Les caméras multispectrales échantillonnent le spectre du visible et/ou de l'infrarouge selon des bandes spectrales étroites. Parmi les technologies disponibles, Les caméras snapshot équipées d'une mosaïque de filtres acquièrent des images brutes à cadence vidéo. Ces images brutes nécessitent un processus de dématriçage permettant d'estimer l'image multispectrale en pleine définition. Dans ce manuscrit nous examinons les méthodes de dématriçage multispectrale et proposons une nouvelle méthode basée sur l'image panchromatique. De plus, nous mettons en évidence l'influence de l'illumination sur les performances de dématriçage, puis nous proposons des étapes de normalisation rendant ce dernier robuste aux propriétés d'acquisition. Les résultats expérimentaux montrent que notre méthode fournit de meilleurs résultats que les méthodes classiques.Afin d'effectuer une analyse de texture, nous étendons les opérateurs basés sur les motifs binaires locaux aux images de texture multispectrale au détriment d'exigences de mémoire et de calcul accrues. Nous proposons alors de calculer les descripteurs de texture directement à partir d'images brutes, ce qui évite l'étape de dématriçage tout en réduisant la taille du descripteur. Afin d'évaluer la classification sur des images multispectrales, nous avons proposé la première base de données multispectrale de textures proches dans les domaines spectraux du visible et du proche infrarouge. Des expériences approfondies sur cette base montrent que le descripteur proposé a à la fois un coût de calcul réduit et un pouvoir de discrimination élevé en comparaison avec les descripteurs classiques appliqués aux images dématriçées. / Multispectral cameras sample the visible and/or the infrared spectrum according to narrow spectral bands. Available technologies include snapshot multispectral cameras equipped with filter arrays that acquire raw images at video rate. Raw images require a demosaicing procedure to estimate a multispectral image with full spatio-spectral definition. In this manuscript we review multispectral demosaicing methods and propose a new one based on the pseudo-panchromatic image. We highlight the influence of illumination on demosaicing performances, then we propose pre- and post-processing normalization steps that make demosaicing robust to acquisition properties. Experimental results show that our method provides estimated images of better objective quality than classical ones.Multispectral images can be used for texture classification. To perform texture analysis, we extend local binary pattern operators to multispectral texture images at the expense of increased memory and computation requirements. We propose to compute texture descriptors directly from raw images, which both avoids the demosaicing step and reduces the descriptor size. In order to assess classification on multispectral images we have proposed the first significant multispectral database of close-range textures in the visible and near infrared spectral domains. Extensive experiments on this database show that the proposed descriptor has both reduced computational cost and high discriminating power with regard to classical local binary pattern descriptors applied to demosaiced images.

Dans les derniers 20 ans, les expériences de traction sur molécule unique par l’action d’une force mécanique ont donné plein d’informations autour des propriétés mécaniques des biomolécules, des modifications structurelles induites par des contraintes mécaniques, ainsi qu’éclaircir les mécanismes d’adhésion et décohésion des paires ligand-recepteur. Suivant cette analyse microscopique, outre que révéler des propriétés biologiques intéressantes, plusieurs de ces systèmes ont montré une nouvelle face, celle de nouveaux matériaux aux propriétés parfois uniques, et ont notamment induit des spéculations sur leur possibles utilisations dans des dispositif de nanotechnologie. Dans cette thèse, par le biais de simulations de dynamique moléculaire, notamment avec les méthodes dites “steered molecular dynamics” et “umbrella sampling”, nous avons réalisé des études concernant : (a) la caractérisation structurelle et mécanique de fragments d’ADN atypiques, comme le tétramère dénommé i-motif, ainsi que (b) la reconstruction des profils d’énergie libre de la liaison et dissociation entre des paires bromodomaine – queues d’histone acétylés (H3 et H4). Nous avons ainsi étudié la structure moléculaire de ces nanostructures particulières d’ADN, formées par l’intercalation de quatre brins d’ADN en un tétramère, et nous en avons déterminé pour la première fois les propriétés mécaniques de base : module de Young, module de flexion, longueur de persistance, et résistance mécanique. Dans la dernière partie du travail, nous avons étudié la manière d’appliquer ces mêmes méthodes à l’étude de paires ligand-recepteur dans le processus de transcription de l’ADN. Nous avons montré que les expériences simulées de traction, dans lesquelles la paire ligand-recepteur est séparée de manière contrôlée par une force mécanique aux extrémités, peuvent donner des informations sur l’hypersurface d’énergie libre. Nous avons essayé, avec un partiel succès, l’application au cas de l’interaction entre bromodomaines et queues d’histones, dans des conditions comparables aux expériences. / In the past 20 years, single-molecule pulling experiments of biomolecules under mechanical forces provided a wealth of information about the mechanical properties of such molecules, and the structural changes that may happen under stress in mechanical proteins, as well as shedding light upon many receptor-ligand binding and unbinding mechanism. Upon such microscopic analysis, besides revealing interesting biological properties, many such systems appeared as unique novel materials, and suggested routes to include such materials in nanotechnology assembly processes. This thesis reports on our studies of the structural and mechanical characterization of DNA i-motif and free-energy based profiling of bromodomain and acetylated histone tails (H3 and H4) binding and dissociation, by using molecular dynamics simulations, and in particular steered “molecular dynamics” and “umbrella sampling” methods. We studied the molecular structure of a peculiar class of DNA-based nanostructures, the i-motif, resulting from the intercalation of four DNA strands into a tetramer, and obtained for the first time its basic mechanical properties: Young’s modulus, bending modulus, persistence length and mechanical toughness. In a final part of the work, we also studied the applicability of the same computational methods to ligand-binding interactions in DNA trasncription. We showed that simulated pulling experiments on ligand-binding pairs, in which the pair is taken apart in a controlled way, can give informations about its free-energy landscape. We attempted, with mixed success, the application to the case of bromodomain-histone tail interactions under conditions comparable to the experiments.

Understanding the mechanisms that regulate gene expression is a major challenge in biology. One of the most important tasks in this challenge is to identify the transcription factors binding sites (TFBS) in DNA sequences. The common representation of these binding sites is called “motif” and the discovery of TFBS problem is also referred as motif finding problem in computer science. Despite extensive efforts in the past decade, none of the existing algorithms perform very well. This dissertation focuses on this difficult problem and proposes three new methods (MotifEnumerator, PosMotif, and Enrich) with excellent improvements. An improved pattern-driven algorithm, MotifEnumerator, is first proposed to detect the optimal motif with reduced time complexity compared to the traditional exact pattern-driven approaches. This strategy is further extended to allow arbitrary don’t care positions within a motif without much decrease in solvable values of motif length. The performance of this algorithm is comparable to the best existing motif finding algorithms on a large benchmark set of samples. Another algorithm with further post processing, PosMotif, is proposed to use a string representation that allows arbitrary ignored positions within the non-conserved portion of single motifs, and use Markov chains to model the background distributions of motifs of certain length while skipping these positions within each Markov chain. Two post processing steps considering redundancy information are applied in this algorithm. PosMotif demonstrates an improved performance compared to the best five existing motif finding algorithms on several large benchmark sets of samples. The third method, Enrich, is proposed to improve the performance of general motif finding algorithms by adding more sequences to the samples in the existing benchmark datasets. Five famous motif finding algorithms have been chosen to run on the original datasets and the enriched datasets, and the performance comparisons show a general great improvement on the enriched datasets.

Multiple polymerase chain reaction (multiple PCR) is one of the most important techniques in molecular biology. The selection of a suitable set of primers is very important for multiple PCR experiments. The primer selection problem is to minimize the number of primers required to amplify a set of DNA sequences. If the minimum set can be used to amplify the entire target DNA sequences, the experimental costs and time will be reduced. But the primer selection problem was proved to be an NP-complete problem. In this thesis, we develop an efficient heuristic algorithm for selecting a set of primer candidates, each may be able to amplify more than one target sequence. Those primers are called universal primers. The universal primer finding can be viewed as the local motif finding in our method. We modify the score function of the original Gibbs sampler method to find local motifs. The new score function is added a new parameter, weight parameter. The weight parameter can guide the Gibbs sampler method to find local motifs with the local view. Then, the complementary sequences of those local motifs are input into the binary integer programming. Thus we can reduce the size of the solution space. We also test our method on some artificial domains and two gene families. All the results show that we get some improvements on the problem.

RECK(reversion-inducing cysteine-rich protein with Kazal motifs) encodes a membrane-anchored glycoprotein of about 110 kDa with multiple epidermal growth factor-like repeat, four N-glycosylation sites and three Kazal-like domains. RECK functions as a tumor suppressor gene which may inhibit the release and activation of MMP-2 and MMP-9. Previous studies indicated that RECK-mediated suppression of tumor cell invasion is regulated by glycosylation of RECK in human tumor cell lines. However, the anti-cancer action of other functional domains of RECK have not been studied. In the study, We investigated the effects of different functional domains of RECK protein on the invasion of tumor cell lines and on the activation of matrix metalloproteinase. We constructed bacterial expression vector and secretory mammalian expression vector which could produce full-length, Kazal-like motifs 1~3, Kazal-like motifs 2~3 and CKM5 polypeptides. Recombinant proteins were purified and used for treatment of human lung cancer cell lines. We found that treatment of K23 and RECK recombinant proteins resulted in suppression of invasive ability and MMP activity. Moreover,K23 and RECK proteins were found to inhibit the secretion of matrix metallo- protease-9 (MMP-9). K23 also formed a complex with MMP-9 and inhibited its proteolytic activity noncompetitively. Experimental metastasis assay revealed that there were fewer tumor nodule formation in the lungs injected with A549 cells stably expressing K23 than control vector. Thus, these findings indicate that the K23 domain of RECK functions as an inhibitor of tumor invasion and metastasis.

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No description available.

This study of the universal persistence of the mandala motif covers the mandala concept, external mandalas, architectural mandalas, and current manifestations.

The major purpose of this thesis is to present a discussion of the motif of the faithful wife as it appears in the domestic drama of the Elizabethan Age; in addition, an account of the literary history of the theme will be given, in order that the use made of the story in Elizabethan drama may be correctly evaluated.

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.