Abstract Building an embedded system from an idea to a product is a slow and expensive process requiring a lot of expertise. Depending on the developer’s expertise, the required quantity and price level of the final product, and the time and money available for development, the developer can build a device from different granularity of components, ranging from ready-made platforms, kits, and modules to individual components. Generally, solutions requiring less expertise, time and money produce products with higher production costs. The main contribution of this thesis is the EOC (Embedded Object Concept) and Atomi II Framework. EOC utilizes common object-oriented methods used in software by applying them to small electronic modules, which create complete functional entities. The conceptual idea of the embedded objects is implemented with the Atomi II framework, which contains several techniques for making the EOC a commercially feasible implementation. The EOC and the Atomi II Framework decreases the difficulty level of making embedded systems by enabling a use of ready-made modules to build systems. It enables automatic conversion of a device made from such modules into an integrated PCB, lowering production costs compared to other modular approaches. Furthermore, it also enables an automatic production tester generation due to its modularity. These properties lower the number of skills required for building an embedded system and quicken the path from an idea to a commercially applicable device. A developer can also build custom modules of his own if he possesses the required expertise. The test cases demonstrate the Atomi II Framework techniques in real world applications, and demonstrate the capabilities of Atomi objects. According to our test cases and estimations, an Atomi based device becomes approximately 10% more expensive than a device built from individual components, but saves up to 50% time, making it feasible to manufacture up to 10-50k quantities with this approach.

Os Xenarthra representam um clado de mamíferos eutérios. Pouco se sabe sobre a evolução morfológica craniana do grupo. Esta tese iniciou os estudos relativos a esta questão com base na genética quantitativa, na morfometria e na sistemática, e teve por objetivos específicos: 1) avaliar empiricamente se as matrizes de variância e covariância fenotípica (matriz-P) dos diversos gêneros de Xenarthra estudados podem ser utilizadas como substitutas das respectivas matrizes de variância e covariância genética aditiva (matriz-G), uma vez que não existem matrizes-G estimadas para os Xenarthra, e também se elas podem ser utilizadas em estudos macroevolutivos; 2) testar se a diversificação morfológica craniana no grupo ocorreu somente através de deriva genética; e 3) compreender como a relação entre os caracteres morfológicos (módulos) e a magnitude geral de integração podem influir na evolução morfológica craniana. Além destes objetivos focados na evolução do grupo, também foi escopo desta tese inferir o hábito alimentar de taxa fósseis do final do Pleistoceno/início do Holoceno para melhorar o conhecimento sobre a ecologia de alguns grupos fósseis. O banco de dados utilizado foi composto por medidas lineares de aproximadamente 1150 espécimes adultos, representando 12 dos 14 gêneros atuais e sete dos diversos gêneros extintos de Xenarthra. Com base nesses dados, matrizes-P de variância e covariância e de correlação foram estimadas para cada gênero. Essas matrizes foram posteriormente comparadas par a par para avaliar a semelhança na estrutura das diferentes matrizes. Também a partir dessas matrizes, foram obtidas as variâncias entre e intra populações para testar se a diversificação morfológica ocorreu de acordo com a expectativa teórica de diversificação sob a ação exclusiva de deriva genética. As mesmas matrizes-P foram comparadas a diferentes matrizes teóricas de hipóteses de modularidade craniana. As matrizes teóricas expressaram a relação entre os caracteres com base no desenvolvimento e/ou desempenho de função compartilhado pelas partes do crânio. Para cada matriz-P de correlação calculou-se a magnitude geral de integração. Além disto, a dieta dos grupos extintos foi inferida através de análises de funções discriminantes a partir da relação entre forma e função dos animais atuais. Os resultados obtidos indicam que as matrizes-P dos diversos gêneros são similares entre si, o que sugere que matrizes-P podem ser utilizadas tanto como substitutas das matrizes-G quanto no contexto macroevolutivo. Os resultados obtidos refutaram a hipótese nula da diversificação morfológica craniana ocorrendo somente por deriva genética, ao menos nos níveis mais inclusivos da filogenia dos Xenarthra. Consequentemente, a seleção natural provavelmente atuou neste processo de diversificação. Os resultados também sugeriram que o crânio desse grupo está organizado em módulos, sendo os módulos mais conspícuos os relacionados à face. Além disso, foi detectada grande variação na magnitude geral de integração entre gêneros. A variação no padrão modular, mas principalmente na magnitude geral de integração, faz com que os gêneros apresentem diferenças nas possíveis capacidades de responder de forma alinhada às pressões seletivas. Por último, as análises morfofuncionais indicaram elevada diversidade de hábitos alimentares entre os Xenarthra extintos / Xenarthra are an eutherian mammal clade and little is known about their cranial morphological evolution. This thesis has initiated studies related to this topic and, based on quantitative genetics, morphometrics and systematics, aimed to: 1) empirically assess if the phenotypic variance and covariance matrices (P-matrix) of several genera can be used as surrogates for their respective additive genetic variance and covariance matrices (G-matrix), since G-matrices for Xenarthra are not available, and also if P-matrices can be used in macroevolutionary studies; 2) test whether the skull morphological diversification within the group occurred only through genetic drift; and 3) understand how the relationship between the traits (modules) and overall magnitude of integration may influence cranial morphological evolution. Besides these objectives focused on the evolution of the group, it was also within the scope of this thesis to infer the feeding habits of late Pleistocene/early Holocene fossil taxa to better understand the ecology of some fossil groups. The database used consist of linear measurements of approximately 1150 adult specimens, representing 12 of the 14 extant genera and seven of the several extinct genera of Xenarthra. The data gathered were used to estimate variance/covariance and correlation P-matrices for every genus. These matrices were compared between pairs of genera to evaluate the matrices\' structural similarities. Based on these matrices, within and between population variances were obtained and it was tested whether morphological diversification was in accordance to the theoretical expectation of diversification under genetic drift alone. The same matrices were compared to theoretical matrices expressing modularity hypotheses. These theoretical matrices represent the relationship among traits in reference to the shared development and/or function of different skull\'s anatomical regions (modules). For every correlation P-matrix the overall magnitude of integration was calculated. Moreover, the extinct groups\' diet was inferred through discriminant function analysis relying on the relationship between form and function of extant animals. Results indicate that P-matrices from several genera were structurally similar. This suggests that P-matrices can be used as surrogates of their G-matrices and in the macroevolutionary context. Results refuted the null hypothesis of cranial morphological diversification occurring only due to genetic drift, at least in more inclusive levels of Xenarthran phylogeny. Consequently, natural selection probably acted on this diversification process. The results also suggested that the Xenarthran skull is organized in modules, and the most conspicuous modules are in the face region. A large variation in the overall magnitude of integration among genera was detected. The variation in the modular pattern, but especially in the overall magnitude of integration, allows genera to differ in their potential capacity to respond aligned with selective pressures. Finally, morphofunctional analyses indicate a high diversity of feeding habits among extinct Xenarthra

Despite reasonable advances in public policies for housing in the last two decades, Brazil's current housing deficit is 5.6 million housing units. In São Paulo, Brazil's largest city, an estimated one fifth of the population of 17.5 million is currently living in inadequate housing conditions, like the "favelas" (Shanty Towns) (IBGE). The favelas' houses are made from scrap materials such as wood and metal sheeting, they do not have services such as sanitation, water or electricity, and the settlements are usually very overcrowded. The gigantic rate of illegal occupation of urban land has lead to disastrous consequences not only to the people who live in them, but to society as a whole, and to environment sustainability. At most countries, including Brazil, social housing has little to do with diversity and uniqueness of living. Social housing is influenced by functionalism and the economic cost effectiveness of the production process. Unfortunately, new urban areas are still being built using the same traditional ideas, which results largely in a very functionalistic approach of repetitiveness. One unit is repeated into a row of identical blocks. This concept is still used in most of the new Brazilian urban areas. As a result those areas become monotonous and repetitive, lacking identity and uniqueness. This Thesis objective is to expose the negative impacts of the present social housing mass production model, and then to analyze the possibilities of a coherent alternative to housing based on identity, sense of community and uniqueness present at the favelas, which could consistently improve the dwellings and the built environment. The main idea is to find inspiration on the Brazilian favelas to develop a new concept for social housing. In spite of all the physical, environmental, economic and social problems, favelas are an example of coherent housing production processes where dwellers autonomously decide about the design, building and use of their dwellings. They also are usually linked to a strong sense of community no longer found elsewhere. The pattern of these large areas shows an uncontrolled growth of residential units, which leads to a vast, seemingly chaotic, but yet very structured way of living. (Vanderfeesten) The analysis of this pattern of structures is a very strong foundation to develop a modular system of building blocks. The main idea is to create an urban housing environment consisting of modular blocks to provide a "favela-based" pattern. Multiple modules typologies will be designed in order to correspond to each family's needs. The arrangement of the modules will result in open walkways, small streets, larger open areas and a vast amount of balconies, roof terraces, parks, and gardens. As a result there is a great opportunity for social interaction. The main goal is to design a housing neighborhood where each house is unique in its structural composition, providing a way of living in which social interaction is promoted while maintaining each individuals identity through the uniqueness of each unit.

Dans cette thèse, nous développons un nouveau modèle de déformation pour étudier les formes. Les déformations, et les difféomorphismes en particulier, jouent un rôle fondamental dans l'étude statistique de formes, comme un moyen de mesurer et d'interpréter les différences entre des objets similaires. Les difféomorphismes résultent généralement d'une intégration d'un flot régulier de champs de vitesses, dont les paramètres n'ont jamais encore vraiment permis de contrôler localement les déformations. Nous proposons un nouveau modèle dans lequel les champs de vitesses sont construits grâce à la combinaison de quelques champs de vecteurs locaux et interprétables. Ces champs de vecteurs sont générés à l'aide d'une structure que nous appelons module de déformation. Un module de déformation génère un champ de vecteurs d'un type particulier (e.g. homothétie) choisi à l'avance: cela permet d'incorporer des contraintes dans le modèle de déformation. Ces contraintes peuvent correspondre à un savoir que l'on a sur les formes étudiées, ou à un point de vue à partir duquel on veut étudier ces formes. Dans un premier chapitre nous définissons les modules de déformation et nous en donnons des exemples variés. Nous expliquons également comment construire facilement un module de déformation adapté à des contraintes complexes en combinant des modules de déformations simples. Ensuite nous construisons des grandes déformations modulaires en tant que flot de champs de vecteurs générés par un module de déformation. Les champs de vecteurs générés par un module de déformation sont paramétrés par deux variables : une géométrique (descripteur géométrique) et une de contrôle. Nous associons également un coût à chaque couple de descripteur géométrique et de contrôle. Dans un deuxième chapitre nous expliquons comment utiliser un module de déformation donné pour étudier des formes. Nous construisons tout d'abord une structure sous-Riemannienne sur l'espace défini comme le produit de l'espace de formes et de celui des descripteurs géométriques. La métrique sous-Riemannienne vient du coût choisi : nous munissons le nouvel espace d'une métrique choisie, qui en générale n'est pas le pull-back d'une métrique sur les champs de vecteurs mais tient compte la manière dont les champs de vecteurs sont construits à partir des contraintes. Grâce à cette structure nous définissons une distance sous-Riemannienne et nous montrons l'existence des géodésiques (trajectoires dont la longueur vaut la distance entre les points de départ et d'arrivée). L'étude des géodésiques se ramène à un problème de contrôle optimal, elles peuvent être obtenues grâce à un formalisme Hamiltonien. En particulier nous montrons qu'elles peuvent être paramétrées par une variable initiale, le moment. Après cela nous présentons les grandes déformations modulaires optimales transportant une forme source sur une forme cible. Nous définissons également l'atlas modulaire d'une population de formes par la donnée d'une forme moyenne et d'une grande déformation modulaire par forme. Dans la discussion nous étudions un modèle alternatif dans lequel les géodésiques sont paramétrées en dimension plus petite. Dans un troisième chapitre nous présentons l'algorithme implémenté pour obtenir les grandes déformations ainsi que la descente de gradient estimant les atlas. Dans un dernier chapitre nous présentons plusieurs exemples numériques grâce auxquels nous étudions certains aspects de notre modèle. En particulier nous montrons que le choix du module de déformation utilisé influence la forme moyenne, et que choisir un module de déformation adapté permet d'effectuer simultanément des recalages rigides et non linéaires. Dans le dernier exemple nous étudions des formes sans a priori, nous utilisons donc un module correspondant à des contraintes faibles et nous montrons que l'atlas obtenu est toujours intéressant. / This thesis is dedicated to the development of a new deformation model to study shapes. Deformations, and diffeormophisms in particular, have played a tremendous role in the field of statistical shape analysis, as a proxy to measure and interpret differences between similar objects but with different shapes. Diffeomorphisms usually result from the integration of a flow of regular velocity fields, whose parameters have not enabled so far a full control of the local behaviour of the deformation. We propose a new model in which velocity fields are built on the combination of a few local and interpretable vector fields. These vector fields are generated thanks to a structure which we name deformation module. Deformation modules generate vector fields of a particular type (e.g. a scaling) chosen in advance: they allow to incorporate a constraint in the deformation model. These constraints can correspond either to an additional knowledge one would have on the shapes under study, or to a point of view from which one would want to study these shapes. In a first chapter we introduce this notion of deformation module and we give several examples to show how diverse they can be. We also explain how one can easily build complex deformation modules adapted to complex constraints by combining simple deformation modules. Then we introduce the construction of modular large deformations as flow of vector fields generated by a deformation module. Vector fields generated by a deformation module are parametrized by two variables: a geometrical one named geometrical descriptor and a control one. We build large deformations so that the geometrical descriptor follows the deformation of the ambient space. Then defining a modular large deformation corresponds to defining an initial geometrical descriptor and a trajectory of controls. We also associate a notion of cost for each couple of geometrical descriptor and control. In a second chapter we explain how we can use a given deformation module to study data shapes. We first build a sub-Riemannian structure on the space defined as the product of the data shape space and the space of geometrical descriptors. The sub-Riemannian metric comes from the chosen cost: we equip the new (shape) space with a chosen metric, which is not in general the pull-back of a metric on vector fields but takes into account the way vector fields are built with the chosen constraints. Thanks to this structure we define a sub-Riemannian distance on this new space and we show the existence, under some mild assumptions, of geodesics (trajectories whose length equals the distance between the starting and ending points). The study of geodesics amounts to an optimal control problem, and they can be estimated thanks to an Hamiltonian framework: in particular we show that they can be parametrized by an initial variable named momentum. Afterwards we introduce optimal modular large deformations transporting a source shape into a target shape. We also define the modular atlas of a population of shapes which is made of a mean shape, and one modular large deformation per shape. In the discussion we study an alternative model where geodesics are parametrized in lower dimension. In a third chapter we present the algorithm that was implemented in order to compute these modular large deformations and the gradient descent to estimate the optimal ones as well as mean shapes. In a last chapter we introduce several numerical examples thanks to which we study specific aspects of our model. In particular we show that the choice of the used deformation module influences the form of the estimated mean shape, and that by choosing an adapted deformation module we are able to perform in a satisfying and robust way simultaneously rigid and non linear registration. In the last example we study shapes without any prior knowledge, then we use a module corresponding to weak constraints and we show that the atlas computation still gives interesting results.

The study of human cranial morphology has a long and contentious history. This study is the first large scale analysis of ecoregion specific human cranial modularity and integration. It utilizes an analysis of morphometric craniofacial variation and ecoregion affinity to better understand the environmental contribution to biological shape. This study tested three hypotheses. First, that there was variation in craniofacial shape that was linked to an individual’s ecoregion. Second, that there were ecoregion specific patterns of cranial modularity. And third, that the patterns of cranial integration (or the level of covariation between any two modules) were also associated with an individual’s ecoregion, and that different environments would result in different patterns of modular dependence and independence. Three-dimensional scans of 298 human crania were collected from museums, representing four higher level ecoregions and 11 lower-level ecoregions. Each cranium was mapped and placed within two hierarchical ecoregions. By examining ecoregions, instead of individual climatic variables, this analysis gives a more complete picture of how the environment is influencing cranial variation. Modules, or relatively independent morphological regions of the crania, were identified and their level of integration was assessed for every ecoregion. Modular integration is an analysis of the relative strength of the covariation between any two modules, and previous research theorized that changes in integration reflected changes in modular independence during development (Bastir and Rosas, 2005; Hall, 2005; Raff, 1996). The variation in strength between modules, both intrapopulation and interpopulation, were assessed and various explanations were explored. This analysis found that each ecoregion exhibited significantly different craniofacial shape from one another. Patterns of integration were also variable by ecoregion, suggesting that the ecological shape variation observed was solidified early in development. This study also identified the presence of a nasal module in each ecoregion. Overall, the findings of this study demonstrate that human crania are variable by ecoregion and that environmental conditions have led to ecoregion specific patterns of cranial modular integration. / Anthropology

Wireless sensor networks used in smart cities and elsewhere collect large amounts of sensor data that needs to be made available to respective audiences and have proper visualization. There is a lack of mobile applications capable of visualizing sensor data coming from multiple sources using different protocols and data formats in a clear way; an application that is easy for anyone to use. This paper will present the development and evaluation of Smart City IoT which is an Android application for visualization of IoT data collected from wireless sensor networks. The resulting application Smart City IoT is designed to be modular to the core to allow for easy extension with new sensor types, communication protocols and data formats. It demonstrates that an Android application can be developed to support multiple sources with different protocols and have a unified visualization without requiring extensive set up. / Trådlösa sensornät som används i smarta städer och på annat håll samlar in stora mängder data som behöver göras tillgängliga för respektive publik och använda sig av lämpliga visualiseringar. Det är brist på mobila applikationer som är kapabla att visualisera sensordata som kommer från flera källor med olika protokoll och data format på ett tydligt sätt; en applikation som är enkel att använda. Den här rapporten kommer att presentera utvecklingen och valideringen av Smart City IoT vilket är en applikation till Android för att visualisera IoTdata hämtat från trådlösa sensor-nätverk. Den resulterande applikationen Smart City IoT är designad för att vara modulär i sin kärna för att tillåta enkel utbyggnad av nya sensortyper, kommunikationsprotokoll och dataformat. Den demonstrerar att en applikation för Android kan utvecklas med stöd för flera källor, med olika protokoll och ha en gemensam visualisering utan att kräva en omfattande konfiguration.

This thesis argues that a peace-oriented struggle has emerged in Peshawar from within the non–state space and is demonstrated at the empirical level by various associations in that space. The struggle to embrace peace and reject different forms of violence, by this associational life in Peshawar is what we call an ‘emergent civil society’. The thesis argues against those who claim that civil society cannot exist or flourish in a non-western environment. Civil Society in Peshawar is emergent, as the empirical evidence suggests, but within an overarching tendency to root this in a local cultural identity. The latter is, however, imbued with values, belief systems, and gender roles, which limit the search for peace. Two examples are the dominance of a hyper masculinity and religious orthodoxies, which undermine forms of associationalism which might promote peace. To find an indigenous cultural identity, the ‘emergent civil society’ navigates, not without tensions, across three different worldviews that includes cultural (Pakhtunwali), religious (Islam) and, to a certain extent, liberal (human rights) perspectives. The tensions between different perspectives become more frictional when the ‘emergent civil society’ advocates women’s rights and religious pluralism, which is resisted by the antithetical forces of masculinity and religious orthodoxies. Amidst these contestations, the ‘emergent civil society’, while resisting these antithetical forces, pressurizes the state also to provide favourable conditions to continue its peace-oriented struggle. This thesis, however, suggests that the ‘emergent civil society’ also needs an in-ward looking tendency to self reflect on certain challenges that seem to impact the potential for growth and development of an associational life, which can fully embrace the social conditions for peace.

Since the cognitive revolution during the last century the mind has been conceived of as being computer-like. Like a computer, the brain was assumed to be a physical structure (hardware) upon which a computational mind (software) was built. The mind was seen as a collection of independent programs which each have their own specific tasks, or modules. These modules took sensory input "data" and transduced it into language-like representations which were used in mental computations. Recently, a new conception of the mind has developed, grounded cognition. According to this model, sensory stimulus is saved in the original format in which it was received and recalled using association mechanisms. Rather than representations being language-like they are instead multimodal. The manipulation of these multimodal representations requires processing distributed throughout the brain. A new holistic model for mental architecture has developed in which the concerted activity of the brain's modal systems produces functional systems which are intimately codependent with one another. The purpose of this thesis is to explore both the modular and multimodal theories of mental architecture. Each will be described in detail along with their supporting paradigms, cognitivism and grounded cognition. After my expositions I will offer support for my own position regarding these two theories before suggesting avenues for future research.

Bergman showed that systems of projections of algebras in a variety will satisfy a certain property if the variety has a near-unanimity term. The converse of this theorem was left open. This paper investigates this open question, and shows that in a locally finite variety, Bergman's Condition implies congruence modularity. / Thesis / Master of Science (MSc)

Resting-state functional MRI(rs-fMRI) represents a powerful means to assess brain functional connectivity in healthy subjects and in neuropsychiatric patients. Aberrant functional connectivity has been observed in subjects affected by Alcohol Use Disorders (AUD) and other forms of substance dependence, a major health issue worldwide with limited treatment options. Despite intense investigation, the specific neuronal substrates involved and the functional implications of aberrant connectivity in these patients remain unknown. Moreover, it is unclear whether treatment can reverse these alterations, and normalize functional connectivity. Several methodological and conceptual questions in the analysis of functional connectivity are still open, and contribute to this uncertainty. Functional connectivity is defined in terms of correlated MR-signal fluctuations, and in-scanner patient motion and other nuisance signals can introduce spurious correlations, thus representing substantial confounding factors. At a more general level, understanding the effects of complex conditions, like AUD, on brain connectivity and their functional implications requires a deep comprehension of the brain organizational principles at multiple scales, a tremendous challenge that is at the heart of modern neuroscience. In this PhD dissertation I address some of the outstanding questions in the analysis and interpretation of aberrant functional connectivity in AUD. To this end, I have embraced the formalism of graph-theory, a powerful framework to assess the effects of alcohol abuse on the local and global topological organization of resting state connectivity. On the methodological side, I have investigated the effects of subject’s motion on the structure of resting state networks, and compared efficacy of different approaches to remove motion-related confounds. Moreover, I demonstrate the importance of network sparsification to remove spurious connections from the graph while maximizing the structural information that can be extracted from the system. Leveraging these methodological developments, I have evaluated functional alterations in different samples of AUD patients. In two independent studies, I demonstrated specific alterations in the topological organization of the insular cortex and subcortical basal structures in recently detoxified alcoholics. Interestingly, protracted abstinence appears to partially normalize functional connectivity, thus suggesting that alcohol-induced alterations in connectivity may be amenable to treatment. Based on these findings, I have studied the effects on brain functional networks of a putative novel treatment based on deep Transcranial Magnetic Stimulation (TMS). Specifically, I analyzed resting state connectivity in AUD patients subjected to repetitive TMS of the bilateral insula and of the anterior cingulate cortex (ACC), and demonstrated treatment-induced changes that may underlie the efficacy of this potential treatment in surrogate clinical read-outs.