potentially become an effective, early-acting therapeutic agent to prevent progression of DR. In addition, these metabolites could potentially be used as reliable biomarkers for monitoring response to therapy and for predicting risk of developing or progressing DR. Finally, the work presented in this dissertation supports the concept that early intervention for treating DR will restore balance and stabilize cellular interactions within the NVU, thereby reversing the chronic stressors (e.g., extreme conditions of metabolic insufficiency in retinal ischemic areas) that ultimately drive development and progression of retinal pathology.Fundação para a Ciência e a Tecnologia (FCT

Wavelet-Based Cancer Drug Recommender System

A natureza molecular do cancro serve de base para estudos sistemáticos de genomas cancerígenos, fornecendo valiosos insights e permitindo o desenvolvimento de tratamentos clínicos. Acima de tudo, estes estudos estão a impulsionar o uso clínico de informação genómica na escolha de tratamentos, de outro modo não expectáveis, em pacientes com diversos tipos de cancro, possibilitando a medicina de precisão. Com isso em mente, neste projeto combinamos técnicas de processamento de imagem, para aprimoramento de dados, e sistemas de recomendação para propor um ranking personalizado de drogas anticancerígenas. O sistema é implementado em Python e testado usando uma base de dados que contém registos de sensibilidade a drogas, com mais de 310.000 IC50 que, por sua vez, descrevem a resposta de mais de 300 drogas anticancerígenas em 987 linhas celulares cancerígenas. Após várias tarefas de pré-processamento, são realizadas duas experiências. A primeira experiência usa as imagens originais de microarrays de DNA e a segunda usa as mesmas imagens, mas submetidas a uma transformada wavelet. As experiências confirmam que as imagens de microarrays de DNA submetidas a transformadas wavelet melhoram o desempenho do sistema de recomendação, otimizando a pesquisa de linhas celulares cancerígenas com perfil semelhante ao da nova linha celular. Além disso, concluímos que as imagens de microarrays de DNA com transformadas de wavelet apropriadas, não apenas fornecem informações mais ricas para a pesquisa de utilizadores similares, mas também comprimem essas imagens com eficiência, otimizando os recursos computacionais. Tanto quanto é do nosso conhecimento, este projeto é inovador no que diz respeito ao uso de imagens de microarrays de DNA submetidas a transformadas wavelet, para perfilar linhas celulares num sistema de recomendação personalizado de drogas anticancerígenas

Refactoring de diagramas de clases UML

Se denomina refactoring al proceso de reestructurar software orientado a objetos aplicando una secuencia de transformaciones que preservan la funcionalidad del mismo a fin de mejorar alguna métrica. Es una actividad esencial para controlar la evolución del software facilitando futuras adaptaciones y extensiones. Cobró importancia en procesos de desarrollo como XP (eXtreme Programming) que requiere de la reestructuración de modelos y código existentes a partir de pasos pequeños y sistemáticos (Beck, 2000). También es fundamental en el contexto de técnicas de ingeniería reversa de sistemas legacy. Algunas herramientas CASE UML proveen facilidades, si bien limitadas, para el refactoring sobre código, es decir ligado a la sintaxis de un lenguaje de programación en particular. Actualmente OMG (Object Management Group) promueve desarrollos de software basados en UML (OMG, 2004) a partir de una arquitectura Model Driven (MDA, 2004). MDA define un framework para modelar que separa la especificación de la funcionalidad del sistema de su implementación sobre una plataforma en una tecnología específica. La idea clave es la automatización de transformaciones de modelo-a-modelo. En este contexto se vuelven esenciales las técnicas de refactoring para mejorar los modelos de los distintos niveles de abstracción de un diseño. En esta investigación se propone el refactoring de diagramas de clases UML enriquecidos con expresiones OCL (Warmer y Kepple, 2003) a partir de un sistema transformacional basado en reglas y estrategias. El objetivo de este sistema transformacional es proveer asistencia para los refactorings de modelo-a-modelo mediante la aplicación de reglas de transformación que preservan la funcionalidad del modelo original. Las transiciones entre versiones se realizan de acuerdo a reglas precisas basadas en la redistribución de clases, atributos, operaciones y asociaciones del diagrama. Durante el proceso de transformación, se necesitan estrategias para guiar la aplicación de las reglas de transformación que permiten construir un nuevo diagrama UML. Se describen en la sección 2 los trabajos relacionados. La sección 3 presenta el sistema de transformación y un conjunto de reglas y estrategias para reestructurar clases y asociaciones. Finalmente la sección 4 concluye y discute futuros trabajos

Approximation of degenerate partial differential equations arising in finance

Doutoramento em Matemática Aplicada à Economia e GestãoEsta dissertação estuda a discretização de equações diferenciais parciais degeneradas com aplicações às Finanças. Em particular, o problema de Cauchy para uma equação diferencial parcial linear de segunda ordem é discretizado nas variáveis espaciais para os casos de coeficientes limitados e ilimitados. A semi-discretização é considerada para a versão multidimensional da EDP e também para o caso particular de uma dimensão espacial. A aproximação à solução da EDP é obtida com recurso a métodos básicos de diferenças finitas em versões discretas de espaços de Sobolev e de Sobolev ponderados. São deduzidos resultados de existência e unicidade para a solução generalizada do problema semi-discretizado. Finalmente, é dada uma estimativa para a taxa de convergência da solução do problema semi-discretizado para a solução do problema exacto correspondente. São obtidos resultados mais fortes para o caso especial de uma dimensão no espaço.This thesis focuses on the discretization of degenerate partial differential equa- tions arising in Finance. In particular, the Cauchy problem for a second order linear parabolic PDE is discretized in the spatial variables for both the bounded and unbounded coefficient cases. The semi-discretization is considered for the general multi-dimensional version of the PDE and also for the particular one-dimensional case. The approximation to the PDE problem solution is obtained by using basic finite difference methods in discrete Sobolev and weighted Sobolev spaces. Existence and uniqueness results for the generalized solution to the semi- discretized problem are deduced. Finally, we give an estimate for the rate of convergence of the solution of the semi-discretized problem to the solution of corresponding the exact problem. Stronger results are deduced for the special case of one dimension on space.info:eu-repo/semantics/publishedVersio

Obesidade Infantil: Estudo em Crianças num ATL

A obesidade infantil apresenta uma tendência crescente, devido essencialmente aos maus hábitos alimentares e ao sedentarismo. Por isso, é cada vez mais relevante determinar as causas e consequências deste fenómeno. Procede-se ao enquadramento, em termos teóricos, do conceito de obesidade infantil e da sua relação com os fatores de risco/proteção, como os hábitos alimentares, a atividade física e o sedentarismo, procurando fazer a ligação entre o que se passa em casa e na escola. Define-se brevemente o enquadramento metodológico, a partir da caracterização da população em estudo – crianças que frequentam Atividade de Ocupação de Tempo Livre (ATL) –, com idades entre os 6 e os 10 anos, até à definição de objetivos e hipóteses a analisar, bem como o instrumento de recolha de informação apropriado para atingir esses objectivos. A análise dos dados recolhidos permite estudar a relação entre os hábitos alimentares, a atividade física e o sedentarismo com a obesidade infantil observada na amostra, verificando-se que as crianças com obesidade almoçam mais na escola e menos em casa, vão mais a locais com fast-food, comem menos vegetais e menos vezes sopa, mas também consomem menos doces; não há uma relação entre os hábitos de atividade física e a obesidade, e, quanto à relação entre as atividades sedentárias e a obesidade, observa-se o contrário do esperado, sendo a prática das atividades sedentárias inferior para as crianças que apresentam níveis de obesidade

Motivation, interaction and perceived learning: assessing the impact of an urban game with 7th grade geography students

The increasing development of mobile technology devices is revolutionizing education. In this context emerge the mobile location-based games. This research was carried out in an effort to understand the importance of mobile location-based games in informal learning and involved the design of an urban game - “MobiGeo”. MobiGeo was implemented for an outdoor pedagogical activity and enrolled a group of 173 seventh grade geography students. In order to collect data, a questionnaire was developed and validated measuring three dimensions related to educational games: motivation, interaction and perceived learning. Results show that this urban game was an adequate activity to use in informal learning environments because it engaged students in gaming with high degrees of motivation and interaction. In fact, while solving the tasks proposed by MobiGeo, students´ developed their perceptions of learning, consolidating and acquiring new knowledge about the European Union.CIEC – Research Centre on Child Studies, IE, UMinho (FCT R&D unit 317), PortugalNational Funds through the FCT (Foundation for Science and Technology) and co-financed by European Regional Development Funds (FEDER) through the Competitiveness and Internationalization Operational Program (POCI) through CIEC (Research Centre on Child Studies, of the University of Minho) with the reference POCI-01-0145-FEDER-00756