Entre as temporalidades de diferentes processos locais, este estudo etnográfico aprofunda-se em entender como esses diferentes ritmos relacionam-se e modulam as atividades de pescadores e de outros habitantes (humanos e não-humanos) na vila do Pontal do Leste - Ilha do Cardoso, Cananeia - SP. Relações essas sempre em processo de co-constituição, co-respondencia, co-evolução entre humanos e não-humanos, nunca formados e preexistentes de antemão. As percepções desses processos são fundamentais para o entendimento do comportamento de alguns animais não-humanos e plantas, das condições de tempo, da geomorfologia insular e da ecologia eólico-hídrica local, resultando em caracterizações sensíveis, que serão desdobradas nessa etnografia. Portanto, nessa malha de relações composta por paisagens multiespécies, onde diversas linhas de movimentos são traçadas por seres e processos, o intuito deste estudo foi descrever como essas linhas encontram-se e contaminam-se. E, acima de tudo, como esses encontros são traduzidos pelos habitantes e visitantes da vila. / Among the temporalities of different local processes, this ethnographic study deepens in understanding how these different rhythms relate and modulate the activities of fishermen and other inhabitants (human and non-human) in the village of Pontal do Leste - Cardoso Island, Cananeia - SP. These relations are always in the process of co-constitution, coresponse, co-evolution between humans and nonhumans never formed and preexisting inadvance. The perceptions of these processes are fundamental to the understanding of the behavior of some non-human animals and plants, of the weather conditions, insular geomorphology and local wind-hydric ecology, resulting in sensitive characterizations that will be unfolded in this ethnography. Therefore, in this meshwork of relationships composed of multispecies landscapes, where several lines of movement are traced by beings and processes, the purpose of this study was to describe how these lines meet and become contaminated. And, above all, how these meetings are translated by the inhabitants and visitors of the village.

Esta dissertação trata das características próprias dos problemas de projeto de desenvolvimento de produtos. Os objetivos deste trabalho foram revisar parte da literatura publicada sobre a natureza dos problemas de projeto; confirmar, na prática, a mudança na definição dos componentes do problema ao longo da sua resolução; e propor uma estrutura que auxilie a escolha de ferramentas de geração de alternativas. São apresentados os resultados de uma observação do processo projetual realizado por estudantes de graduação da Engenharia e do Design, trabalhando conjuntamente. A dissertação é estruturada na forma de três artigos encadeados. Os resultados da revisão bibliográfica conformam o primeiro artigo, referente ao capítulo dois deste documento. A observação dos grupos de estudantes está no segundo artigo, referente ao capítulo três. A contribuição busca facilitar a tradução dos requisitos de um projeto em conceitos de um produto, através da proposição de uma matriz que cruza as dimensões dos problemas de projeto de produtos manufaturados industrialmente e algumas ferramentas conhecidas para a geração de alternativas. Essa matriz se encontra no terceiro artigo, referente ao capítulo quatro do documento. No quinto e último capítulo são elaboradas as conclusões do estudo, que apontam para a recursividade da atividade de definir um problema paralelamente ao seu processo de resolução. / This study is about the nature of design problems. Its objectives are: to review part of the literature about the topic; to confirm, with empirical basis, the changes in the components of design problem through the resolution process; and present a framework that helps choosing concept generating tools. The empirical data were obtained from observation and verbal protocols of graduation students from Engineering and Design courses working together. This research is presented in three linked articles, setting chapters two, three and four of this document. Chapter two represents the literature review. The observation of the students corresponds to chapter three. The contribution appears in chapter four, where the design problem dimensions are crossed with tools for concept generation. Lastly, in the fifth chapter, the conclusions pointed out to the recursiveness in the problem definition and solution generation process.

L'évolution moléculaire, basée sur l'étude des données de séquençage, s'est imposée comme une approche majeure pour l'étude de l'Histoire des organismes vivants (notamment à travers les arbres phylogénétiques). Ses méthodes classiques reposent sur un découpage des génomes en entités supposées indépendantes : les gènes. Or, les gènes n'évoluent pas indépendamment : au sein de l'histoire des espèces qui le portent, l'histoire d'un gène s'inscrit. En outre, leur position le long des chromosomes fait qu'ils partagent des événements de mutations structurales (duplications, pertes de fragments chromosomiques) avec les gènes proches. Enfin, leur potentielle fonction biologique les amène à être influencés par (et à influencer en retour) l'évolution d'autres gènes. Je montre que ne pas prendre en compte ces relations d'inter-dépendances évolutives (de coévolution) lors de l'inférence d'arbres de gènes résulte en une suresti mation des différences entre les arbres des différents gènes ainsi qu'entre les arbres des gènes et l'arbre des espèces. Des modèles permettent déjà d'intégrer la coévolution des gènes avec les espèces à la reconstruction des arbres de gènes. Par ailleurs, on connaît des modèles décrivant l'évolution des relations entre gènes, néanmoins sans intégrer ces informations à la reconstruction des arbres de gènes. Je reprends ces avancées et les combine au sein d'une méthode qui modifie les arbres de gènes selon un critère qui prend en compte les séquences ainsi que des relations de coévolution avec les espèces et d'autres gènes. Cette méthode, appliquée à des mammifères et des champignons, permet de produire des histoires de gènes cohérentes entre elles / Molecular evolution, based on the study of sequencing data, established itself as a fundamental approach in the study of the history of living organisms (noticeably through the inference of phylogenetic trees). Classical molecular evolution methods rely on the decomposition of genomes into entities that are supposed independent: genes. However we know that genes do not evolve independently: their potential biological function lead them to be influenced by (and influence) the evolution of other genes. Moreover, their position along chromosomes imply that they share events of structural mutations (duplication, loss of a chromosome fragment) with neighbouring genes. Similarly, a gene individual history inscribes itself in the history of the species that bears it. I show that not taking into account this inter-dependency relationships (co- evolutionary relationships) during the inference of gene trees results in an overesti- mation of the differences between gene trees as well as between gene tree and species tree. Modelling efforts these last year have allowed the integration of gene and species co-evolution information to the reconstruction of gene trees. Besides, researchers have proposed models describing the evolution of the relationships linking genes, but without integration of this information in the tree building process. My works aim to combine these advances in a method that modify gene trees according to a criterion that integrates sequence information and information coming from co-evolution relationships. This method, applied to mammals and fungi, leads to gene histories that are more congruent (simpler adjacency histories, longer events of loss or transfer, ...)

Au cours de cette thèse, nous avons développé un outil pour détecter la coévolution, c'est à dire l'évolution conjointe de différentes entités biologiques (nucléotides, acides aminés, fonctions biologiques), à différentes échelles (moléculaire, organe). Cet outil s'applique sur des arbres phylogénétiques sur lesquels des évènements évolutifs (mutations, gains/pertes de fonctions biologiques) sont placés. Nous nous plaçons dans un cadre abstrait dans le but de travailler sur les processus conduisant à l'apparition d'évènements évolutifs au sens large le long des lignées d'un arbre phylogénétique. Cet outil est constitué de deux parties distinctes, chacune ayant ses propres spécificités.D'une part, nous avons produit une première méthode simple, très efficace, permettant de détecter parmi un très grand nombre de tels processus, quelles paires d'évènements semblent apparaître de manière conjointe dans l'arbre. Grâce à un formalisme mathématique utilisant les propriétés de l'algèbre bilinéaire, des calculs exacts d'espérance, de variance et même de distributions de probabilités sont possibles et permettent d'associer à ces paires détectées des p-values exactes, rendant cette méthode très précise.D'autre part, nous avons développé un modèle de coévolution entre de tels processus évolutifs. Ce modèle mathématique limite considérablement le nombre de paramètres utilisés et nous a permis de calculer et d'optimiser une fonction de vraisemblance. Cette optimisation revient à rechercher les paramètres du modèles expliquant au mieux les données contemporaines observées, et nous permet ainsi, toujours selon notre modèle, d'établir le scénario le plus probable ayant mené aux données observées.Cette seconde méthode est plus gourmande en temps de calcul, ce qui invite à associer les deux méthodes dans un pipeline nous permettant de traiter efficacement un grand nombre de paires avant d'aller plus loin dans notre étude et tester les paires les plus encourageantes à l'aide de notre modèle mathématique, dans le but de décrire un scénario interprétable dans un contexte biologique. Nous avons testé cet outil à l'aide de simulations, avant de l'appliquer à deux exemples biologiques très différents : le lien entre intracellularité et perte de flagelle chez Escherichia coli, et l'étude de toutes les paires de nucléotides dans des séquences d'ARNr 16S d’un échantillon de gamma-entérobactéries. / In this thesis, we have developed a tool to detect co-evolution, ie the joined evolution of different biological entities (nucleotides, amino acids, organic functions), on different scales (molecular, organ). This tool is applied to phylogenetic trees on which evolutionary events (mutations, gain / loss of biological functions) are placed. We consider an abstract framework in order to work on the processes leading to the emergence of evolutionary events along the lineages of a phylogenetic tree. This tool consists of two separate parts, each with its own specificities.On the one hand, we have produced a first simple, highly effective method to detect from a very large number of such processes, which pairs events seem to appear jointly in the tree. Using a mathematical formalism using the properties of the bilinear algebra, exact calculations of expectancy, variance and even probability distributions are possible and allow to associate exact p-values to these pairs, making this method very precise.On the other hand, we have developed a model of coevolution between such evolutionary processes. This mathematical model severely limits the number of parameters used and allows us to calculate and maximize a likelihood function. This optimization is similar to searching the parameters of a model explaining the best the observed contemporary data, and allows us as well, according to our model, to determine the most likely scenario that led to the observed data.This second method requires more computing time, which invites to combine the two methods in a pipeline allowing us to efficiently process a large number of pairs before proceeding further in our study and test the most promising pairs using our mathematical model in order to describe a scenario interpreted in a biological context. We have tested this tool by using simulations, before applying it to two very different biological examples: the link between intracellularity and loss of flagellum in Escherichia coli, and the study of all the pairs of nucleotides in sequences 16S rRNA of a sample of gamma-Enterobacteria.

No description available.

<p>  </p> <p>Predators and parasites are critical, interconnected members of the community and have the potential to influence host populations. Predators, in particular, can have direct and indirect impacts on disease dynamics. By removing hosts and their parasites, predators alter both host and parasite populations and ultimately shape disease transmission. Our ability to accurately predict disease dynamics requires understanding the ecological effects of predation on prey and host densities and its role in the coevolution of host resistance and parasite virulence. While the impact of predators on disease dynamics has received considerable attention, research has focused on selective predation on infected prey. There is, however, substantial evidence that some predators avoid infected prey, preferentially attacking uninfected individuals. Such different strategies of prey selectivity by predators modulate host-parasite interactions, changing the fitness payoffs both for hosts and their parasites. I use empirical results and theoretical predictions as a framework to discuss the mechanisms by which predation for infected versus uninfected individuals can affect disease dynamics. First, by integrating hypotheses from behavioral ecology and disease ecology, I outlined novel perspectives that complement the prevailing view of selective predation of infected individuals (Chapter 1). Then, exploring short-term ecological outcomes and long-term host-parasite coevolution, I investigated patterns of <em>Daphnia dentifera</em> host population densities and host susceptibility over several generations under different types of predation pressure, including selective predation on infected and uninfected individuals (Chapter 2). Finally, building on the results of this research, I developed a high school project-based lesson plan that facilitates the instruction of the nature of science, implementing on-going ecological research in activities to improve student learning based on a constructivist approach to learning (Chapter 3). Together this research highlights the differential ecological and evolutionary outcomes of host-parasite interactions under varying community contexts.</p>

The interaction between pollinators and flowers affects the fitness of both pollinators and flowering plants, which can result in the co-evolution of pollinator and floral traits. Some pollination systems contain flower-dwelling ambush predators that attack visiting pollinators. This interaction could result in co-evolution of predator and pollinator traits as is typical in predator-prey systems. The presence of these predators could also have indirect negative fitness effects on flowering plants by killing or deterring pollinators. This raises the possibility that predator and floral traits also co-evolve. Furthermore, it is possible that this system is best described as a three-species game where predator, pollinator, and floral traits all co-evolve. The ultimate goal of my thesis is to explore this possibility. This is achieved in Chapter 5, which consists of a game theory model of the co-evolution of floral colour with predator and pollinator behavioural strategies. This model is novel, both within the pollination context described here and within a wider context. Furthermore this model is the first to propose that the evolution of floral colour might be affected by the presence of flower-dwelling ambush predators. This is particularly significant given that there has been little discussion about what floral traits might be adaptations to the presence of these predators. A secondary goal of this thesis is to explore how pollinators detect and respond to the presence of flower-dwelling ambush predators as an important subcomponent of predator-pollinator-flower co-evolutionary dynamic. Chapter 2 demonstrates that bumblebees avoid evidence of past predation events, and Chapter 3 demonstrates that the honeybee recruitment dance is affected by exposure to cues of predation risk in a way that should reduce the colony's exposure to predators. Chapter 4 is a model that suggests novel factors that might affect how a population of pollinators distributes itself between predator-free and predator-containing flowers. / Thesis / Doctor of Philosophy (PhD)

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Software Product Lines (SPLs) are a successful approach to software reuse in the large. Even though tools exist to create SPLs, their evolution is widely unexplored. Evolving an SPL manually is tedious and error-prone as it is hard to avoid unintended side-effects that may harm the consistency of the SPL. In this thesis, the conceptual basis of a system for the evolution of model-based SPLs is presented, which maintains consistency of models and feature mapping. As basis, a novel classification is introduced that distinguishes evolutions by their potential to harm the mapping of an SPL. Furthermore, multiple remapping operators are presented that can remedy the negative side-effects of an evolution. A set of evolutions is complemented with appropriate remapping operations for the use in SPLs. Finally, an implementation of the evolution system in the SPL tool FeatureMapper is provided to demonstrate the capabilities of the presented approach when co-evolving models and feature mapping of an SPL.

Software Product Lines (SPLs) are a successful approach to software reuse in the large. Even though tools exist to create SPLs, their evolution is widely unexplored. Evolving an SPL manually is tedious and error-prone as it is hard to avoid unintended side-effects that may harm the consistency of the SPL. In this thesis, the conceptual basis of a system for the evolution of model-based SPLs is presented, which maintains consistency of models and feature mapping. As basis, a novel classification is introduced that distinguishes evolutions by their potential to harm the mapping of an SPL. Furthermore, multiple remapping operators are presented that can remedy the negative side-effects of an evolution. A set of evolutions is complemented with appropriate remapping operations for the use in SPLs. Finally, an implementation of the evolution system in the SPL tool FeatureMapper is provided to demonstrate the capabilities of the presented approach when co-evolving models and feature mapping of an SPL.:1 Introduction 1.1 Motivation for Evolving Software Product Lines 1.2 Outline of the Thesis 2 Background and Scope 2.1 Concepts and Terminology 2.1.1 Software Product Lines 2.1.2 Model-Driven Software Development 2.1.3 FeatureMapper 2.2 Scope 2.3 Related Work 3 Evolution of Software Product Lines 3.1 Evolutions 3.1.1 Evolutions in the Problem Space 3.1.2 Evolutions in the Solution Space 3.2 Classification Systems for Evolutions 3.2.1 Classification by Behavior Preservation 3.2.2 Classification Systems in the Literature 3.2.3 Classification by Semantical Extent of Model Changes 3.3 Remapping Operations 3.3.1 Remapping in the Problem Space 3.3.2 Remapping in the Solution Space 3.4 Classification and Remapping of Evolutions 3.4.1 Classification and Remapping of Problem Space Evolutions 3.4.2 Classification and Remapping of Solution Space Evolutions 4 A Framework for Evolutions in FeatureMapper 4.1 Relevant Technology 4.1.1 Refactory 4.1.2 EMFText 4.2 Implementation 4.2.1 Implementation of the Evolutions System 4.2.2 Implementation of the Remapping System 4.2.3 Implementation of the User Interface System 4.2.4 Implementation of the Test Suite 4.3 Possibilities for Extension 4.3.1 Adding New Evolutions 4.3.2 Adapting Existing Evolutions 5 Example Project 5.1 Initial Situation in 2001 5.2 First Revision in 2006 5.2.1 Removing the Cassette Player 5.2.2 Adding an MP3 CD Player 5.2.3 Adding a Personal Navigation Device 5.2.4 Changing the Implementation of the UI Builder 5.2.5 Summary of the Changes of the First Revision in 2006 5.3 Second Revision in 2011 5.3.1 Creating a Multi-Format CD Player 5.3.2 Enhancing Voice Recognition to Control the Audio Player 5.3.3 Restructuring Personal Navigation Maps 5.3.4 Changing the Implementation of the CD Player 5.3.5 Summary of the Changes of the Second Revision in 2011 5.4 Conclusion of the Example Project 6 Conclusion 6.1 Summarized Findings 6.2 Limitations and Drawbacks 6.3 Possibilities for Future Work 6.4 Theoretical and Practical Contributions A Object Remapping Specification (*.orspec) A.1 Object Remapping Specification Model A.2 Object Remapping Specification Syntax B DocBooklet (*.docbooklet) B.1 DocBooklet Model B.2 DocBooklet Syntax C NavMap (*.navmap) C.1 NavMap Model C.2 NavMap Syntax List of Figures List of Tables List of Listings Bibliography