La métagénomique comparative est dite de novo lorsque les échantillons sont comparés sans connaissances a priori. La similarité est alors estimée en comptant le nombre de séquences d’ADN similaires entre les jeux de données. Un projet métagénomique génère typiquement des centaines de jeux de données. Chaque jeu contient des dizaines de millions de courtes séquences d’ADN de 100 à 200 nucléotides (appelées lectures). Dans le contexte du début de cette thèse, il aurait fallu des années pour comparer une telle masse de données avec les méthodes usuelles. Cette thèse présente des approches de novo pour calculer très rapidement la similarité entre de nombreux jeux de données. Les travaux que nous proposons se basent sur le k-mer (mot de taille k) comme unité de comparaison des métagénomes. La méthode principale développée pendant cette thèse, nommée Simka, calcule de nombreuses mesures de similarité en remplacement les comptages d’espèces classiquement utilisés par des comptages de grands k-mers (k > 21). Simka passe à l’échelle sur les projets métagénomiques actuels grâce à un nouvelle stratégie pour compter les k-mers de nombreux jeux de données en parallèle. Les expériences sur les données du projet Human Microbiome Projet et Tara Oceans montrent que les similarités calculées par Simka sont bien corrélées avec les similarités basées sur des comptages d’espèces ou d’OTUs. Simka a traité ces projets (plus de 30 milliards de lectures réparties dans des centaines de jeux) en quelques heures. C’est actuellement le seul outil à passer à l’échelle sur une telle quantité de données, tout en étant complet du point de vue des résultats de comparaisons. / Metagenomics studies the genomic content of a sample extracted from a natural environment. Among available analyses, comparative metagenomics aims at estimating the similarity between two or more environmental samples at the genomic level. The traditional approach compares the samples based on their content in known identified species. However, this method is biased by the incompleteness of reference databases. By contrast, de novo comparative metagenomics does not rely on a priori knowledge. Sample similarity is estimated by counting the number of similar DNA sequences between datasets. A metagenomic project typically generates hundreds of datasets. Each dataset contains tens of millions of short DNA sequences ranging from 100 to 150 base pairs (called reads). In the context of this thesis, it would require years to compare such an amount of data with usual methods. This thesis presents novel de novo approaches to quickly compute the similarity between numerous datasets. The main idea underlying our work is to use the k-mer (word of size k) as a comparison unit of the metagenomes. The main method developed during this thesis, called Simka, computes several similarity measures by replacing species counts by k-mer counts (k > 21). Simka scales-up today’s metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Experiments on data from the Human Microbiome Project and Tara Oceans show that the similarities computed by Simka are well correlated with reference-based and OTU-based similarities. Simka processed these projects (more than 30 billions of reads distributed in hundreds of datasets) in few hours. It is currently the only tool able to scale-up such projects, while providing precise and extensive comparison results.

Even today, many genes are without any known homolog. These "orphans" are found in all species, from Viruses to Prokaryotes and Eukaryotes. For a portion of these genes, we might simply not have enough data to find homologs yet. Some of them are imported from taxonomically distant organisms via lateral transfer; others have homologs, but mutated beyond the point of recognition. However, a sizeable fraction of orphan genes is unambiguously created via "de novo" mechanisms. The study of such novel genes can contribute to our understanding of the emergence of functional novelty and the adaptation of species to new ecological niches. In this work, we first survey the field of orphan studies, and illustrate some of the common issues. Next, we analyze some of the intrinsic properties of orphans proteins, including secondary structure elements and Intrinsic Structural Disorder; specifically, we observe that in young proteins the relationship between these properties and the G+C content of their coding sequence is stronger than in older proteins. We then tackle some of the methodological problems often found in orphan studies. We find that using evolutionarily close species, and sensitive, state-of-the art homology recognition methods is instrumental to the identification of a set of orphans enriched in de novo created ones. Finally, we compare how intrinsic disorder is distributed in bacteria versus eukaryota. Eukaryotic proteins are longer and more disordered; the difference is to be attributed primarily to eukaryotic-specific domains and linker regions. In these sections of the proteins, a higher frequency of the disorder-promoting amino acid Serine can be observed in Eukaryotes. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 4: Manuscript.</p>

This thesis is representing teoretic approach to the modeling of supply chain. Supply chain is displayed as distribution network and transformed to the model of linear programming. This model of LP is optimized. For optimazing is applied also method De Novo and the illustrative example used for models helps us with comparison of results.

One of the main goals of computational methods is to identify reasonable geometries for target materials. Organometallic complexes have been investigated in this dissertation research, entailing a significant challenge based on transition metal diversity and the associated complexity of the ligands. A large variety of theoretical methods have been employed to determine ground state geometries of organometallic species. An impressive number of transition metals entailing diverse isomers (e.g., geometric, spin, structural and coordination), different coordination numbers, oxidation states and various numbers of electrons in d orbitals have been studied. Moreover, ligands that are single, double or triple bonded to the transition metal, exhibiting diverse electronic and steric effects, have been investigated. In this research, a novel de novo scheme for structural prediction of transition metal complexes was developed, tested and shown to be successful.

Orientador : Marcelo Siqueira Ridenti / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Filosofia e Ciencias Humanas / Made available in DSpace on 2018-07-31T22:41:21Z (GMT). No. of bitstreams: 1 Jorge_MarinaSoler_M.pdf: 9608144 bytes, checksum: 0f06dfdc9415196117a14ba5aa8a86c8 (MD5) Previous issue date: 2002 / Resumo: Esta dissertação analisa as relações que os cineastas provenientes do movimento conhecido como CINEMA NOVO estabelecem com a Empresa Brasileira de Filmes S/A - EMBRAFILME - criada pelo Estado Militar em 1969 para o financiamento, a coprodução e mais tarde para a distribuição de filmes brasileiros. Apesar destes cineastas terem participado ativamente do período de efervescência artística e revolucionária prégolpe e posicionarem-se publicamente contra a ditadura estabelecida em 1964, eles exercem grande influência no interior da EMBRAFILME, principalmente a partir de 1974. A ligação de artistas de esquerda com um projeto cultural de um regime autoritário de direita dá a este segmento da indústria cultural brasileira uma especificidade que procuramos compreender e discutir / Abstract: This dissertation deals with the relations between the moviemakers of CINEMA NOVO and EMBRAFILME- Empresa Brasileira de Filmes S/A -, which was created by the Military State in 1969 to finance, produce and later distribute Brazilian films. Although these moviemakers had actively taken part in the artistic and revolutionary effervescence pre-coup d 'état and had also openly declared themselves against the dictatorship established in 1964, they had great influence in Embrafilme, mainly Erom 1974 onwards. The link between such left-wing artists and a cultural project supported by an authoritarian govemment gives to this segment of the Brazilian cultural industry a specificitythat we try to understand and discuss / Mestrado / Mestre em Sociologia

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The evolutionary history of genes across different species is a subject of research interest. For human genes, there is a particular focus on investigating the possible origins of genes. However, there has been limited research on the development process from an evolutionary perspective. Additionally, most previous studies have focused on model organisms and representative organisms from various eras, with less attention given to primates, which are evolutionarily more closely-related to humans. With the advancement of whole genome sequencing of primates, investigating the genes of various primate species has become a viable possibility. This dissertation work integrates computational insights into the topics of primate and human gene emergence, conservation, and loss. Specifically, this series of studies contributes to three aspects of the topic: (1) the environmental conditions in evolution history that are associated with the emergence of primate and human de novo genes, (2) the evolutionary dynamics of human cancer genes in primates, and (3) gene conservation and loss in primates. Results reveal that primate and human de novo genes and cancer genes share similarities in the time of emergence, peaking later than random human genes and tending to occur in local warm periods in the context of an overall trend of decreasing global surface temperature. Cancer genes are more conserved in their evolutionary origins than random human genes, with two peaks of emergence, one before primates and the other within 20 million years, and have different patterns within the two time periods. Genes with high expression in the human brain exhibit more conservation in their evolutionary origins than those in the immune system or random genes. On the other hand, genes expressed highly in the mouse brain tend to be either prevalent in primates or specific to mouse. Overall, this dissertation work charts the evolutionary history of a number of distinct primate and human genes, elucidates the potential association of ancient environmental factors with primate genomes, provides insights into the origin, conservation, and emergence of cancer genes in primates, as well as examines the conservation and loss of genes in different tissues. The hope is that these results will contribute to a greater understanding of the picture of gene evolution in primate and human genomes. / Doctor of Philosophy / Genes can be seen as tiny instructions inside human bodies that tell individuals how to grow and what they will look like. They are very important to understand how the human body works and to keep every person healthy. Each individual inherits genes from their parents, who carry on the genes from their parents (the individual's ancestors). Similarly, the entire human species collectively has inherited genes from our evolutionary ancestors. Each individual may also have genes that are unique to them due to reasons such as mutations. For a group of species or related species, this may also happen, resulting in genes called de novo genes. In this dissertation human de novo genes, which are unique to humans (Homo sapiens), and primate de novo genes, which are more broadly unique to the primates, are examined. Here, primates include several evolutionarily related species, including apes, monkeys, and humans. This dissertation first explored the emergence of primate and human de novo genes, as well as cancer genes that play certain roles in human cancer, in relation to global surface temperatures estimated at the time. The results suggested that these genes emerged more often during local warmer periods within the general trend of declining temperature in the recent 13 million years. Secondly, this series of studies looked at cancer genes compared to random human genes and found that many human cancer genes were inherited from primate ancestors. For those human cancer genes that were not inherited from such early ancestors, most have emerged within the last 20 million years. Lastly, genes highly expressed in the human brain were examined, and it was found that many such genes were also inherited from primate ancestors, more than those highly expressed in the immune system and random human genes. Genes that are highly expressed in the mouse brain, on the other hand, are often either inherited from common ancestors of mouse and primate or mouse de novo genes.

[pt] Essa dissertação desenvolve uma reflexão sobre a possibilidade, ou não, do novo crente realizar uma verdadeira conversão cristã. Denominamos novo crente aqueles que transitam entre as igrejas, hoje, buscando desenvolver uma religiosidade com matizes próprios. A teologia cristã percebe que o homem pósmoderno pode encontrar-se numa situação de não-salvação devido às características de sua época, entre elas: individualismo, fechamento para a partilha dos dons e para a vida comunitária, egoísmo acentuado etc. A pesquisa evidencia a necessidade da vida comunitária no processo de verdadeira conversão cristã. Essa reflexão irá mostrar que tal situação de não salvação, atinge todo ser humano porque pecador. Mas mostrará que a proposta da salvação pela Graça de Deus mediante Jesus Cristo também é universal, e provoca uma mudança de comportamento e de atitudes conformadas com o Mestre por aqueles que se dispõem a segui-Lo. Essa questão encontra sua relevância à medida que interpela os cristãos, responsáveis pelo anúncio do Evangelho, a uma tomada de posição frente à mobilidade religiosa. A Igreja Católica deverá assumir a tarefa de rever sua linguagem teológica e sua pregação, bem como suas práticas pastorais, aceitando enfrentar os desafios que a mobilidade religiosa impõe à Igreja, a fim de acolher o novo crente numa atitude de autêntica conversão a Jesus Cristo. / [en] The present dissertation develops a reflection about the possibility, or impossibility, for the new believer to accomplish a truly Christian conversion. We designate new believer those who pass through the churches, seeking to unfold religiousness with their own resources. The Christian theology perceives that the post-modern man can find himself in a non-salvation condition due to characteristics of his time, among them we find: individualism, unavailability to share gifts and to deal with communitarian life, significant selfishness etc. The research also shows the need for the communitarian life in the process of the actual Christian conversion. Our thoughts will indicate that this non-salvation condition reaches every human being as a sinner. However it will present that the proposal of salvation by means of God`s Grace through Jesus Christ is also universal and instigates a change of behavior and resigned attitudes towards the Master by those who make themselves attainable to follow Him. This matter achieves its relevance as it stimulates the Christians, responsible for the Gospel`s announcement, to position themselves regarding the religious mobility. The catholic church shall take on the task of revising its theological language and its preaching as well as its pastoral exercise, with the purpose of welcoming the new believer in a expression of authentic conversion to Jesus Christ.

O DOPS-SP (Departamento de Ordem Política e Social do Estado de São Paulo) foi criado em 1924 com o objetivo de organizar informações sobre a vigilância dos suspeitos do que o Estado brasileiro via como criadores da desordem política e/ou social. Sob essa categoria estariam, sobretudo, os comunistas, socialistas e anarquistas. Contudo, para além dessa esfera mais conhecida de inimigos, o DOPS registrou em seus arquivos as atividades de um amplo espectro da sociedade. Entre estes estavam os militantes - ou suspeitos de militância do movimento integralista. Estes foram fichados principalmente durante o período do Estado Novo, mas também depois. Institucionalmente, os integralistas, após o período da Ação Integralista Brasileira (AIB) entre 1932 e 1937, passaram a ser reprimidos e investigados durante o Estado Novo. Após a queda da ditadura, organizaram o Partido de Representação Popular (PRP), organização que subsistiu até 1965, quando vários de seus membros entraram na Aliança Renovadora Nacional (ARENA), sustentáculo do regime militar. Toda essa trajetória está retratada em pastas da série Dossiês organizada pelo DOPS paulista, e cujas datas-limites são 1938 e 1981. Analisar como os integralistas foram vistos e investigados pelo DOPS-SP ao longo de quatro décadas, bem como a própria trajetória integralista nesse período, estão entre as minhas metas para este trabalho. / DOPS-SP (Departamento de Ordem Política e Social do Estado de São Paulo, the São Paulo State political police) was founded in 1924 in order to organize information about the suspects surveillance that Brazilian government regarded as political and/or social troublemakers. Under this category were mostly comunistas, socialists and anarchists. However, far beyond this more known sphere of enemies, DOPS recorded in their files the activities of a wide spectrum of society. Among these were partisans or suspects of the Brazilian Integralist movement. These were blacklisted mainly during Vargas Estado Novo period, but also later. Institutionally, the Integralists, after the Ação Integralista Brasileira (AIB) period between 1932 and 1937, have been repressed and investigated during Estado Novo. After dictatorships fall, they organized the Peoples Representation Party (PRP), that continued until 1965, when many of its members joined the National Renewal Alliance (ARENA), the military regime mainstay. All this history is portrayed in the DOPS-organized « Dossiês » series folders, whose limits-dates are 1938 and 1981. To analyze how the Integralists were seen and investigated by DOPS-SP over four decades, as well as the Integralist trajectory during this period are among my goals for this work.

Cette thèse aborde l’institutionnalisation du système socio-technique qui a permis la mobilité automobile entre 1920 et 1950 au Portugal, un pays qui au départ n’est pas producteur de véhicules automobiles et demeure périphérique technologiquement, par l’étude de deux aspects qui sont complémentaires : la régulation de la circulation des automobiles et l’adaptation des routes aux nouveaux véhicules motorisés. C’est une étude sur l’appropriation et la construction de ce système en fonction des actions menées par les usagers, les ingénieurs, les législateurs, les clubs automobiles, les services de voirie ou les organes de l’administration routière. Pendant la période analysée et malgré des taux de motorisation assez faibles, le système socio-technique est institutionnalisé et stabilisé, accompagnant et dialoguant avec la définition des standards internationaux et en créant des structures qui ont influencé le développement de ce système pendant la deuxième moitié du XXe siècle.La façon dont l’institutionnalisation du système a été menée à terme a non seulement permis une augmentation importante du transport routier commercial (au détriment du développement des chemins de fer), mais a aussi protégé une culture élitiste de l’usage des voitures particulières et le développement du tourisme automobile, visible dans la régulation de la circulation et dans la construction de routes touristiques avec des caractéristiques techniques et des budgets spéciaux. Elle a aussi permis le développement de l’ingénierie routière au Portugal avec la création d’un organe autonome d’administration routière et avec la formation de plusieurs ingénieurs qui ont construit une oeuvre que s’est approprié le discours de l’Estado Novo comme un symbole de sa réalisation et de sa modernité. Ces acteurs ont participé à l’élaboration de connaissances techniques ainsi qu’aux négociations de normes sociales et morales et à la construction de représentations au niveau des pratiques des usagers, des discours et de la matérialité de ce système. / This dissertation focuses on the institutionalization of the sociotechnical system, underlying automobility, in Portugal, from 1920 to 1950. By taking into consideration that the country was technologically peripheral and originally no automobiles were locally manufactured, this work developed along two complementary aspects: the regulation of automobile circulation and the adaptation of roads to the new vehicles. This is a study focusing on the appropriation and construction of this system through the interventions of users, engineers, legislators, automobile clubs, road services and administration. In the period under consideration, despite the low rates of motorization, the sociotechnical system institutionalized and stabilized, by following and discussing the definition of international standards and creating structures, which influenced the development of this system, during the second half of the nineteenth century.The way in which the institutionalization of the car system developed allowed not only an increase in commercial road transport in detriment of railways, but also protected an elitist culture regarding the use of private cars and the development of automobile tourism, as shown by circulation regulations and in the construction of tourism roads with special technical and budgetary characteristics. It also allowed the development of road engineering in Portugal, with the creation of an independent organ for road administration and the training of engineers whose works were appropriated by the rhetoric of the dictatorial regime known as New State (Estado Novo) as a symbol of its own accomplishments and modernity. All these actors participated in the construction of a technical discourse and in the negotiations of social and moral norms, as well as of representations at the level of the users’ practices, discourses and the materiality of the sociotechnical car system.Key-words: Sociotechnical system; automobile mobility, Portugal, Estado Novo, roads, motorists.