<p>In this thesis we investigate two operational models of name-passing calculi: one based on coalgebra, and one based on enriched automata. We develop a semantic framework for modelling the open bisimulation in <i>π</i>-calculus, hyperbisimulation in Fusion calculus, and the first semantic interpretation of <i>FOλ</i>⁽<i>nabla</i>⁾ logic.</p><p>We consider a category theoretic model where both “variables” and “names”, usually viewed as separate notions, are particular cases of the more general notion of <i>atoms</i>. The key aspect of this model is to consider functors over the category of irreflexive and symmetric finite relations. The models previously proposed for the separate notions of “variables” and “names” embed faithfully in the new one, and initial algebra/final coalgebra constructions can be transferred from the formers to the latter.</p><p>Moreover, the new model admits a definition of <i>distinction-aware</i> simultaneous substitutions. As a substantial application example, we give the first semantic interpretation of Miller-Tiu's <i>FOλ</i>⁽<i>nabla</i>⁾ logic. <i>FOλ</i>⁽<i>nabla</i>⁾ logic is designed for reasoning about operational semantics of languages with binding.</p><p>On the operational level, a contribution of the thesis is to extend an automata-based model for a variety of name-passing calculi with their associated notion of equivalence. HD-automata, a syntax-independent operational model, has been successfully applied for modelling e.g. early and late bisimulation in <i>π</i>-calculus and hyperbisimulation in Fusion calculus. However, current HD-automata are not adequate for modelling open bisimulation because they can not handle distinction-preserving substitutions. We solve this technical problem by integrating the notion of distinction into the definition of named sets, the basic building blocks of HD-automata. Finally, we discuss the relationship between HD-automata with distinctions, and <b>D</b>-LTS. </p>

Concurrency is concerned with systems of multiple computing agents that interact with each other. Bisimilarity is one of the main representatives of these. Concurrent Constrain Programming (ccp) is a formalism that combines the traditional and algebraic view of process calculi with a declarative one based upon first-order logic. The standard definition of bisimilarity is not completely satisfactory for ccp since it yields an equivalence that is too fine grained. By building upon recent foundational investigations, we introduce a labeled transition semantics and a novel notion of bisimilarity that is fully abstract w.r.t. the observational equivalence in ccp. When the state space of a system is finite, the ordinary notion of bisimilarity can be computed via the partition refinement algorithm, but unfortunately, this algorithm does not work for ccp bisimilarity. Hence, we provide an algorithm that allows us to verify strong bisimilarity for ccp, modifying the algorithm by using a pre-refinement and a partition function based on the irredundant bisimilarity. Weak bisimilarity is a central behavioral equivalence in process calculi and it is obtained from the strong case by taking into account only the actions that are observable in the system. Typically the standard partition refinement can also be used for deciding weak bisimilarity simply by using Milner's reduction from weak to strong; a technique referred to as saturation. We demonstrate that the above-mentioned saturation technique does not work for ccp. We give a reduction that allows us to use the ccp partition refinement algorithm for deciding this equivalence.

The main purpose of this research was to investigate new medical applications of femtosecond laser ablation. A near-infrared femtosecond laser was tested and proved to be able to overcome the existing limitations and outperform the conventional long-pulse lasers in the areas of human urinary calculus (kidney stone) lithotripsy and skin treatment. The two primary objectives of my research are: 1) to investigate the feasibility of using femtosecond pulsed laser radiation to ablate urinary calculus of various compositions. The laser-calculus interaction mechanism was characterized using pump probe imaging and fast flash imaging. A novel fiber delivery system was developed to transmit and focus high energy femtosecond pulses for urinary calculus lithotripsy. The successful demonstration of the femtosecond laser lithotripsy provided a promising treatment method better than the existing long-pulse laser lithotripsy in a few different aspects, including less collateral damage to surrounding tissue, small-size debris and more controlled experimental condition. 2) to investigate the depth limitation of femtosecond subsurface ablation in scattering skin sample and develop a prototype tissue optical clearing device to enhance femtosecond beam penetration for deeper subsurface cavitation production in the skin. The successful demonstration of the device has potential benefits to new femtosecond-based therapies for reshaping or removing subcutaneous tissues. / text

A psi-calculus is an extension of the pi-calculus with nominal data types for data structures, logical assertions, and conditions. These can be transmitted between processes and their names can be statically scoped as in the standard pi-calculus. Expressiveness and therefore modelling convenience significantly exceed those of other formalisms: psi-calculi can capture the same phenomena as other extensions of the pi-calculus, and can be more general, e.g. by allowing structured channels, higher-order formalisms such as the lambda calculus for data structures, and predicate logic for assertions. Ample comparisons to related calculi are provided and a few significant applications are discussed. The labelled operational semantics and definition of bisimulation is straightforward, without a structural congruence. Minimal requirements on the nominal data and logic are established in order to prove general algebraic properties of psi-calculi. The purity of the semantics is on par with the pi-calculus. The theory of weak bisimulation is established, where the tau actions are unobservable. The notion of barb is defined as the output label of a communication action, and weak barbed equivalence is bisimilarity for tau actions and preservation of weak barbs in all static contexts. It is proved that weak barbed equivalence coincides with weak bisimulation equivalence. A symbolic transition system and bisimulation equivalence is presented, and shown fully abstract with respect to bisimulation congruence in the non-symbolic semantics. The symbolic semantics is necessary for an efficient implementation of the calculus in automated tools exploring state spaces, and the full abstraction property means processes are bisimilar in the symbolic setting if they are bisimilar in the original semantics. Psi-calculi remove the necessity of proving general properties every time a new mobile process calculus is defined. By properly instantiating the framework the properties are guaranteed to hold, thus removing the need to do tedious and error-prone proofs.

In this thesis we investigate two operational models of name-passing calculi: one based on coalgebra, and one based on enriched automata. We develop a semantic framework for modelling the open bisimulation in π-calculus, hyperbisimulation in Fusion calculus, and the first semantic interpretation of FOλ(nabla) logic. We consider a category theoretic model where both “variables” and “names”, usually viewed as separate notions, are particular cases of the more general notion of atoms. The key aspect of this model is to consider functors over the category of irreflexive and symmetric finite relations. The models previously proposed for the separate notions of “variables” and “names” embed faithfully in the new one, and initial algebra/final coalgebra constructions can be transferred from the formers to the latter. Moreover, the new model admits a definition of distinction-aware simultaneous substitutions. As a substantial application example, we give the first semantic interpretation of Miller-Tiu's FOλ(nabla) logic. FOλ(nabla) logic is designed for reasoning about operational semantics of languages with binding. On the operational level, a contribution of the thesis is to extend an automata-based model for a variety of name-passing calculi with their associated notion of equivalence. HD-automata, a syntax-independent operational model, has been successfully applied for modelling e.g. early and late bisimulation in π-calculus and hyperbisimulation in Fusion calculus. However, current HD-automata are not adequate for modelling open bisimulation because they can not handle distinction-preserving substitutions. We solve this technical problem by integrating the notion of distinction into the definition of named sets, the basic building blocks of HD-automata. Finally, we discuss the relationship between HD-automata with distinctions, and D-LTS.

Mice homozygous for the disrupted renal type 11a sodium/phosphate (Na/Pi) cotransporter gene, Npt2, (Npt2 KO) exhibit renal Pi wasting and hypercalciuria, predisposing factors for renal stone formation. We observed that Npt2 KO mice, but not wild-type littermates form renal stones. The renal stones were evident in newborn, weanling and adult mice and composed of calcium (Ca) and Pi. The presence of renal calcification correlated with the absence of Npt2 gene expression and the presence of genes responsible for the synthesis (1alpha-hydroxylase) and catabolism (24-hydroxylase) of 1,25-dihydroxyvitamin D, whose elevated levels contribute to the hypercalciuria and renal calcification in Npt2 KO mice. The renal calcification was associated with increased osteopontin (OPN) mRNA expression and colocalized with OPN, the latter associates with renal stones in vivo and inhibits Ca mineralization in vitro). These data demonstrate that hyperphosphaturia and hypercalciuria, secondary to Npt2 gene disruption, are sufficient for the development of renal calcification.

This thesis deals with the algorithmic undecidability (unsolvability) of provability in some non-classical logics. In fact, there are two natural variants of this problem. Fix a logic, we can study its set of theorems or its consequence relation, which is a more general problem. It is well-known that both these problems can be undecidable already for propositional logics and we provide further examples of such logics in this thesis. In particular, we study propositional substructural logics which are obtained from the sequent calculus LJ for intuitionistic logic by dropping structural rules. Our main results are the following. First, (finite) consequence relations in some basic non-associative substructural logics are shown to be undecidable. Second, we prove that a basic associative substructural logic with the contraction rule, which is notorious for being hard to handle, has an undecidable set of theorems. Since the studied logics have natural algebraic semantics, we also obtain corresponding algebraic results which are interesting in their own right.

Les comportements des processus concurrents peuvent être exprimés en utilisant des calculs de processus, des langages formels simples qui permettent de démontrer des résultats mathématiques précis sur les interactions entre processus. Un exemple très simple est CCS, un autre exemple est le pi-calcul, plus expressif grâce à un mécanisme de communication de canaux. Dans ce dernier, on peut instaurer un système de types (pour raffiner l'analyse aux environnements plus contraints) et encoder le lambda-calcul (qui représente les calculs séquentiels).Certains de ces calculs, comme CCS ou des variantes du pi-calcul comme les calculs de fusions, ont une certaine propriété de symétrie. On utilise dans un premier temps cette symétrie comme un outil, pour prouver que deux encodages du lambda-calcul dans le pi-calcul sont en fait équivalents.Cette preuve nécessitant un système de types et une forme de symétrie, on se pose la question de l'existence d'un système de types pour les autres calculs symétriques, notamment les calculs de fusion, à laquelle on répond par la négative avec un théorème d'impossibilité.En analysant ce théorème, on découvre un contrainte fondamentale de ces calculs qui empêche l'utilisation des types, à savoir la présence d'une notion de relation d'équivalence entre les canaux de communication. Le relâchement de cette contrainte pour obtenir une relation de pré-ordre engendre un calcul intéressant qui recouvre des notions importantes du pi-calcul, absentes dans les calculs de fusion : les types et les noms privés. La première partie de la thèse se concentre sur l'étude de ce calcul.La deuxième partie de la thèse se concentre sur la bisimulation, une méthode pour établir l'équivalence de deux agents dans des langages d'ordre supérieur, par exemple le pi-calcul ou le lambda-calcul. Une amélioration de cette méthode est la théorie des techniques modulo, très puissante, mais qui malheureusement s'applique uniquement aux systèmes de premier ordre, comme les automates ou CCS.Cette thèse s'applique alors à décrire les langages d'ordre supérieur en tant que systèmes du premier ordre. On récupère ainsi la théorie générale des techniques modulo pour ces langages, en prouvant correctes la correspondance induite et les techniques spécifiques à chaque langage. On détaille les tenants et aboutissants de cette approche, pour fournir les outils nécessaires à son utilisation pour d'autres langages d'ordre supérieur. / The behaviours of concurrent processes can be expressed using process calculi, which are simple formal languages that let us establish precise mathematical results on the behaviours and interactions between processes. A very simple example is CCS, another one is the pi-calculus, which is more expressive thanks to a name-passing mechanism. The pi-calculus supports the addition of type systems (to refine the analysis to more subtle environments) and the encoding of the lambda-calculus (which represents sequential computations).Some of these calculi, like CCS or variants of the pi-calculus such as fusion calculi, enjoy a property of symmetry. First, we use this symmetry as a tool to prove that two encodings of the lambda-calculus in the pi-calculus are in fact equivalent.This proof using a type system and a form of symmetry, we wonder if other existing symmetric calculi can support the addition of type systems. We answer negatively to this question with an impossibility theorem.Investigating this theorem leads us to a fundamental constraint of these calculi that forbids types: they induce an equivalence relation on names. Relaxing this constraint to make it a preorder relation yields another calculus that recovers important notions of the pi-calculus, that fusion calculi do not satisfy: the notions of types and of privacy of names. The first part of this thesis focuses on the study of this calculus, a pi-calculus with preorders on names.The second part of this thesis focuses on bisimulation, a proof method for equivalence of agents in higher-order languages, like the pi- or the lambda-calculi. An enhancement of this method is the powerful theory of bisimulations up to, which unfortunately only applies for first-order systems, like automata or CCS.We then proceed to describe higher-order languages as first-order systems. This way, we inherit the general theory of up-to techniques for these languages, by proving correct the translations and up-to techniques that are specific to each language. We give details on the approach, to provide the necessary tools for future applications of this method to other higher-order languages.

A urolitíase ocorre com relativa freqüência dentre as afecções que acometem o trato urinário inferior de cães e gatos. Urólitos são agregados de material cristalino e matriz que se forma em um ou mais locais no trato urinário quando a urina torna-se supersaturada com substâncias cristalogênicas. A constituição dos urólitos pode ser decorrente de deposição de um único tipo mineral ou de minerais diferentes que se depositam em camadas (laminações) ou simplesmente agregam-se à pedra. Dependendo do tipo mineral e sua distribuição no urólito, este pode ser classificado em simples (apenas uma camada com predomínio - >70% - de um único tipo mineral), misto (também apenas uma camada identificável, porém sem predomínio de um único mineral) ou composto (presença de mais de uma camada de composição mineral diferente). Atualmente existem dois métodos de análise da composição mineral de cálculo: análise qualitativa e quantitativa, porém apenas a quantitativa permite a determinação do percentual das diferentes composições minerais, além de ser um método mais sensível e específico. Este estudo teve como objetivo analisar os casos de urolitíase canina que tiveram seus cálculos analisados quantitativamente, atendidos no Hospital Veterinário da Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo (FMVZ-USP). Foram analisados 161 urólitos provenientes de 156 cães (5 animais apresentaram recidiva), durante o período de fevereiro de 1999 a janeiro de 2007. Todas as análises foram realizadas no Minnesota Urolith Center, baseada nos métodos de microscopia de luz polarizada, espectroscopia infravermelha e espectroscopia por raios-X com dispersão de energia. Apenas 30,2% (106) dos urólitos eram simples, 1,9% (3) mistos e 67,9% (47) eram compostos. Apesar desse predomínio de urólitos compostos, a avaliação individual desses revelou que 64 de 106 urólitos compostos continham em todas as suas camadas, predomínio (>70%) de um mesmo tipo mineral: 26 continham estruvita, 35 oxalato de cálcio (mono ou dihidratado) e três de urato (urato ácido de sódio e urato ácido de amônio). Tais urólitos, apesar de classificados como compostos poderiam ser manejados como urólitos simples. Por outro lado, 30 urólitos compostos tinham a região interna minerais passíveis de dissolução, mas que seria impedida por uma camada mineral externa não passível de dissolução. O inverso ocorreu em 3 amostras (apenas a camada mais externa seria passível de dissolução) e outras duas amostras apresentaram deposição sequencial de minerais passíveis de dissolução, porém, que exigiriam protocolos distintos. Assim, o conhecimento da composição de todas as camadas (núcleo, pedra, parede e superfície) que compõe o urólito é essencial para o entendimento da formação do cálculo e conseqüentemente para a indicação do tratamento adequado, assim como para a prevenção de recidivas. / Urolithiasis is a relatively common urinary tract disorder of dogs and cats. Whenever urine becomes oversaturate with cristallogenic substances, uroliths may be formed from crystalline material and protein matrix. Uroliths may be composed from only one kind or from different types of minerals, which can be deposited in layers or aggregate forming a stone. They can be classified according to their mineral type and distribution in: simple (only one layer and more than 70% of a single mineral), mixed (one identifiable layer, without predominance of a mineral type) or coumpound (more than one layer of different mineral types). Currently, there are two methods of urolith analyses: quantitative and qualitative analysis. However, only quantitative analysis allows determination of the mineral composition with accuracy, and it is a more sensitive and specific test. One hundred and sixty one canine uroliths were obtained from the Hospital of the School of Veterinary Medicine and Zootechny of University of São Paulo (FMVZ-USP) and were submitted to Minnesota Uroliths Center for quantitative analysis from February 1999 to January 2007. All uroliths were analyzed using polarizing light microscopy, infrared spectroscopy and energy dispersive X-ray spectroscopy. One hundred and six (30,2%) were simple uroliths, 3 (1,9%) mixed, and 47 (67,9%) were compound. Despite the predominance of compound uroliths, individual urolithevaluation revealed that 64 of 106 compound uroliths had a predominant mineral type (>70%) in all layers: 26 were struvite, 35 calcium oxalate (mono or dihydrate) and 3 were urate (sodium acid urate and ammonium acid urate). These uroliths, despite being classified as compound uroliths, could be assumed as simple uroliths. However, 30 compound uroliths had dissoluble inner layers, but the outer layer would prevent them from being dissovable. Three samples had the opposite (outer layer could be dissoluted, but inner layer could not) and 2 other samples had required two different protocols for medical dissolution. Knowledge the composition of all layers (nidus, stone, shell and surface crystals) is essential to understand the urolith etiology and a key factor to successful therapy and prevent recurrence.

OBJETIVOS: O aumento da expectativa de vida tem gerado um envelhecimento populacional global, fazendo com que a proporção de indivíduos com mais de 60 anos de idade cresça mais rapidamente do que as demais faixas etárias. A incidência de litíase urinária em indivíduos idosos tem aumentado nos últimos anos, principalmente em nações industrializadas. Aspectos particulares do envelhecimento orgânico aumentam a morbidade associada à litíase urinária em idosos, tornando a prevenção e o tratamento clínico ainda mais relevantes nessa faixa etária. Nosso objetivo é analisar a avaliação metabólica de homens idosos portadores de cálculos renais. MATERIAIS E MÉTODOS: Realizamos um estudo clínico tipo caso-controle. Os critérios de inclusão foram: indivíduos do sexo masculino com mais de 60 anos de idade, com antecedente de cólica renal ou diagnóstico incidental de litíase urinária após os 60 anos (grupo caso); no grupo controle foram incluídos pacientes da mesma faixa etária sem antecedente de cólica renal ou diagnóstico incidental de litíase renal. Todos os participantes foram submetidos à anamnese e aqueles selecionados realizaram perfil metabólico para diagnóstico de litíase urinária: dosagem sérica de cálcio total, cálcio ionizado, ácido úrico, fósforo, glicemia, uréia, creatinina e paratormônio (PTH); coleta de urina para urocultura e pH urinário, e amostras de urina de 24 horas para quantificação do volume e dosagem de cálcio, citrato, creatinina, ácido úrico e sódio. Foram também submetidos à radiografia simples de abdome e ultrassonografia do aparelho urinário. Os indivíduos do grupo caso realizaram dois perfis metabólicos completos de urina de 24 horas, enquanto os do grupo controle somente um perfil. Os resultados foram submetidos à análise estatística. RESULTADOS: Cento e dez indivíduos foram convocados e, após aplicação dos critérios de inclusão, 70 foram selecionados. Cinquenta e um indivíduos concluíram a investigação clínica, sendo 25 no grupo caso e 26 no controle. Cinquenta e seis por cento dos pacientes do grupo caso apresentaram hipocitratúria comparados a 15,4% do grupo controle (p=0,002). A determinação de sódio em urina de 24 horas também apresentou diferença estatisticamente significativa entre casos e controles: 64% versus 30,8%, respectivamente (p=0,017). Estes resultados foram submetidos à análise de regressão logística univariada e múltipla, respectivamente, e mantiveram seus níveis de significância. CONCLUSÃO: A hipocitratúria e a hipernatriúria são os principais distúrbios metabólicos apresentados por indivíduos idosos do sexo masculino portadores de cálculo urinário / PURPOSES: Rise in life expectancy has caused a global populational ageing and people older than 60-years have increased more than any other age group. The incidence of urinary lithiasis in aging people has increased during the last years, mainly in developed nations. Some aspects concerning organic ageing increase morbidity related to urolithiasis in older individuals making prevention and medical management of urinary stones relevant in this age group. Our objective is to evaluate metabolic parameters in men older than 60 years with urinary stones. MATERIALS AND METHODS: A case-control study was performed. Inclusion criteria were: men older than 60- years old with renal pain episodes or incidental diagnosis of urinary lithiasis beginning after 60-years old (case arm). Control group was constituted by patients older than 60 years without renal colic past or diagnosis of urolithiasis. Patients were recruited from a database from the Urologic Clinic at University of São Paulo Medical School Hospital. Each individual was submitted to anamnesis and those selected underwent a metabolic evaluation for urinary stones: serum dosages of total and ionized calcium, uric acid, phosphorus, glucose, urea, creatinine and parathyroid hormone (PTH); urine culture and urinary pH. Twenty four hour urine samples were obtained for volume quantification and for calcium, citrate, creatinine, uric acid and sodium dosages. An abdominal x-ray and ultrasonography were performed in all patients. Case arm patients underwent two complete metabolic urinary investigations while control arm individuals to only one. All results were submitted to statistical analysis. RESULTS: One hundred and ten individuals were called up for initial evaluation and 70 were selected. Fifty-one individuals concluded the whole clinical investigation: 25 in the case arm and 26 in the control arm. Hypocitraturia was present in 56% of case arm patients and 15,4% of the control arm patients (p=0,002). Hypernatriuria in 24-hour urine samples was found in 64% of case arm patients and in 30,8% of control arm patients (p=0,017). These results were submitted to univariate and multiple logistic regressions and maintained their levels of significancy. CONCLUSION: Hypocitraturia and hypernatriuria are the main metabolic disorders among aging men with urolithiasis