With the ever increasing amount of high-throughput molecular profile data, biologists need versatile tools to enable them to quickly and succinctly analyze their data. Furthermore, pathway databases have grown increasingly robust with the KEGG database at the forefront. Previous tools have color-coded the genes on different pathways using differential expression analysis. Unfortunately, they do not adequately capture the relationships of the genes amongst one another. Structure Enrichment Analysis (SEA) thus seeks to take biological analysis to the next level. SEA accomplishes this goal by highlighting for users the sub-pathways of a biological pathways that best correspond to their molecular profile data in an easy to use GUI interface.

Imitating Matter examines the work of four nineteenth-century American figures for whom the science of matter served as a crucial interlocutor on questions of social and historical change. In several decades stretching to either side of the U.S. Civil War, Frederick Douglass, Henry David Thoreau, Emily Dickinson, and an enslaved potter and poet named Dave, known to scholars as Dave the Potter, all made powerful and original efforts to write to the heart of reform and to reckon with inchoate conditions arising in areas of new social growth. Each of these figures contended in their own ways with the means and possibilities of creating a substantial break with racial slavery in the United States, and, as Imitating Matter uncovers, each assigned a central place in their investigations of reform to the transformability, ongoing creativity, and capacity for emergence that they associated with matter. Instead of understanding matter as inert or inanimate, these thinkers adapted contemporary scientific notions about principles of life, growth, and development integral to matter to formulate the prospects and challenges of historical change, aligning the efforts of human reformers with a capacity for new beginnings ontologically rooted in matter’s prolific becoming. In turn, naturalizing social change to varying degrees led these figures to grapple with conceptual challenges, like halting and protracted timespans, the frustrations of orchestrating distributed interventions in belief, and prolific examples of the non-arrival of change in the decades after Emancipation. Recent scholarship on nineteenth-century American thought has identified an investment in vitalist materialism shared amongst scientists, writers, and intellectuals of many persuasions; Imitating Matter reveals the rich threads of relation that nineteenth-century writers conducted between matter and politics and adumbrates a phase in American progressive thinking informed by matter’s agitations. Chapter 1, “Dave the Potter’s Crises of Keeping: Preservative Transformation and National Survival,” reads Dave the Potter’s late couplets, written between 1858 and 1862, through his earlier work’s focus on material transformations. Examining Dave’s extant inscribed stoneware jars, created for his legal owners in South Carolina between c. 1830 and 1862, this chapter identifies a logic of keeping-by-transforming enacted in Dave’s poetic couplets and in the clay bodies of the jars on which his writing appears. The late crisis couplets of 1858-62 identify a threat of national dissolution unless the nation can be preserved through the saving actions of “listening” and “repentance,” positioning the possibility of national reform next to a litany of other activated preservative transformations, which allow materials to endure by fundamentally altering their substance. Like clay turning into stoneware in a scorching kiln, animal flesh turning into salted meat or leather through submersion, and underground bodies turning into fossils, the nation, placed in proximity to these materials susceptible to dissolution but saved by transformation, was likewise envisioned preserved through substantial internal change. By casting the nation’s survival in proximate terms to the losing and keeping of earthly and animal matter, Dave used the chemistry of material mutation to think through the possibility of historical change. Chapter 2, “Thoreau, Milton, the Teeming Earth, and the Institutions on It,” interprets the manifold connections built by Henry David Thoreau in essays, lectures, Walden (1854), and the journals, between radical antislavery thinking, on the one hand, and what he called the “radical” constitution of matter, on the other. This chapter first sketches the relationships that Thoreau constructs between a matter characterized by emergence and the human political capacity to begin anew, most visible in the phenomena that Thoreau calls “wild” – namely, mountaintops, swamps, Walden Pond, mud, the song of the wood-thrush, the insides of elms, and the early morning hours. This chapter then demonstrates that the apprehensions of vital, animate matter that ensue in these moments, inflected with John Milton’s vitalist monism and matter’s strange capacities for emergence in Paradise Lost, also inform the politics of Thoreau’s antislavery essays written after the passage of the Fugitive Slave Law (1850) and John Brown’s raid (1859). Thoreau’s ontologically rooted vision of political reform was underwritten by a radicalism that he saw inherent in nature, matter constantly betraying old forms and put new ones into circulation. Fleshing out the Miltonic inheritance in Thoreau’s thinking also adumbrates the regular associations that Thoreau makes between John Brown and the English Revolution – another literary and political moment in which an ontology of animate matter was understood to have consequences for politics and historical transformation. Chapter 3, “Uttering like the Earth: Frederick Douglass’s Reform Theory” elucidates the rich theories of reform found in Frederick Douglass’s wartime “picture lectures” (“Age of Pictures,” “Lecture on Pictures,” “Life Pictures,” and “Pictures and Progress”). Instead of understanding Douglass’s “pictures” as photographs and daguerreotypes, as many recent interpreters have done, I piece together the influence of Ludwig Feuerbach and Thomas Carlyle’s theories of projection-fetishism on Douglass’s lectures, in order to show that their strangely behaving “pictures” are beliefs uttered and made corporeal. Douglass improvised on the projective dynamics described by Feuerbach and Carlyle – whereby believers invent their own devotional objects by projecting them outward and becoming susceptible to their influence – in order to argue that a post-emancipation national shift in structures of feeling around race and freedom would depend on the ability of reformers to give powerful corporeal form to a belief in Black freedom. While the picture lectures are often read as digressions from Douglass’s wartime oratory, this chapter reads them as continuous with Douglass’s many wartime speeches that diagnose a hazardous deficit of belief among northern Republicans – a wartime failure to imagine racial equality that would leave the emancipationist project exposed in later years. Douglass’s theory of social change by way of “picturing” took the ongoing “utterance” of the earth and of “ever-moving matter” as a paradigmatic model for the materialization of belief by reformers, finding “progressive lessons” in the earth’s regular expansions of existence. Chapter 4, “‘To Denizen Denied’: Failed Emergence in Emily Dickinson’s Affective Chronology of Reconstruction,” tracks a rhetoric of emergence in Emily Dickinson’s coded writing on Black freedom and national reform from the early war years through the 1880s. In the early 1860s, in poems and in her correspondence with writer, naturalist, activist, and colonel of the first Union regiment of ex-slaves, T. W. Higginson, Dickinson wrote about a prospective harvest of Black freedom emerging from the war, and in particular from the action of the Black soldier. This chapter argues that after the war, as Reconstruction advanced, Dickinson returned to writing about Black freedom in the same natural register, her poems of absent harvest and disappointing bloom responding to the non-arrival of substantial national change. During the Reconstruction years, like other poets and artists in the Republican-leaning periodicals that she preferred, Dickinson responded to news of Emancipation’s failures and incompletions, her postwar poetry and correspondence with Higginson registering a trajectory of feeling from the anticipated promises of the war years to the unaccomplished transformations of the years after. While Dickinson has been read as a Civil War poet, this chapter helps show the ways in which she is also a poet of Reconstruction.

Dissertation presented in ful lment of the requirements for the degree of: Master of Science in Physics 2016 / The Phase-II upgrade of the Large Hadron Collider at CERN in the early 2020s will enable an order of magnitude increase in the data produced, unlocking the potential for new physics discoveries. In the ATLAS detector, the upgraded Hadronic Tile Calorimeter (TileCal) Phase-II front end read out system is currently being prototyped to handle a total data throughput of 5.1 TB/s, from the current 20.4 GB/s. The FPGA based Super Read Out Driver (sROD) prototype must perform an energy reconstruction algorithm on 2.88 GB/s raw data, or 275 million events per second. Due to the very high level of pro ciency required and time consuming nature of FPGA rmware development, it may be more e ective to implement certain complex energy reconstruction and monitoring algorithms on a general purpose, CPU based sROD co-processor. Hence, the feasibility of a general purpose ARM System on Chip based co-processing unit (PU) for the sROD is determined in this work. A PCI-Express test platform was designed and constructed to link two ARM Cortex-A9 SoCs via their PCI-Express Gen-2 x1 interfaces. Test results indicate that the latency of the PCI-Express interface is su ciently low and the data throughput is superior to that of alternative interfaces such as Ethernet, for use as an interconnect for the SoCs to the sROD. CPU performance benchmarks were performed on ve ARM development platforms to determine the CPU integer, oating point and memory system performance as well as energy e ciency. To complement the benchmarks, Fast Fourier Transform and Optimal Filtering (OF) applications were also tested. Based on the test results, in order for the PU to process 275 million events per second with OF, within the 6 s timing budget of the ATLAS triggering system, a cluster of three Tegra-K1, Cortex-A15 SoCs connected to the sROD via a Gen-2 x8 PCI-Express interface would be suitable. A high level design for the PU is proposed which surpasses the requirements for the sROD co-processor and can also be used in a general purpose, high data throughput system, with 80 Gb/s Ethernet and 15 GB/s PCI-Express throughput, using four X-Gene SoCs.

La tomographie par rayons X ou CT pour "Computed Tomography" est un outil puissant pour caractériser et localiser les défauts internes et pour vérifier la conformité géométrique d’un objet. Contrairement au cas des applications médicales, l’objet inspecté en Contrôle Non Destructif (CND) peut être très grand et composé de matériaux de haute atténuation, auquel cas l’utilisation d’une trajectoire circulaire pour l’inspection est impossible à cause de contraintes dans l’espace. Pour cette raison, l’utilisation de bras robotisés est l’une des nouvelles tendances reconnues dans la CT, car elle autorise plus de flexibilité dans la trajectoire d’acquisition et permet donc la reconstruction 3D de régions difficilement accessibles dont la reconstruction ne pourrait pas être assurée par des systèmes de tomographie industriels classiques. Une cellule de tomographie X robotisée a été installée au CEA. La plateforme se compose de deux bras robotiques pour positionner et déplacer la source et le détecteur en vis-à-vis. Parmi les nouveaux défis posés par la tomographie robotisée, nous nous concentrons ici plus particulièrement sur la limitation de l’ouverture angulaire imposée par la configuration en raison des contraintes importantes sur le mouvement mécanique de la plateforme. Le deuxième défi majeur est la troncation des projections qui se produit lorsque l’objet est trop grand par rapport au détecteur. L’objectif principal de ce travail consiste à adapter et à optimiser des méthodes de reconstruction CT pour des trajectoires non standard. Nous étudions à la fois des algorithmes de reconstruction analytiques et itératifs. Avant d’effectuer des inspections robotiques réelles, nous comptons sur des simulations numériques pour évaluer les performances des algorithmes de reconstruction sur des configurations d’acquisition de données. Pour ce faire, nous utilisons CIVA, qui est un outil de simulation pour le CND développé au CEA et qui est capable de simuler des données de projections réalistes correspondant à des configurations d’acquisition définies par l’utilisateur. / X-ray computed tomography (CT) is a powerful tool to characterize or localize inner flaws and to verify the geometric conformity of an object. In contrast to medical applications, the scanned object in non-destructive testing (NDT) might be very large and composed of high-attenuation materials and consequently the use of a standard circular trajectory for data acquisition would be impossible due to constraints in space. For this reason, the use of robotic arms is one of the acknowledged new trends in NDT since it allows more flexibility in acquisition trajectories and therefore could be used for 3D reconstruction of hardly accessible regions that might be a major limitation of classical CT systems. A robotic X-ray inspection platform has been installed at CEA LIST. The considered system integrates two robots that move the X-ray generator and detector. Among the new challenges brought by robotic CT, we focus in this thesis more particularly on the limited access viewpoint imposed by the setup where important constraints control the mechanical motion of the platform. The second major challenge is the truncation of projections that occur when only a field-of-view (FOV) of the object is viewed by the detector. Before performing real robotic inspections, we highly rely on CT simulations to evaluate the capability of the reconstruction algorithm corresponding to a defined scanning trajectory and data acquisition configuration. For this purpose, we use CIVA which is an advanced NDT simulation platform developed at CEA and that can provide a realistic model for radiographic acquisitions and is capable of simulating the projection data corresponding to a specific CT scene defined by the user. Thus, the main objective of this thesis is to develop analytical and iterative reconstruction algorithms adapted to nonstandard trajectories and to integrate these algorithms in CIVA software as plugins of reconstruction.

Este trabalho teve o propósito de avaliar a relação entre a cartilagem alar e a abertura piriforme a partir de imagens de tomografia computadorizada cone-beam e a relação do nariz com o padrão esquelético vertical da face. A pesquisa foi realizada com 96 imagens de indivíduos de ambos os sexos (49 masculino e 47 feminino), com idades entre 18 e 65 anos classificados de acordo com sua tipologia facial. Para a realização das marcações e mensurações de interesse foi utilizado o software OsiriX. A tipologia facial foi acessada através de três metodologias: índice facial, ângulo goníaco e proporção entre as alturas faciais. No corte axial da imagem de tomografia computadorizada, foram aferidas quatro grandezas lineares: largura do nariz externo, distância entre as inserções alares, extensão da base da abertura piriforme e máxima largura da abertura piriforme. Todas as grandezas foram mensuradas por dois examinadores em concordância. A análise dos resultados obtidos mostrou que há correlação entre as larguras do nariz externo e da abertura piriforme e entre a base da cavidade nasal e a distância entre as inserções alares. A largura da abertura piriforme aumenta proporcionalmente mais que a do nariz. Além disso, a tipologia facial longa associa-se à largura nasal. / The aim of this study was to evaluate the relationship between the alar cartilage and the pyriform aperture using cone-beam computed tomography (CT) imaging, and the relationship between the morphology of the nose and the vertical skeletal pattern of the face. 96 images of subjects (49 male and 47 female), aged 18-65 years classified according to the vertical skeletal pattern of the face were used in this study. The OsiriX software was used to measure the structures of interest. The facial pattern was obtained according to three techniques: facial index, gonial angle, and facial proportions. From an axial section of the CT imaging, four measurements were performed: nasal width, distance between the alar insertions, extension of the base of the pyriform aperture and width of the pyriform aperture. All measurements were obtained by two calibrated examiners. There is correlation between the nasal width and the breadth of the pyriform aperture, and between the base of the nasal cavity and the distance between the alar insertions. The width of the pyriform aperture proportionally increases more than the nasal breadth. Furthermore, the long face type is associated with nasal width.

Intrinsecamente, todo procedimento cirúrgico apresenta um certo índice de intercorrências e/ou complicações associadas. Hemorragias, infecções, parestesias ou disestesias e perda primária dos implantes são algumas das intercorrências e complicações mais comuns relacionadas a procedimentos cirúrgicos para implantodontia. Este estudo avaliou retrospectivamente o índice de intercorrências e complicações após cirurgia para a instalação de implantes dentais osteointegráveis. Foram avaliados, retrospectivamente, 660 prontuários clínicos de pacientes submetidos à instalação de implantes osteointegráveis no período 8 anos atendidos na Área de Cirurgia Buco-Maxilo-Facial da Faculdade de Odontologia de Piracicaba - Unicamp. Os resultados demonstraram que houve um maior índice de intercorrências e complicações quando os pacientes eram atendidos por alunos de especialização (p= 0,015) e quando o exame por imagem realizado era somente a radiografia panorâmica convencional (p= 0,011). Os resultados demonstraram também um maior índice de intercorrências e complicações nos pacientes quando estes eram submetidos a procedimentos cirúrgicos de reconstrução óssea alveolar (p< 0,0001). A presença de infecção pós-operatória influenciou significativamente para o aumento no índice de perda primária de implantes (p< 0,0001). / Intrinsically, every surgical procedure presents a certain rate of associated intercurrences and/or complications. Hemorrhages, infections, paresthesias or dysesthesias and primary loss of implants are some of the most common intercurrences and complications related to surgical procedures in implant dentistry. This study conducted a retrospective evaluation of the rate of intercurrences and complications related to patients submitted to osseointegratable dental implant placement. A retrospective evaluation was made of 660 clinical record charts of patients submitted to osseointegratable dental implants in the period of 8 years, attended in the Oral and Maxillofacial Surgery Department of Piracicaba Dental School - Unicamp. The results showed that there was a higher rate of intercurrences and complications when patients were attended by residents (p= 0.015) and when the panoramic radiograph was the only preoperative image exam requested (p= 0.011). The results also showed a higher rate of intercurrences and complications in patients when they were submitted to surgical procedures of alveolar bone reconstruction (p< 0.0001). The presence of post-operative infection had a significant influence on the increase in the primary loss of implants (p< 0.0001).

Por muito tempo, fruto da filosofia antiga e, de certa forma, também da renascentista, a democracia foi erigida a um modelo de ídolo, um regime perfeito que deveria ser seguido pelos modelos reais. O trabalho de Nietzsche, nessa seara, rompeu com a ideia dos ídolos, dentre eles a democracia, identificando como químera a crença em tais tradições ou modelos perfeitos. Embora seu trabalho tenha sido útil nesse tocante, é certo que Nietzsche é um desconstrutivista. Por essa razão, cabe-nos analisar a questão da idolatria democrática e, com base na genealogia nietzschiana, tentar construir um modelo realizável de democracia. Nas atuais circunstâncias institucionais, a identificação de um modelo de democracia que apresenta graves falhas e ranhuras é imprescindível para saber até que ponto se busca atingir um modelo democrático, ou se a busca, na verdade, representa uma ilusão vivenciada em pleno seio da democracia. Na verdade, a crise institucional brasileira se deve em grande parte às frustrações decorrentes de se perquirir um modelo inalcançável e desafinado com a realidade democrática nacional. E é justamente na fuga de uma democracia idolatra que se mostra pleno o caminho para superação dos fundamentos das insatisfações populares, realçando-se com mais profundidade os aspectos peculiares da democracia em processo brasileira. A própria crise de representatividade é um dos aspectos, como se verá, em que a perspectiva ideal apenas serve para agredir ainda mais a já combalida instituição da representação popular. Sem uma democracia possível, o país lutará eternamente para tentar remediar um ciclo infinito de crise, atacando suas consequências, jamais as causas. O objetivo deste trabalho, para além da descontrução de Nietzsche, foi abordar, de maneira exemplar, alguns aspectos em que o ídolo democracia não advoga em prol das nossas instituições e, na prática, analisar a viabilidade de uma reforma política realista. / For a long time, fruit of ancient and, in a way, renaissancist philosophy, democracy was built into an \"idol\" model, a perfect regimen that should be followed by the real models. Nietzche\'s work, in that field, broke through the idol concept, among them, democracy, seeing like chimera the belief in such traditions or perfect models. Although his work has been helpful in this particular issue, it\'s certain that Nietzsche exercises a deconstruction method. That\'s why it\'s up to us to analyze the democratic idolatry issue and, based on Nietzsche\'s genealogy, try to built an achivable democracy \"model\". In the current institutional circumstances. The identification of a model of democracy that has serious flaws and grooves is essential to know to what extent it seeks to achieve a democratic model, our if the ssek, as a matter of fact, represents an illusion experienced in deep core of democracy. Actually, the institutional brazillian crises is being caused by the frustrations arising from assert an unattainable and discord model with the national democratic reality. And it\'s precisely in the escape from an idolater democracy that the full path to overcoming the fundamentals of popular dissatisfaction shows itself, deeply highlightining the peculiar aspects of the processing brazillian democracy. The crisis of representation, itself, is one of the aspects, as we will see, wherein the optimal approach only serves to further harm the already battered institution of popular representation. Without a possible democracy, the country will fight forever to try to remedy an endless cycle of crisis, attacking its consequencies, never the reasons. The aim of this thesis, beyond Nietzsche deconstructive method, was approach, in an exemplary manner, some aspects where the idol democracy does not advocate on behalf of our institutions and, in practice, examine the feasibility of a realistic political reform.

The evolution of novel protein functions and protein families is a fundamental question within both evolutionary biology and biochemistry. While many gene families follow predictable patterns of molecular tinkering, many protein families exist with completely novel functions now essential. The guanylate kinase protein interaction domain (GKPID) of the membrane associated guanylate kinases (MAGUK) represents a model system for the study of protein evolution in which a protein scaffolding domain has evolved from a nucleotide kinase ancestor. Here we elucidate the ancient mechanisms by which these new functions evolved by combining ancestral protein reconstruction with in vitro and cell-biological molecular experiments. We found that the GKPID's capacity to serve as a mitotic spindle-orienting scaffold evolved by duplication and divergence of an ancient guanylate kinase enzyme before the divergence of animals and choanoflagellates. Re-introducing a single historical substitution into the ancestral guanylate kinase is sufficient to abolish the ancestral enzyme activity, confer the derived scaffolding function, and establish the capacity to mediate spindle orientation in cultured cells. This substitution appears to have revealed a latent protein-binding site, rather than constructing a novel interaction interface, apparently by altering the dynamics or conformational occupancy of a hinge region that determines whether the binding site is exposed or hidden. Three further substitutions also conveyed a measure of ligand specificity to phosphorylated Pins, which is necessary in metazoan spindle orientation pathways. These findings show how a small number of simple, ancient genetic changes caused the evolution of novel molecular functions crucial for the evolution of complex animals and laid the groundwork for an entirely new family of metazoan scaffolding proteins. This dissertation contains previously unpublished, co-authored material.

L'Imagerie par Résonance Magnétique (IRM) nécessite des outils pour gérer le mouvement physiologique et autre du sujet. La création des images par l'IRM comporte trois étapes: l'acquisition de données avec une séquence d'impulsions, la reconstruction d'images, et le post-traitement. Les techniques adaptatives de reconstruction d'images visent à intégrer des informations liées au mouvement dans le processus de génération d'images à partir de données acquises, ceci dans le but de compenser les artéfacts et problèmes provoqués par le mouvement. L'IRM dynamique avec rehaussement de contraste est une technique destinée à l'estimation de la fonction des organes, en suivant le passage d'un produit de contraste dans le corps. Les problèmes dus au mouvement, surtout dans l'application thoraco-abdominale de cette technique, se présentent sous forme d'artéfacts de mouvement et de décalages. Une nouvelle méthode de reconstruction d'images, DCE-GRICS (Reconstruction généralisée dynamique avec rehaussement de contraste par inversion d'un système couplé), a été développée pour résoudre ces problèmes. Le mouvement est estimé avec un modèle linéaire non rigide basé sur les signaux physiologiques issus de capteurs externes. Les changements d'intensité causés par le passage de l'agent de contraste sont rendus avec un modèle linéaire de changement de contraste basé sur le fonctions B-spline. Cette méthode a été appliquée et validée sur l'imagerie de la perfusion myocardique. Les inexactitudes causées par le mouvement dans les courbes intensité-temps sont compensées, afin de rendre plus fiable le post-tratement des courbes pour l'estimation de la perfusion myocardique. / Magnetic Resonance Imaging (MRI) requires tools for managing physiological and other motion of the patient. The generation of MR images consists of three steps: data acquisition with a pulse sequence, image reconstruction and image post-processing. Adaptive image reconstruction techniques aim at integrating motion information into the process of image generation from the acquired data, in order to compensate for motion-induced artefacts and problems. Dynamic contrast-enhanced (DCE) MRI is a technique designed for assessing the function of organs, by following dynamically the passage of a contrast agent in the body after a bolus injection. Motion-induced problems, especially in abdominal and thoracic DCE-MRI, consist of motion artefacts and misregistration. A new image reconstruction method, DCE-GRICS (Dynamic Contrast-Enhanced Generalized Reconstruction by Inversion of Coupled Systems), has been developed for solving these issues. Motion is estimated with a non rigid linear model based on physiological signals obtained from external sensors. Dynamic intensity changes caused by the passage of the contrast agent are described using a linear contrast change model based on B-splines. The method is applied and validated on myocardial perfusion imaging. Motion-induced inaccuracies in intensity-time curves are compensated, in order to allow for more reliable myocardial perfusion quantification by curve post-processing.

<div>Near-Field Acoustical Holography (NAH) is an inverse process in which sound pressure measurements made in the near-field of an unknown sound source can be used to reconstruct the sound field so that source locations can be identified. Usually a large number of measurements is required for the usual NAH methods since a large number of parameters in the source or field model need to be determined. However, a large-scale microphone measurement is costly and hard to perform, so the use of NAH is limited by practical experimental conditions. In the present work, with the motivation of decreasing the number of microphone measurements required, and thus facilitating the measurement process, two sparse Equivalent Source Method (ESM) algorithms were studied: i.e., Wideband Acoustical Holography (WBH) and l_1-norm minimization. Based on these two algorithms, a new hybrid NAH procedure was proposed and demonstrated.To study and verify the above mentioned algorithms, simulations of different sources were conducted and then experiments were conducted on different sources: i.e., a loudspeaker cabinet and a diesel engine.</div>