Thesis (M.S.)--University of Michigan, 2002. / Includes bibliographical references.

Parmi les écrits du compositeur viennois Arnold Schoenberg, nombreuses sont les occurrences d’un concept d’idée musicale [musikalische Gedanke] dont l’emploi polysémique paraît problématique à bien des égards. Celui-ci peut en effet se rapporter à l’oeuvre entière aussi bien qu’à une simple partie de sa forme, mais encore n’être qu’un objet possible de la nature dont la forme historique est elle-même contingente. Or, au-delà d’un usage commun issu de la terminologie formaliste du XIXe siècle, l’idée musicale est manifestement portée ici par une démarche réflexive, ni résolument prescriptive ni seulement descriptive, dont la cohérence et la portée peuvent être révélés par une étude compréhensive des quelques manuscrits – rarement explorés et jamais édités en langue française – où se réunissent les observations d’un compositeur soucieux de déterminer les lois d’une pensée « purement musicale ».À l’époque de la Première Guerre Mondiale, toute une décennie durant laquelle se joue pour Schoenberg un retournement à la fois esthétique et idéologique, les bouleversements historico-culturels accompagnent la révélation de la nature problématique d’une relation de sons pour « qui attend mieux de la musique qu’un peu de douceur et de beauté ». Car en effet, si les premières oeuvres atonales avaient été vécues comme une libération, comme une émancipation vis-à-vis de contraintes imposées de l’extérieur et constituant autant d’entraves à un idéal d’expression, bien vite se fit jour la question de la com-position, de sa possibilité logique. En ce sens, si le retrait de la tonalité a pu se justifier comme l’aboutissement d’un processus historique, il s’est révélé a posteriori n’être que l’acte inaugural indispensable d’une véritable pensée critique en musique, celle qui entreprend d’accorder l’art des sons aux principes et limites de la raison humaine. L’emploi schoenbergien de l’idée musicale révèle alors une pensée universelle de la relation musicale – tonale ou non –, développée selon une stricte analogie avec les formes discursives de la connaissance en général. Loin de ne refléter alorsqu’un système compositionnel personnel ou la technique spécifique d’une école, celle-ci déborde largement du champ musical. Par ce qu’elles impliquent logiquement au sujet de l’unité, de la représentation ou encore du temps, les réponses suggérées par le compositeur manifestent une profonde affinité avec une modernité critique qui interroge le penser au temps de la crise de l’idéalisme / Many of the writings of the Viennese composer Arnold Schoenberg deal with an ambivalent concept of musical idea [musikalische Gedanke] whose occurrences seem problematic in many ways. It may indeed relate to the entire work as well to a simple part of its form, but it can also be a possible object of nature whose historical form is itself contingent. However, beyond its common use coming from the technical terminology of the nineteenth century, the musical idea is clearly driven here by a decidedly reflexive approach, neither purely prescriptive nor only descriptive, whose scope and consistency can be exposed through a comprehensive study of the few manuscripts – seldom investigated and never published in French – where are gathered the observations of a composer concerned about the laws of a “purely musical” thought. At the time of the First World War, a decade during which occurs for Schoenberg an aesthetical and ideological reversal, historico-cultural changes accompany the revelation of the problematic nature of a relation of sounds for who “expects better from music than some kind of sweetness and beauty.” Indeed, if early atonal works had been experienced as a liberation, an emancipation from external constraints, obstacles to an ideal of expression, promptly emerged the issues of com-position, of its logical possibility. In this sense, if the withdrawal of tonality may have been justified as result of a historical process, it has been only the opening act of an authentic critical thought in music, one that undertakes to square the art of sounds to theprinciples and limits of human reason. Schoenberg’s use of the musical ideal then reveals a universal thought of the musical relationship – tonal or not –, developed according to a strict analogy with the discursive forms of conceptual knowledge. But far from reflecting only a personal compositional system or the specific technic of a School, it goes far beyond the musical field. Through what they imply logically about unity, representation, time, the answers suggested by the composer show a deep affinity with a critical modernity, one questioning the thinking at the time of the crisis of idealism

Les résultats d’expériences de microarray furent décriés par le manque de concordance inter-expériences. Les listes immenses de gènes résultant de filtrages statistiques sont difficiles à exploiter. La Food and Drug Administration a montré que le choix d’indicateurs de filtrage de gènes était la source d’une grande disparité entre expériences de microarray issus de laboratoires indépendants. Dans ce contexte, nous avons développé une méthode de sélection basée sur la modélisation de l’allure de la courbe d’expression avec le Log2 du « fold-change » entre les points de cinétique. En effet, des gènes co-régulés au cours d’une cinétique temporelle présentent des courbes d’expression d’allure similaire alors que leur niveau d’expression peut être différent. Nous avons validé la méthode grâce à 2 expériences indépendantes de microar-ray étudiant la différenciation des ovaires d’embryons de souris. Ainsi, nous avons obtenu une liste réduite et pertinente de gènes exprimés. Puis, une analyse de ces résultats dans le cas de la différenciation ovarienne nous a permis d’identifier 9 nouveaux gènes candidats validés in silico et restant à être testés biologiquement. / Microarray results were blamed because of their lack of concordance. Moreover, the huge candidate gene lists from statistical filterings are not useful for biologists. FDA proved that the lack of reliability between microarray experiments came from the choice of gene filtering indicators. In this context, a filtering method was developed based on expression curve shape modelling with the use of Log 2 of fold-change between kinetic points. Actually, the co-regulated genes display similar expression shape but with heterogeneous expression level.Our method was developed and validated thanks to two independent microarray experiments (Affymetric®) from mouse embryonic ovaries. Therefore, a short and relevant list of genes was obtained. Thus, a study of results linked to ovarian differentiation permitted to identify nine new candidate genes that were in silico validated. These genes might be biologically tested (i.e. RT PCR) by the scientific community.

This thesis proposes a new way to analyze facial expressions through 3D scanned faces of real-life people. The expression analysis is based on learning the facial motion vectors that are the differences between a neutral face and a face with an expression. There are several expression analysis based on real-life face database such as 2D image-based Cohn-Kanade AU-Coded Facial Expression Database and Binghamton University 3D Facial Expression Database. To handle large pose variations and increase the general understanding of facial behavior, 2D image-based expression database is not enough. The Binghamton University 3D Facial Expression Database is mainly used for facial expression recognition and it is difficult to compare, resolve, and extend the problems related detailed 3D facial expression analysis. Our work aims to find a new and an intuitively way of visualizing the detailed point by point movements of 3D face model for a facial expression. In our work, we have created our own 3D facial expression database on a detailed level, which each expression model has been processed to have the same structure to compare differences between different people for a given expression. The first step is to obtain same structured but individually shaped face models. All the head models are recreated by deforming a generic model to adapt a laser-scanned individualized face shape in both coarse level and fine level. We repeat this recreation method on different human subjects to establish a database. The second step is expression cloning. The motion vectors are obtained by subtracting two head models with/without expression. The extracted facial motion vectors are applied onto a different human subject’s neutral face. Facial expression cloning is proved to be robust and fast as well as easy to use. The last step is about analyzing the facial motion vectors obtained from the second step. First we transferred several human subjects’ expressions on a single human neutral face. Then the analysis is done to compare different expression pairs in two main regions: the whole face surface analysis and facial muscle analysis. Through our work where smiling has been chosen for the experiment, we find our approach to analysis through face scanning a good way to visualize how differently people move their facial muscles for the same expression. People smile in a similar manner moving their mouths and cheeks in similar orientations, but each person shows her/his own unique way of moving. The difference between individual smiles is the differences of movements they make.

In Cellulomonas fimi the cenB gene encodes a secreted endoglucanase (EngB) involved in the degradation of cellulose. The cenB gene carried on a 5.6 kb C fimi DNA fragment encodes a polypeptide of Mr 110,000 in Escherichia coli. The level of expression of the gene was significantly increased by replacing its normal transcriptional and translational regulatory signals with those of the E. coli lac operon. The intact EngB polypeptide is not required for enzymatic activity: active polypeptides of Mr 95,000 and 82,000 also appear in E. coli and a deletion mutant of cenB encodes an active polypeptide of Mr 72,000. The intact and truncated EngB both bind to microcrystalline cellulose. A simple, rapid affinity chromatography procedure on Avicel was developed for the purification of intact EngB and of the 72,000 deletion derivative. Alignment of the amino-terminal amino acid sequence of the purified intact EngB from E. coli with the partial nucleotide sequence of the cloned C. fimi DNA showed that the mature EngB is preceded by a sequence encoding a putative signal polypeptide of 32 amino acids, a translational initiation codon and a sequence resembling an E. coli ribosome binding site 4 nucleotides before the initiation codon. The signal peptide functions and is correctly processed in E. coli, even when its first 15 amino acids are replaced by the first 7 amino acids of β-galactosidase. The truncation of EngB does not affect its export to the periplasm of E.coli. In the intact EngB, 25% of the residues are hydroxyamino acids. It displays features common to endo-β-1 ,4-glucanases, since it has a high activity on carboxymethylcellulose. The kinetic parameters for carboxymethylcellulose hydrolysis of both intact and truncated EngB are not significantly different. C. fimi protease cleaves intact EngB, in a specific manner, to generate two polypeptides of Mr 65,000 and 43,000; the former has the capacity to bind Avicel. A polyclonal antibody raised against the purified intact EngB recognizes a C. fimi extracellular protein of M 110,000 as well as 5 polypeptides of lower molecular weight. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

Au-delà de l'information génétique contenue dans la séquence de l'ADN des cellules, il existe une mémoire cellulaire, dite épigénétique comprenant l'ensemble des circuits génétiques avec rétroactions positives permettant d'amplifier ou de maintenir une réponse cellulaire dans le temps. Nous nous sommes intéressés, à travers deux exemples, aux boucles de rétrocontrôle positif comme élément de réponse à un signal, permettant de fixer, de manière à la fois dynamique et robuste, le comportement cellulaire. Dans un premier temps, nous avons identifié une boucle d'auto-amplification dans la production de vitellogénine chez la truite et permettant d'expliquer l' « effet mémoire de la vitellogénèse » (une seconde stimulation à l'œstradiol induit une plus forte production de vitellogénine et plus rapidement que lors de la première stimulation, alors même que le niveau de vitellogénine retombe à zéro entre les deux stimulations). Le modèle que nous proposons implique un récepteur tronqué à l'œstradiol possédant une activité basale même en l'absence de son ligand, permettant de maintenir la cellule dans un état d'aptitude à répondre sans pour autant produire de vitellogénine. Dans un deuxième temps, nous nous sommes intéressés à une des causes possibles provoquant la transition épithélio-mésenchymateuse (EMT), responsable des métastases dans les cancers. L'EMT témoigne d'un état plus agressif des cellules tumorales et s'accompagne notamment d'un changement du métabolisme des cellules cancéreuses, diminuant la part de la phosphorylation oxydative au profit de la glycolyse (effet Warburg). Cela entraîne une baisse d'efficacité de la production d'ATP, obligeant les cellules à prélever davantage de nutriments dans leur milieu. Cette observation a suscité le développement de thérapies basées sur la privation de glucose et qui, a priori, devraient nuire principalement aux cellules cancéreuses. Nous avons étudié les effets d'un faible contenu cellulaire en ATP sur la transformation cellulaire. Nous avons observé qu'un traitement par un analogue non métabolisable du glucose diminue drastiquement le contenu en ATP des cellules ayant passé l'EMT et induit des changements morphologiques et génétiques orientés vers le phénotype mésenchymateux. La protéine MKL1, cofacteur de transcription dont l'activité est régulée par la polymérisation de l'actine, pourrait être un relais génétique entre l'état métabolique cellulaire et le maintien de l'EMT. Ces résultats suggèrent de fortes connections entre l'EMT et le niveau énergétique des cellules, faisant d'une privation d'énergie une cause possible de l'aggravation du phénotype mésenchymateux et remettant en cause les bienfaits sur le long terme de thérapies visant à « affamer » les cellules tumorales. / Beyond the genetic information contained in the DNA sequence of cells, there is a cellular memory called epigenetic, including genetic circuits with positive feedback loops amplifying or maintaining cellular states in time. We studied through two examples, the positive feedback loops as part of response to a signal, able to set cell behavior, in a dynamic and robust way. As a first step, we identified a self-amplification loop in the production of trout vitellogenin explaining the "vitellogenesis memory effect" (a second estradiol stimulation induces higher and faster vitellogenin production than during the first stimulation, even though the vitellogenin level falls to zero between the two stimuli). The model we propose involves a truncated estradiol receptor, with a basal activity even in the absence of its ligand, which is able to maintain the cell in an estrogen-responsive state without producing vitellogenin. In a second step, we studied one of the possible causes leading to the epithelial-mesenchymal transition (EMT), involved in cancer metastasis. The EMT reflects a more aggressive state of tumor cells and is associated with a particular change in the metabolism of cancer cells, reducing the part of oxidative phosphorylation in favor of glycolysis (Warburg effect). This leads to a reduction in the efficiency of ATP production, forcing the cells to take more nutrients from their environment. This observation led to the development of treatments based on glucose deprivation which should mainly affect cancer cells. We studied the effects of a low cellular ATP content on cell transformation. We observed that a treatment with a non-metabolizable glucose analogue drastically reduces the ATP content of cells that had undergone EMT and induces morphological and genetic changes enforcing the mesenchymal phenotype. We identified the transcriptional coactivator MKL1, whose activity is regulated by actin polymerization, as a possible genetic link between the cellular metabolic state and maintenance of EMT. These results suggest strong connections between the EMT and the energy level of the cells, and raise serious questions about the benefits of the long-term therapy "starving" tumor cells, considering that energy deprivation could aggravate the mesenchymal cell phenotype.

Leishmania major (L. major) is an intra-macrophage protozoan parasite which differentiates from a promastigote to an amastigote upon transmission from its insect vector at 25°C to its mammalian host at 37°C. This temperature shift occurs in the same range as that used to elicit the heat shock response in prokaryotes and higher eukaryotes in which the induction of genes encoding heat shock proteins is seen. Ubiquitin is a heat inducible protein and one of the most conserved eukaryotic proteins known. Genomic libraries made from major DNA were initially screened with the ubiquitin gene from yeast. DNA sequence analyses of positive clones revealed at least 5 ubiquitin coding elements arranged head to tail without intervening sequences. The predicted protein sequence showed that ubiquitin in Leishmania differs from that of yeast and barley at 5 out of 76 amino acid positions and from that of human at only 2 positions. Further characterization revealed another ubiquitin encoding locus believed to carry only one ubiquitin encoding element. Comparisons of ubiquitin mRNA levels from L. major grown at 26°C, 37°C, and 42°C suggest that ubiquitin gene expression in these particular parasites is constitutive and that prolonged exposure at a non-lethal temperature results in a reduction of ubiquitin-specific mRNA. However, a direct correlation between parasite differentiation and ubiquitin gene expression was not defined as it could not be determined whether the described experimental conditions actually established differentiated states of L. major. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

An important goal of Educational Data Mining is to provide data and visualization about students’ state of knowledge and students’ affective states. The combination of these provides an understanding of the easiness or hardness of the concepts being taught and the student’s comfortability in it. While various studies have been conducted on estimating students’ knowledge and affect, little research has been done to transform this collected (Raw) data into meaningful information that is more relatable to teachers, parents and other stakeholders, i.e. Non-Researchers. This research seeks to enhance existing Teacher Tools (An application designed within the MathSpring - An Intelligent Tutoring system) to generate a live dashboard for teachers to use in the classroom, as their students are using MathSpring. The system captures student performance and detects students’ facial expressions, which highlight students emotion and engagement, using a deep learning model that detects facial expressions. The live dashboard enables teachers to understand and juxtapose the state of knowledge and corresponding affect of students as they practice math problem solving. This should help teachers understand students’ state of mind better, and feed this information back to act and alter their instruction or interaction with each student in a personalized way. We present results of teachers' perceptions of the usefulness of the Live Dashboard, through a qualitative and quantitative survey.

Le combat contre les infections bactériennes reste un enjeu majeur de santé publique notamment avec la dissémination des Entérobactéries productrices de carbapénèmases, capables d’hydrolyser l’ensemble des β-lactamines. On assiste à l’émergence de certains clones épidémiques, se distinguant par leur distribution mondiale, leur forte transmissibilité et leur capacité à persister chez les patients. L’exemple le plus parlant est le cas du clone de Klebsiella pneumoniae appartenant au « sequence type » (ST) 258 et responsable de la diffusion mondiale de la carbapénèmase KPC (Klebsiella Pneumoniae Carbapenemase) portée majoritairement par des plasmides de la famille InFIIk. Les raisons du succès de ce clone et de l’association KPC/IncFIIk/ST258 ne sont pas encore totalement élucidées. Par ailleurs, il n’existe pas de corrélation entre le niveau d’expression d’une carbapénèmase, la sensibilité in vitro de la souche vis à vis des carbapénèmes et l’efficacité clinique d’un traitement par ces molécules. Les phénomènes d’héterorésistance aux carbapénèmes sont fréquents chez les souches produisant KPC, mais l’impact clinique est inconnu. Les mécanismes de régulation de l’expression des carbapénèmases ne sont pas élucidés.Les objectifs de cette thèse résident dans l’analyse des facteurs génétiques associés à la diffusion et la persistance de clones multi-résistants ainsi que l’analyse de l’expression des β-lactamases associées.La première partie de ce travail porte sur l’analyse de l’évolution in vivo d’une souche de K. pneumoniae ST258 produisant KPC ayant persisté chez un patient pendant près de 5 ans. L’analyse comparative des génomes provenant de 17 isolats a permis de mettre en évidence une diversification génétique importante ainsi que la sélection de mutations modifiant la virulence de la souche et sa sensibilité aux antibiotiques. Afin de caractériser les raisons du succès de certains plasmides portant KPC, une analyse transcriptomique d’une souche de Escherichia coli TOP10 transformée par un plasmide multi-réplicon IncFIIk-IncFIB exprimant KPC-2, a été réalisée en présence ou non d’imipénème. Les gènes les plus exprimés dans ces conditions sont les gènes de résistance aux antibiotiques et certains gènes essentiels à la réplication du plasmide. La présence d’imipénème affecte peu la transcription des gènes plasmidiques mais induit un stress oxydatif important dans l’ensemble de la souche. Par ailleurs, l’analyse de l’expression du gène blaKPC-2 dans différentes espèces par 5’-RACE a permis de révéler que ce gène de résistance est sous la dépendance de plusieurs promoteurs, dont la force diffère selon le fond génétique. Cette caractéristique pourrait expliquer le succès de certains isoformes du transposon Tn4401 permettant une meilleure expression du gène blaKPC-2, dans certaines espèces. Les outils développés dans cette thèse ont également été appliqués à l’analyse d’un clone d’Enterobacter kobei ST125 dont la céphalosporinase naturelle ACT-28 possède une activité d’hydrolyse accrue vis à vis de l’imipénème. Enfin, l’analyse du génome de la première souche Shewanella sp. produisant une BLSE de type CTX-M-15 a permis de révéler la présence d’un nouveau variant oxacillinase chromosomique avec activité carbapénèmase, appelé OXA-535. OXA-535 est proche d’OXA-436, un autre variant carbapénèmase porté par un plasmide ayant déjà disséminé chez les Entérobactéries. L’analyse de l’environnement génétique des gènes blaOXA-535 et blaOXA-436 confirme le rôle du genre Shewanella comme progéniteur des carbapénèmases de classe D. Ce travail contribue à une meilleure compréhension de la diffusion de certains clones multi-résistants et des mécanismes contrôlant l’expression des gènes de résistance aux β-lactamines. / Multidrug resistant bacteria and in particular carbapenemase-producing Enterobacteriaceae remain a major health public challenge. Some successful clones are emerging globally, due to their high transmissibility and their ability to colonize and persist in patients over time. Genomic analyses revealed that the dissemination of KPC carbapenemase is closely related to the spread of Klebsiella pneumoniae of the sequence-type (ST) 258 and to few successful plasmids linked to IncFIIk family. However, the reasons of the association between K. pneumoniae ST258, IncFIIk plasmids and KPC that led to the rapid spread of this clone are currently unknown.Furthermore, there is no correlation between expression level of a carbapenemase-encoding gene, in vitro susceptibility to carbapenems and efficiency of a carbapenem-based treatment. Most of the time, KPC-producing K. pneumoniae exhibit a heteroresistant phenotype with carbapenems, but its clinical impact remains unknown. The mechanisms underlying the regulation of carbapenemases expression remain to be explored.The objectives of the thesis are to obtain deeper insights into genomic plasticity of carbapenemase–producing clones, and into the expression of their β-lactamases.The first part of this work was dedicated to the in vivo evolution of a single strain of KPC-producing K. pneumoniae ST258 that colonized a patient for almost 5 years. Genomic comparison of 17 isolates revealed a remarkable diversification with occurrence of several mutations with impact on bacterial virulence and susceptibility to antibiotics.Several studies extensively described the genetic structures of blaKPC-carrying plasmids, but information regarding gene expression at the whole plasmid level are lacking. Accordingly, we performed RNA-seq on Escherichia coli TOP10 transformed with an IncFIIk-IncFI blaKPC-2-carrying plasmid, with or without imipenem exposure. In both conditions, plasmid-encoded genes related to antimicrobial resistance and involved in plasmid replication were the most expressed. Imipenem exposure led to a more general response with overexpression of E. coli numerous chromosome-encoded genes involved in oxidative stress response. In addition, analysis of blaKPC-2 gene expression in several species using 5’RACE revealed the presence of several promoters whose strength depends on the bacterial genetic background. This could promote higher expression of blaKPC-2 gene and explain the association of some isoforms of Tn4401 in different species. The tools developed in the frame of this work were also applied to study a single Enterobacter kobei ST125 clone whose natural cephalosporinase (ACT-28) has increased hydrolytic activity towards imipenem. Finally, genomic analysis of the first ESBL-producing Shewanella sp. was performed. It revealed the presence of blaCTX-M-15 and blaSHV-2 genes carried on an IncA/C plasmid and a new chromosomally-encoded oxacillinase variant of OXA-48 with carbapenemase activity, called OXA-535. OXA-535 was found to be closely related to OXA-436, another carbapenemase which has recently spread in Enterobacteriaceae. Analysis of the genetic environment of both blaOXA-48-like genes confirmed the role of Shewanella spp. as progenitors of class D carbapenemases.Overall, this work contributes to a better comprehension of the diffusion of multi-drug resistant clones and of the mechanisms implicated in β-lactamase expression.

Previous studies have suggested that manganese (Mn) deficiency is associated with increased pancreatic amylase activity in rats. The present study investigated whether this increase in amylase activity is a result of increased pancreatic amylase messenger RNA (mRNA) levels. Weanling rats were fed a high carbohydrate diet containing either 39.6 ppm (control) or 0.5 ppm (deficient) manganese for 4 to 8 weeks. Manganese deficiency was confirmed by determining hepatic manganese content which was significantly lower in Mn-deficient rats than in the respective controls. Pancreatic RNA was size-fractionated on formaldehyde gels, and hybridized with 32P-labeled complementary DNAs (cDNA) for amylase and trypsinogen. Amylase mRNA levels were increased significantly in both 4 week (200%) and 8 week (250%) Mn-deficient rats when compared with their respective controls. In contrast, manganese deficiency was not associated with alternations in trypsinogen mRNA levels. Moreover, in vitro translation of the pancreatic mRNA indicated that manganese deficiency increased amylase mRNA levels supporting the Northern Blot analysis. Insulin and corticosterone, hormones known to increase amylase mRNA levels, were not affected by Mn-deficiency. These observations suggest that manganese may participate in the regulation of amylase gene expression.