LES METHODES CLASSIQUES DISPONIBLES POUR MESURER L'ACTIVITE ENZYMATIQUE DE REPARATION DES LESIONS DE L'ADN PAR DES ADN N-GLYCOSYLASES SONT LONGUES ET LABORIEUSES A METTRE EN ŒUVRE (ANALYSE PAR ELECTROPHORESE SUR GEL COUPLEE AU MARQUAGE PAR UN ISOTOPE RADIOACTIF OU ENCORE PAR CHROMATOGRAPHIE LIQUIDE HAUTE PERFORMANCE). NOUS AVONS DEVELOPPE DANS LE PRESENT TRAVAIL, UNE NOUVELLE METHODE DE QUANTIFICATION PRECISE ET AISEE DES ACTIVITES DE REPARATION BASEE SUR UNE DETECTION UTILISANT LE PRINCIPE PHYSIQUE DU FRET (TRANSFERT PAR RESONANCE D'ENERGIE DE FLUORESCENCE). POUR CE FAIRE, UN SUBSTRAT D'ADN ORIGINAL A ETE CONÇU : UNE STRUCTURE AUTOCOMPLEMENTAIRE CONTENANT DES LESIONS SPECIFIQUES DANS LA SEQUENCE DOUBLE BRIN DE L'EPINGLE A CHEVEUX ET, AYANT LES DEUX EXTREMITES MARQUEES PAR DES CHROMOPHORES. L'EXCISION DE LA LESION PAR DES ADN N-GLYCOSYLASES CONDUIT A LA SEPARATION DES BRINS COMPLEMENTAIRES, INDUISANT UNE DIMINUTION DU PROCESSUS DE « QUENCHING » DE FLUORESCENCE. L'EXCISION EST DONC DETECTEE ET QUANTIFIEE PAR L'AUGMENTATION DE L'INTENSITE DU SIGNAL D'EMISSION DU FLUOROPHORE. APRES AVOIR ETABLI LA LINEARITE DE LA REPONSE DU TEST, NOUS AVONS UTILISE CETTE APPROCHE EXPERIMENTALE POUR ACCEDER AUX PARAMETRES CINETIQUES CARACTERISTIQUES DES ENZYMES DE REPARATION. LA VALIDITE DE CES PARAMETRES A ETE CONTROLEE PAR COMPARAISON AVEC LES DONNEES OBTENUES PAR ANALYSE SUR GEL D'ACRYLAMIDE (EGPA). LES POSSIBLES APPLICATIONS DE NOTRE TEST EN TANT QU'OUTIL DE SCREENING POUR LA DETECTION D'ACTIVITE DE REPARATION OU D'INHIBITION ENZYMATIQUE, SUR ENZYMES PURIFIEES OU A PARTIR D'EXTRAITS CELLULAIRES ONT ETE INVESTIGUEES. ENFIN, UN PROJET DE MINIATURISATION DU FORMAT DE LECTURE DANS UN MICROSYSTEME DE TYPE « LAB-ON-A-CHIP » A ETE MENE. L'ENSEMBLE DES RESULTATS OBTENUS PROUVE LA PERTINENCE DE NOTRE METHODE D'ANALYSE EN PHASE HOMOGENE, EN VUE D'EXTENSIONS A L'ANALYSE PARALLELISEE HAUT DEBIT POUR DES APPLICATIONS EN RECHERCHE FONDAMENTALE, BIOMEDICALE ET PHARMACEUTIQUE.

La formation des hadrons est, dans le cadre de la théorie quantique de couleur (QCD), un processus non-perturbatif ; cette caractéristique entraîne d'importantes difficultés théoriques. C'est pourquoi, les mesures expérimentales de fragmentation dans différents noyaux sont une nécessité afin d'obtenir des progrès tangibles dans la compréhension des mécanismes de formation des hadrons. La thèse commence par les bases théoriques nécessaires à une telle approche, suivies des principaux modèles qui lui sont associés.La thèse se poursuit par l'analyse de données de Jefferson Lab obtenues à l'aide d'un faisceau d'électrons de 5 GeV incident sur différentes cibles (2H, C, Al, Fe, Sn et Pb). Les produits de la réaction sont mesurés avec le spectromètre CLAS. Les principaux résultats de cette expérience sont : (a) l'analyse multi-dimensionnelle des observables mesurées, qui permet une meilleure confrontation avec les modèles théoriques et l'extraction d'informations temporelles sur la fragmentation, et (b) l'observation d'une atténuation hadronique non-linéaire en fonction du rayon du noyau cible. Dans une partie plus théorique, le générateur d'événements PyQM, développé dans le but de reproduire les données de la collaboration HERMES, est présenté. Les résultats sont mitigés, en effet la base théorique utilisée ne semble pas s'appliquer au cas étudié, néanmoins certaines caractéristiques des données sont reproduites permettant de comprendre leurs origines parfois inattendues. Enfin, les possibilités d'expériences futures, à Jefferson Lab et dans un collisionneur ion-électron (EIC), sont explorées.

Providing computer-aided support for human analysis of videos has been a battle of extremes. Powerful solutions exist, but they tend to be domain-specific and complex. The user-friendly, simple systems provide little analysis support beyond basic media player functionality. We propose a human-centered, domain-independent solution between these two points. Our proposed model and system, VAST, is based on our experience in two diverse video analysis domains: science and athletics. Multiple-perspective location metadata is used to group related video clips together. Users interact with these clip groups through a novel interaction paradigm ? views. Each view provides a different context by which users can judge and evaluate the events that are captured by the video. Easy conversion between views allows the user to quickly switch between contexts. The model is designed to support a variety of user goals and expertise with minimal producer overhead. To evaluate our model, we developed a system prototype and conducted several rounds of user testing requiring the analysis of volleyball practice videos. The user tasks included: foreground analysis, ambiguous identification, background analysis, and planning. Both domain novices and experts participated in the study. User feedback, participant performance, and system logs were used to evaluate the system. VAST successfully supported a variety of problem solving strategies employed by participants during the course of the study. Participants had no difficulty handling multiple views (and resulting multiple video clips) simultaneously opened in the workspace. The capability to view multiple related clips at one time was highly regarded. In all tasks, except the open-ended portion of the background analysis, participants performed well. However, performance was not significantly influenced by domain expertise. Participants had a favorable opinion of the system?s intuitiveness, ease of use, enjoyability, and aesthetics. The majority of participants stated a desire to use VAST outside of the study, given the opportunity.

Nanobelts are a new class of semiconducting metal oxide nanowires with great potential for nanoscale devices. The present research focuses on the manipulation of SnO₂ nanobelts suspended in ethanol using microfluidics and electric fields. Dielectrophoresis (DEP) was demonstrated for the first time on semiconducting metal oxide nanobelts, which also resulted in the fabrication of a multiple nanobelt device. Detailed and direct real-time observations of the wide variety of nanobelt motions induced by DEP forces were conducted using an innovative setup and an inverted optical microscope. High AC electric fields were generated on a gold microelectrode (~ 20 µm gap) array, patterned on glass substrate, and covered by a ~ 10 µm tall PDMS (polydimethylsiloxane) channel, into which the nanobelt suspension was introduced for performing the DEP experiments. Negative DEP (repulsion) of the nanobelts was observed in the low frequency range (< 100 kHz) of the applied voltage, which caused rigid body motion as well as deformation of the nanobelts. In the high frequency range (~ 1 MHz - 10 MHz), positive DEP (attraction) of the nanobelts was observed. Using a parallel plate electrode arrangement, evidence of electrophoresis was also found for DC and low frequency (Hz) voltages. The existence of negative DEP effect is unusual considering the fact that if bulk SnO₂ conductivity and permittivity values are used in combination with ethanol properties to calculate the Clausius Mossotti factor using the simple dipole approximation theory; it predicts positive DEP for most of the frequency range experimentally studied. A fluidic nanobelt alignment technique was studied and used in the fabrication of single nanobelt devices with small electrode gaps. These devices were primarily used for conducting impedance spectroscopy measurements to obtain an estimate of the nanobelt electrical conductivity. Parametric numerical studies were conducted using COMSOL Multiphysics software package to understand the different aspects of the DEP phenomenon in nanobelts. The DEP induced forces and torques were computed using the Maxwell Stress Tensor (MST) approach. The DEP force on the nanobelt was calculated for a range of nanobelt conductivity values. The simulation results indicate that the experimentally observed behavior can be explained if the nanobelt is modeled as having two components: an electrically conductive interior and a nonconductive outer layer surrounding it. This forms the basis for an explanation of the negative DEP observed in SnO₂ nanobelts suspended in ethanol. It is thought that the nonconductive layer is due to depletion of the charge carriers from the nanobelt surface regions. This is consistent with the fact that surface depletion is a commonly observed phenomenon in SnO₂ and other semiconducting metal oxide materials. The major research contribution of this work is that, since nanostructures have large surface areas, surface dominant properties are important. Considering only bulk electrical properties can predict misleading DEP characteristics.

Les Distributions de Partons Généralisées (GPDs), dont le formalisme a été introduit dans les années 1990, offrent la plus complète description de la structure (en quarks et gluons) du nucléon à ce jour. La Diffusion Compton Profondément Virtuelle (DVCS), qui correspond à l'électroproduction exclusive "dure" de photons sur le nucléon, est un processus clef parmi les réactions donnant accès aux GPDs. Une expérience dédiée à l'étude du DVCS s'est déroulée en 2005 avec le détecteur CLAS de Jefferson Lab, en utilisant un faisceau d'électrons polarisés de 5,776 GeV et une cible d'hydrogène. Pour cette expérience, nous avons construit et utilisé un calorimètre électromagnétique dédié capable de détecter le photon de l'état final. Les données acquises nous ont permis d'étudier le DVCS sur le plus vaste domaine cinématique jamais accédé pour cette réaction jusqu'à présent : 1 < Q² < 4,6 GeV², 0,1 < xB < 0,58, 0,09 < -t < 2 GeV². Les travaux réalisés au cours de cette thèse incluent notamment des travaux de simulation effectués dans le cadre de la préparation de l'expérience, l'étalonnage en temps d'un des sous-systèmes de CLAS, et l'analyse des données dont l'objectif a été l'extraction des sections efficaces non polarisées de la réaction étudiée et de la différence des sections efficaces polarisées, cette dernière observable étant linéairement proportionnelle aux GPDs. Les résultats obtenus sont confrontés aux calculs théoriques du DVCS basés sur une des paramétrisations des GPDs les plus abouties à ce jour.

Aufgabe der Studienarbeit ist die Entwicklung einer Software mit grafischer Benutzeroberfläche, welche es ermöglicht, Farbtesttabellen (color test charts) mit Hilfe des Spektralfotometers Spectrolino der Firma X-Rite Incorporated (ehemals GretagMacbeth GmbH) und dem dazugehörigen XY-Tisch SpectroScan zu messen. Das zu schreibende Programm soll standardisierte und auch nicht standardisierte Testtafeln weitgehend automatisch messtechnisch erfassen können.

In der vorliegenden Arbeit wird eine integrierbare Pumpentechnologie für polymerbasierte mikrofluidische Systeme entwickelt. Ausgehend von den Anforderungen für die Durchführung molekulardiagnostischer Nachweise kommen dabei Fertigungsverfahren zum Einsatz, die sich auch für Einweg-Anwendungen eignen. Das genutzte Aktorprinzip für die integrierten Mikropumpen basiert auf der Elektrolyse von Wasser. Zur besseren technologischen Integrierbarkeit wird das Wasser in Form eines Hydrogels appliziert. Der Elektrolyt wird dabei mit einer Polymermembran mit geringer Wasserdampfdurchlässigkeit verschlossen. Die Membran wird in ihrem plastischen Verformbereich genutzt. Zur Dimensionierung der Mikropumpen und des mikrofluidischen Systems werden analytische und numerische Modelle entwickelt, die eine gute Übereinstimmung mit den Messwerten zeigen. Die Funktionsfähigkeit wird anhand zweier vollständig integriert ablaufender Immunoassays demonstriert. Dabei kommt ein polymerbasierter, optischer Biosensor zum Einsatz.

Oral cancer is the sixth most common cancer worldwide and has been marked by high morbidity and poor survival rates that have changed little over the past few decades. Beyond prevention, early detection is the most crucial determinant for successful treatment and survival of cancer. Yet current methodologies for cancer diagnosis based upon pathological examination alone are insufficient for detecting early tumor progression and molecular transformation. Development of new diagnostic tools incorporating tumor biomarkers could enhance early detection by providing molecular-level insight into the biochemical and cellular changes associated with oral carcinogenesis. The work presented in this doctoral dissertation aims to address this clinical need through the development of new automated cellular analysis methods, incorporating lab-on-a-chip sensor techniques, for examination of molecular and morphological biomarkers associated with oral carcinogenesis. Using the epidermal growth factor receptor (EGFR) as a proof-of-principle biomarker, the sensor system demonstrated capacity to support rapid biomarker analysis in less than one-tenth the time of traditional methods and effectively characterized EGFR biomarker over-expression in oral tumor-derived cell lines. Successful extension from in vitro tumor cell lines to clinically relevant exfoliative brush cytology was demonstrated, providing a non-invasive method for sampling abnormal oral epithelium. Incorporation of exfoliative cytology further helped to define the important assay and imaging parameters necessary for dual molecular and morphological analysis in adherent epithelium. Next, this new sensor assay and method was applied in a small pilot study in order to secure an initial understanding of the diagnostic utility of such biosensor systems in clinical settings. Four cellular features were identified as useful indicators of cancerous or pre-cancerous conditions including, the nuclear area and diameter, nuclear-to-cytoplasm ratio, and EGFR biomarker expression. Further examination using linear regression and ROC curve analysis identified the morphological features as the best predictors of disease while a combination of all features may be ideal for classification of OSCC and pre-malignancy with high sensitivity and specificity. Further testing in a larger sample size is necessary to validate this regression model and the LOC sensor technique, but shows strong promise as a new diagnostic tool for early detection of oral cancer. / text

Optical biosensors are increasingly being considered for lab-on-a-chip applications due to their benefits such as small size, biocompatibility, passive behaviour and lack of the need for fluorescent labels. The light guiding mechanisms used by many of them result in poor overlap of the optical field with the target molecules, reducing the maximum sensitivity achievable. This thesis presents a new platform for optical biosensors, namely slotted photonic crystals, which engender higher sensitivities due to their ability to confine, spatially and temporally, the peak of optical mode within the analyte itself. Loss measurements showed values comparable to standard photonic crystals, confirming their ability to be used in real devices. A novel resonant coupler was designed, simulated, and experimentally tested, and was found to perform better than other solutions within the literature. Combining with cavities, microfluidics and biological functionalization allowed proof-of-principle demonstrations of protein binding to be carried out. High sensitivities were observed in smaller structures than most competing devices in the literature. Initial tests with cellular material for real applications was also performed, and shown to be of promise. In addition, groundwork to make an integrated device that includes the spectrometer function was also carried out showing that slotted photonic crystals themselves can be used for on-chip wavelength specific filtering and spectroscopy, whilst gas-free microvalves for automation were also developed. This body of work presents slotted photonic crystals as a realistic platform for complete on-chip biosensing; addressing key design, performance and application issues, whilst also opening up exciting new ideas for future study.

Polymer foams belong to the solid foams family which are versatile materials, extensively used for a large number of applications such as automotive, packaging, sport products, thermal and acoustic insulators, tissue engineering or liquid absorbents. Composed of air bubbles entrapped in a continuous solid network, they combine the properties of the polymer with those of the foam to create an intriguing and complex material. Incorporating a foam into a polymer network not only allows one to use the wide range of interesting properties that the polymer offers, but also permits to profit from the advantageous properties of foam including lightness, low density, compressibility and high surface-to-volume ratio. Generally, the properties of polymer foams are strongly related to their density and their structure (bubble size and size distribution, bubble arrangement, open vs closed cells). Having a good control over foam properties is thus achieved by first controlling its density and structure.We developed a technique in which solid foams are generated essentially in a two-step process: a sufficiently stable liquid foam with well-controlled structural properties is generated in a first step, and then solidified in a second one. With such a two-step approach, the generation of solid foams can be divided into a number of well-separated sub-tasks which can be controlled and optimised separately. The transition from liquid to solid state is a sensitive issue of a great importance and therefore needs to be controlled with sufficient accuracy. It is essentially composed of three key steps: foam generation, mixing of reactants and foam solidification and requires the optimisation of foam stability in conjunction with an appropriate choice of both foaming time and solidification time. Furthermore, a good homogeneity of the polymer foam calls for a good mixing of the different reactants involved in the foaming and the polymerisation.A particularly powerful demonstration of the advantages of this approach is given by solidifying monodisperse liquid foams generated using millifluidic technique, in which all bubbles have the same size. In a liquid foam, equal-volume bubbles self-order into periodic, close-packed structures under gravity or confinement. As such, monodisperse foams provide simultaneous control over the size and the organisation of the pores in the final solid with an accuracy which is expected to give rise to a better understanding of the structure-property relationship of porous solids and to the development of new porous materials.We therefore aim to explore the new spectrum of properties, which polymer foams offer when we introduce an ordered structure into them since the most widely used polymer foams nowadays have disordered structures. The goal of our study is to demonstrate the feasibility of this two-step approach for different classes of polymers, including biomolecular hydrogel, superabsorbent polymer and polyurethane.For the generation of the structured polymer foams we use Lab-on-a-Chip technologies which allow the "shrinking" of large-scale set-ups to micro/millimetic scale. It permits also to perform "flow chemistry" in which the various liquid and gaseous ingredients of the foam are injected and mixed in a purpose-designed network of the micro- and millifluidic Lab-on-a-Chip. We adjust this approach according to the requirements of each polymer system, i.e. the foaming and the mixing techniques are chosen to fit the properties of each system, and can be exchanged to fit the properties of the studied systems.