A conspiracy theory for clefts : the syntax and interpretation of cleft constructions

O objetivo final deste estudo é contribuir para a discussão sobre qual a medida em que conceitos semânticos e discursivos estão sintaticamente codificados. Mais especificamente, investiga-se se existe alguma correlação consistente entre alguns aspetos interpretativos e sintáticos de quatro construções clivadas do Português Europeu, e como se deve dar conta teoricamente destas potenciais correlações. As clivadas consideradas são as clivadas canónicas, as pseudoclivadas, as clivadas de é que e as clivadas de SER. Sintaticamente podemos distinguir dois tipos: clivadas bioracionais (canónicas e pseudoclivadas) e clivadas mono-oracionais (clivadas de é que e de SER). Todas as estruturas têm um constituinte clivado focalizado que pode constituir tanto um foco informacional como um foco contrastivo, e uma oração clivada que introduz uma pressuposição existencial. Adicionalmente, o constituinte clivado identifica exaustivamente uma posição vazia na oração clivada. Adota-se a semântica alternativa para o foco (Rooth 1985), segundo a qual o foco entoacional contribui uniformemente um conjunto de alternativas na Forma Lógica. Regras pragmáticas operando neste conjunto dão origem a duas implicaturas que podem ser suspensas: pressuposição existencial e exaustividade. Dado que as clivadas de é que e as de SER têm a mesma interpretação que orações não-clivadas, conclui-se que a sua estrutura sintática particular não contribui para estas propriedades interpretativas. Em contrapartida, as clivadas bioracionais, que são orações copulativas especificacionais, têm uma presuposição existencial e uma interpretação exaustiva que não pode ser suspensa, tal como as orações especificacionais não-clivadas. Argumenta-se que isto se deve ao facto de o constituinte clivado identificar uma variável introduzida por uma descrição definida. Demonstra-se que a oração clivada, uma relativa em posição de complemento de um determinador definido nas clivadas canónicas e uma relativa livre nas pseudoclivadas, tem a mesma denotação que um DP definido, e portanto tem uma pressuposição existencial inerente. A interpretação exaustiva deve-se à relação identificacional entre o constituinte clivado e a descrição definida. Além disso, defende-se que em Português Europeu um traço de foco não desencadeia movimento-A’ para um FocP especializado. Os constituintes focalizados movem-se antes por razões independentes do foco. Isto é confirmado pelo facto de apenas o constituinte clivado das clivadas de é que ter propriedades de movimento A’, os outros parecem estar in situ. Propõe-se que o constituinte clivado das clivadas de é que é um tópico com um traço de foco que se move para um TopP. Esta análise dá conta da existência de restrições discursivas semelhantes para tópicos não focalizados e para o constituinte clivado das clivadas de é que. O traço quantificacional de foco arrastado pela topicalização dá origem a efeitos de intervenção, causando a não-recursividade do foco na periferia esquerda e a sua incompatibilidade com movimento de outros constituintes com traços quantificacionais. A análise prediz as restrições de encaixe observadas para as clivadas de é que. Finalmente, desenvolve-se uma análise sintática das clivadas de SER que aproxima estas estruturas das estruturas com partículas de foco. Propõe-se que a cópula é um operador sensível ao foco que é merged juntamente com o constituinte clivado. As restrições distribucionais da cópula devem-se a requisitos selecionais de núcleos.

Stratigraphic interpretation of Well-Log data of the Athabasca Oil Sands of Alberta Canada through Pattern recognition and Artificial Intelligence

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Assessment of climate change statistical downscaling methods: Application and comparison of two statistical methods to a single site in Lisbon

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia do Ambiente

On the Upper Cretaceous age and affinities of Neocyprideis lusitanicus (Ostracoda)

Guernet & Lauverjat (1986) described a new species, Neocyprideis lusitanicus, from sediments deposited near Aveiro, Portugal. For these authors, some associated fossils (Molluscs, planktonic Foraminifera) indicated a Pliocene age. That seemingly was the first record of Neocyprideis in post-Miocene sediments in Europe. A recent study of Upper Cretaceous material from the same region showed an abundant Neocyprideis fauna, associated with Charophyta. These Neocyprideis could be assigned without any doubt to N. lusitanicus. Therefore, N. lusitanicus appears as an Upper Cretaceous species, reworked in much later sediments, not Pliocene but Quaternary, as indicated by the planktonic Foraminifera assemblage. This interpretation is supported by: 1 - the incompatibility of the Neocyprideis (restricted to lacustrine-lagoonal environments) with abundant planktic Foraminifera; 2 - the occurrence of N. lusitanicus with Charophytes and non marine, cretaceous vertebrates but without the same Foraminifera. Neocyprideis lusitanicus is a valid species, clearly different from the other late Cretaceous species (N. coudouxensis and N. murciensis) as well as the Early Miocene described species (N. aquitanica, N. janoscheki).

Advanced image processing techniques for detection and quantification of drusen

Dissertation presented to obtain the degree of Doctor of Philosophy in Electrical Engineering, speciality on Perceptional Systems, by the Universidade Nova de Lisboa, Faculty of Sciences and Technology

Modelling and optimization of the ion exchange membrane bioreactor for removal of anionic pollutants from drinking water streams

Dissertação para obtenção do Grau de Doutor em Engenharia Química, especialidade de Engenharia Bioquímica

Spatial analysis and investigation of fire events occurrences in the Valencian Community, Spain

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Relational navigation and archiving of multimedia information for contemporary dance

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Homogneous time resolved fluorescence: a new technique for detection and quantifications of infliximab in autoimmune patients

RESUMO:As terapias biológicas revolucionaram o tratamento das doenças autoimunes nos últimos anos. Tipicamente têm como alvos mediadores importantes no mecanismo das doenças. Os antagonistas do fator de necrose tumoral-α (TNF-α) são um grupo de agentes biológicos muito prescrito, pois estão indicados no tratamento de doenças imuno-mediadas comuns, tais como artrite reumatoide, artrite idiopática juvenil, artrite psoriática, espondilite anquilosante, doença de Crohn e colite ulcerosa. Com o uso frequente de inibidores do TNF-α, tem-se tornado evidente que estes agentes têm um potencial imunogénico importante, que pode comprometer o prognóstico a longo prazo dos doentes cronicamente tratados. A produção de anticorpos anti-fármaco parece causar falência terapêutica secundária em muitos doentes. Um dos efeitos dos anticorpos anti-fármaco é o aumento da eliminação do fármaco. A eliminação do fármaco, por sua vez, varia entre indivíduos, refletindo diferentes perfis farmacocinéticos. A determinação dos níveis séricos mínimos do agente anti-TNF-α é assim muito informativa e pode auxiliar nas decisões terapêuticas. Contudo, os testes imunológicos para determinar as concentrações séricas do fármaco não estão facilmente disponíveis na prática clínica. De forma a investigar uma nova técnica potencialmente fidedigna e prática para a deteção e quantificação dos agentes biológicos anti-TNF-α, foi testada a técnica por HTRF (homogeneous time-resolved fluorescence resonance energy transfer) para a determinação de concentrações séricas de infliximab. Apesar de apresentar algumas limitações relacionadas com as condições de leitura da fluorescência, esta técnica provou obter resultados próximos das concentrações obtidas por ELISA (enzyme-linked immunosorbent assay) bridging. Adicionalmente, tem a vantagem de ser de execução muito mais fácil e rápida. Deste modo, a técnica por HTRF poderá ser otimizada e tornar-se uma valiosa ferramenta laboratorial para orientar as decisões terapêuticas em doentes autoimunes com falência da terapêutica anti-TNF-α.--------- ABSTRACT: Biologic therapies revolutionized the treatment of autoimmune diseases in the last years. Typically, they target important disease mediators. Tumor necrosis factor-alpha (TNF-α) antagonists constitute a very prescribed group of biologic agents as they are indicated for the treatment of common immune-mediated diseases, such as rheumatoid arthritis, juvenile idiopathic arthritis, psoriatic arthritis, ankylosing spondylitis, Crohn’s disease and ulcerative colitis. With the increasing use of TNF-α inhibitors it has been noticed that they have an important immunogenic potential that can compromise long-term outcomes in chronically treated patients. The production of anti-drug antibodies seems to cause secondary therapeutic failure in many patients. One of the effects of anti-drug antibodies is the enhancement of drug clearance. Drug clearance, in turn, varies among individuals, reflecting different pharmacokinetic profiles. Determination of serum anti-TNF-α drug trough levels is though very informative and could support treatment decisions. However, immunologic assays to determine drug serum concentrations are not readily available in clinical practice. In order to investigate a potentially reliable and practical new technique for detection and quantification of anti-TNF-α biologic agents, homogeneous time-resolved fluorescence resonance energy transfer (HTRF) technique was tested for determination of serum infliximab concentrations. Although presenting some limitations related with fluorescence reading conditions, this technique proved to give results close to the concentrations obtained by the widely used bridging enzyme-linked immunosorbent assay (ELISA). In addition, it has the advantage of being much easier and faster to perform. Thus, HTRF technique can be optimized and become a valuable laboratorial tool to guide treatment decisions in autoimmune patients with anti-TNF-α therapy failure.

Spatial Patterns and Irregularities of the electoral data: general elections in Canada

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Planning and verification of multipath routing protocols

Conventionally the problem of the best path in a network refers to the shortest path problem. However, for the vast majority of networks present nowadays this solution has some limitations which directly affect their proper functioning, as well as an inefficient use of their potentialities. Problems at the level of large networks where graphs of high complexity are commonly present as well as the appearing of new services and their respective requirements, are intrinsically related to the inability of this solution. In order to overcome the needs present in these networks, a new approach to the problem of the best path must be explored. One solution that has aroused more interest in the scientific community considers the use of multiple paths between two network nodes, where they can all now be considered as the best path between those nodes. Therefore, the routing will be discontinued only by minimizing one metric, where only one path between nodes is chosen, and shall be made by the selection of one of many paths, thereby allowing the use of a greater diversity of the present paths (obviously, if the network consents). The establishment of multi-path routing in a given network has several advantages for its operation. Its use may well improve the distribution of network traffic, improve recovery time to failure, or it can still offer a greater control of the network by its administrator. These factors still have greater relevance when networks have large dimensions, as well as when their constitution is of high complexity, such as the Internet, where multiple networks managed by different entities are interconnected. A large part of the growing need to use multipath protocols is associated to the routing made based on policies. Therefore, paths with different characteristics can be considered with equal level of preference, and thus be part of the solution for the best way problem. To perform multi-path routing using protocols based only on the destination address has some limitations but it is possible. Concepts of graph theory of algebraic structures can be used to describe how the routes are calculated and classified, enabling to model the routing problem. This thesis studies and analyzes multi-path routing protocols from the known literature and derives a new algebraic condition which allows the correct operation of these protocols without any network restriction. It also develops a range of software tools that allows the planning and the respective verification/validation of new protocols models according to the study made.

Evolutionary dynamics of Chlamydia trachomatis genome and identification of molecular patterns of hypothetical protein coding genes

The obligate intracellular bacterium Chlamydia trachomatis is a human pathogen of major public health significance. Strains can be classified into 15 main serovars (A to L3) that preferentially cause ocular infections (A-C), genital infections (D-K) or lymphogranuloma venereum (LGV) (L1-L3), but the molecular basis behind their distinct tropism, ecological success and pathogenicity is not welldefined. Most chlamydial research demands culture in eukaryotic cell lines, but it is not known if stains become laboratory adapted. By essentially using genomics and transcriptomics, we aimed to investigate the evolutionary patterns underlying the adaptation of C. trachomatis to the different human tissues, given emphasis to the identification of molecular patterns of genes encoding hypothetical proteins, and to understand the adaptive process behind the C. trachomatis in vivo to in vitro transition. Our results highlight a positive selection-driven evolution of C. trachomatis towards nichespecific adaptation, essentially targeting host-interacting proteins, namely effectors and inclusion membrane proteins, where some of them also displayed niche-specific expression patterns. We also identified potential "ocular-specific" pseudogenes, and pointed out the major gene targets of adaptive mutations associated with LGV infections. We further observed that the in vivo-derived genetic makeup of C. trachomatis is not significantly compromised by its long-term laboratory propagation. In opposition, its introduction in vitro has the potential to affect the phenotype, likely yielding virulence attenuation. In fact, we observed a "genital-specific" rampant inactivation of the virulence gene CT135, which may impact the interpretation of data derived from studies requiring culture. Globally, the findings presented in this Ph.D. thesis contribute for the understanding of C.trachomatis adaptive evolution and provides new insights into the biological role of C. trachomatishypothetical proteins. They also launch research questions for future functional studies aiming toclarify the determinants of tissue tropism, virulence or pathogenic dissimilarities among C. trachomatisstrains.

Production and characterization of Chitin-Glucan Complex by Komagataella pastoris

This thesis was focused on the production, extraction and characterization of chitin:β-glucan complex (CGC). In this process, glycerol byproduct from the biodiesel industry was used as carbon source. The selected CGC producing yeast was Komagataella pastoris (formerly known as Pichia pastoris), due the fact that to achieved high cell densities using as carbon source glycerol from the biodiesel industry. Firstly, a screening of K. pastoris strains was performed in shake flask assays, in order to select the strain of K. pastoris with better performance, in terms of growth, using glycerol as a carbon source. K. pastoris strain DSM 70877 achieved higher final cell densities (92-97 g/l), using pure glycerol (99%, w/v) and in glycerol from the biodiesel industry (86%, w/v), respectively, compared to DSM 70382 strain (74-82 g/l). Based on these shake flask assays results, the wild type DSM 70877 strain was selected to proceed for cultivation in a 2 l bioreactor, using glycerol byproduct (40 g/l), as sole carbon source. Biomass production by K. pastoris was performed under controlled temperature and pH (30.0 ºC and 5.0, respectively). More than 100 g/l biomass was obtained in less than 48 h. The yield of biomass on a glycerol basis was 0.55 g/g during the batch phase and 0.63 g/g during the fed-batch phase. In order to optimize the downstream process, by increasing extraction and purification efficiency of CGC from K. pastoris biomass, several assays were performed. It was found that extraction with 5 M NaOH at 65 ºC, during 2 hours, associated to neutralization with HCl, followed by successive washing steps with deionised water until conductivity of ≤20μS/cm, increased CGC purity. The obtained copolymer, CGCpure, had a chitin:glucan molar ratio of 25:75 mol% close to commercial CGC samples extracted from A. niger mycelium, kiOsmetine from Kitozyme (30:70 mol%). CGCpure was characterized by solid-state Nuclear Magnetic Resonance (NMR) spectroscopy and Differential Scanning Calorimetry (DCS), revealing a CGC with higher purity than a CGC commercial (kiOsmetine). In order to optimize CGC production, a set of batch cultivation experiments was performed to evaluate the effect of pH (3.5–6.5) and temperature (20–40 ºC) on the specific cell growth rate, CGC production and polymer composition. Statistical tools (response surface methodology and central composite design) were used. The CGC content in the biomass and the volumetric productivity (rp) were not significantly affected within the tested pH and temperature ranges. In contrast, the effect of pH and temperature on the CGC molar ratio was more pronounced. The highest chitin: β-glucan molar ratio (> 14:86) was obtained for the mid-range pH (4.5-5.8) and temperatures (26–33 ºC). The ability of K. pastoris to synthesize CGC with different molar ratios as a function of pH and temperature is a feature that can be exploited to obtain tailored polymer compositions.(...)