This study presents two computer vision based algorithms for automated 2D detection of construction workers and equipment from site video streams. The state-of-the-art research proposes semi-automated detection methods for tracking of construction workers and equipment. Considering the number of active equipment and workers on jobsites and their frequency of appearance in a camera's field of view, application of semi-automated techniques can be time-consuming. To address this limitation, two new algorithms based on Histograms of Oriented Gradients and Colors (HOG+C), 1) HOG+C sliding detection window technique, and 2) HOG+C deformable part-based model are proposed and their performance are compared to the state-of-the-art algorithm in computer vision community. Furthermore, a new comprehensive benchmark dataset containing over 8,000 annotated video frames including equipment and workers from different construction projects is introduced. This dataset contains a large range of pose, scale, background, illumination, and occlusion variation. The preliminary results with average performance accuracies of 100%, 92.02%, and 89.69% for workers, excavators, and dump trucks respectively, indicate the applicability of the proposed methods for automated activity analysis of workers and equipment from single video cameras. Unlike other state-of-the-art algorithms in automated resource tracking, these methods particularly detects idle resources and does not need manual or semi-automated initialization of the resource locations in 2D video frames. / Master of Science

Human Artificial Chromosomes (HACs) have been confirmed as viable gene expression vectors and a potential tool for gene therapy. However, standard lipid-based delivery methods pose a developmental barrier. The work presented in this thesis includes the development of a novel and efficient HAC vector system for gene delivery into human cells using Herpes Simplex Virus-1 (HSV-1) amplicon technology. The development of HSV-1 amplicons for HAC delivery is a major step forward in the HAC field. In this study, utilising the technology allowed the generation of HACs at a high efficiency in a range of human cell types, which is a significant step in the development for HAC gene expression systems. Further work also showed a significant difference in HAC stability between cell lines. Real-time PCR analysis determined that Aurora B was over expressed in cell lines in which the HACs were unstable. This correlated with high levels of chromosomal instability and was confirmed by western blot analysis. Since Aurora B is a kinase involved in at least two cell cycle checkpoints, cellular phosphorylation levels were perturbed to mimic that observed in the unstable cells, using okadaic acid, which is both a protein phosphatase inhibitor and activates Aurora B. Treatment of cells showed an increase in both HAC and overall chromosomal instability and an increase in histone H3 Serine 10 and Serine 28 phosphorylation. The project also focussed on the development of a gene expression system using HSV-1 amplicons. Two different strategies were explored. Firstly, one approach involved engineering the HPRT genomic locus into an HSV-HAC vector, by Red mediated recombination for complementing the HPRT deficiency in HPRT- HT1080 cells. As an alternative approach, co-infection of two different HSV-1 HAC amplicons for generating a single HAC gene vector was investigated. Initial experiments utilising the latter approach were the most successful and show promise for generating HAC containing genes via this strategy.

Pour compléter leur cycle de vie, les virus interagissent avec de nombreux facteurs de la cellule-hôte. Le virus Herpès simplex de type 1 (HSV-1) ne fait pas exception. Une récente étude protéomique du virus effectuée par notre laboratoire a permis d’identifier 49protéines cellulaires potentiellement incorporées dans les virions matures d’HSV-1 [1]. Étant donné que certaines de ces protéines peuvent jouer des rôles importants au cours du cycle de vie du virus, elles constituent des cibles de choix pour identifier et caractériser de nouvelles interactions hôte-pathogène dans le contexte d’HSV-1. D’ailleurs le laboratoire a été effectué un criblage aux petits ARN d’interférence qui a démontré qu'au moins 15 des protéines incorporées sont impliqués dans le cycle de réplication de HSV-1 en culture cellulaire (Annexe 1). Des nombreuses études rapportent l'incorporation des protéines de l'hôte dans les virions matures mais très peu abordent l'importance de la fraction des protéines cellulaires incorporée dans les virions pour le cycle virale. Pour vérifier ça, nous avons déplété ces protéines des virions matures extracellulaires en utilisant des petits ARN d’interférence. Par la suite, nous avons utilisé ces virus déplétés pour réinfecter des cellules déplétées ou normales. Cette méthode nous a permis d'identifier pour la première fois 8 protéines (DDX3X, HSPA8, KRT10, MIF, Rab5A, Rab6A, Rab10 et 14-3-3ζ) dont l'absence dans les virions réduit la production virale d'au moins 50%. Pour mieux comprendre à quelle étape du cycle viral ces protéines sont nécessaires, nous avons aussi quantifié les virus intracellulaires, produits des cellules déplétées individuellement des quinze protéines cellulaires. Ainsi, nous avons trouvé que dans nos conditions 7 de ces 8 protéines cellulaires (DDX3X, HSPA8, KRT10, MIF, Rab5A, Rab6A et Rab10) semblent impliquées dans la production des virus intracellulaires, ce qui nous a stimulés à débuter une série de tests plus approfondis de l’entrée d’HSV-1. Les résultats préliminaires, démontrent l’implication dans l’entrée d’HSV-1 d’au moins 3 à 4 de ces protéines (HSPA8, KRT10, Rab5A et Rab10). / To complete their life cycle viruses interact with many factors of the host cell. Herpes simplex virus type 1 (HSV-1) is no exception. A recent proteomic study of the virus carried by our laboratory has identified up to 49 cellular proteins potentially incorporated into the mature virions of HSV-1[1]. Since some of these proteins may play important roles during the viral life cycle, they are interesting targets for identification and characterization of new host-pathogen interactions in the context of HSV-1. To target the proteins that are relevant to the viral life cycle of Herpes, the laboratory performed a screening with small interfering RNAs (siRNAs), which showed that at least 15 incorporated proteins are involved in the replication cycle of HSV- 1 in cell culture (Appendix 1). Numerous studies report the incorporation of host proteins in mature virions but few addresses the importance for the viral infectivity of the fractions of cellular proteins incorporated into the virions. To verify this, we depleted these proteins from the mature extracellular virions using siRNAs. Subsequently, we used these viruses to re-infect depleted or normal cells. This method allowed us to identify for the first time eight proteins (DDX3X, HSPA8, KRT10, MIF, Rab5A, Rab6A, Rab10 and 14-3-3ζ) whose absence in virions reduced viral production by at least 50%. As part of understanding at what stage of the life cycle these proteins are necessary for HSV-1, we tested the infectivity of intracellular depleted viruses. Thus, we found at least seven cellular proteins (DDX3X, HSPA8, KRT10, MIF, Rab5A, Rab6A and Rab10) to have a pronounced effect on the replication of herpes virus, which has stimulated us to begin a series of more in-depth tests of the entry of HSV-1. Preliminary results demonstrate the involvement in the entry of HSV-1 of at least three to four proteins (HSPA8, KRT10, Rab5A and Rab10).

La rencontre entre une couche limite laminaire se développant sur une plaque plane sous une surface libre et un obstacle rectangulaire émergent mène à l’apparition d’une zone de recirculation complexe appelée tourbillon en fer à cheval à l’amont de l’obstacle. Cette zone de recirculation est composée d’un certain nombre de vortex s’enroulant autour de l’obstacle et pouvant présenter des dynamiques variées. Le but de ce travail est de réaliser une étude expérimentale paramétrique du tourbillon en fer à cheval laminaire et faiblement turbulent. Les mesures sont réalisées par PIV et par trajectographies et des méthodes de détection basés sur la décomposition modale (POD) et la détection des points critiques sont utilisées afin de faciliter l’étude de la dynamique tourbillonnaire. Ce manuscrit se propose de : (i) Déterminer l’évolution des caractéristiques du tourbillon en fer à cheval en fonction des paramètres adimensionnels de l’écoulement. (ii) Mettre en place une typologie des différentes dynamiques exhibées. (iii) Déterminer les mécanismes à l’origine de l’apparition de ces différentes dynamiques à l’aide d’un modèle conceptuel. (iv) Et finalement, étudier l’influence de la longueur de l’obstacle sur le tourbillon en fer à cheval. / A laminar boundary layer developing under a free-surface and interacting with an emerging obstacle lead to the creation of a complex recirculation zone called horseshoe vortex upstream from the obstacle. This recirculation zone is composed of a given number of vortices wrapping around the obstacle with various kind of dynamics. The aim of this work is to perform an experimental parametric study of the laminar, and slightly turbulent horseshoe vortex. Measurements are obtained by PIV and trajectographies and detection method based on modal decomposition (POD) and critical points are used to ease the study of the vortex dynamics. This manuscript intends to : (i) Explain the horseshoe vortex main characteristics evolution with the non-dimensional parameters of the flow. (ii) Define a typology of the different observed vortex dynamics. (iii) Identify the physical mechanisms at the origin of those dynamics through the use of a conceptual model. (iv) And finally, show the influence of the obstacle length on the horseshoe vortex.

B virus (Macacine herpesvirus 1, Cercopithecine herpesvirus 1, herpes B virus) is an Old World monkey simplex virus endemic in macaques. B virus infection in its natural host, macaque, is very similar to HSV-­‐1 infection in humans causing mild or asymptomatic infection. On the other hand, zoonotic infection in humans results in death in the absence of early initiation of antiviral drugs. Viruses evade host immune responses in order to survive and propagate. Most herpes viruses including HSV-­‐1 down-­‐regulate major histocompatibility complex class I (MHC class I) surface expression on infected cells in order to prevent CD8+ T-­‐cell recognition and subsequent cell lysis. MHC class I molecules bind to the inhibitory receptors of NK cells and prevent NK cell activity. Thus, this mechanism protects HSV-­‐1 infected cells from CD8+ T-­‐cell lysis, making them sensitive to natural killer (NK) cell cytotoxicity. To investigate if B virus pathogenicity is a result of novel immune evasion mechanisms employed by B virus, we determined NK cell regulation during B virus infection. To this end, our experiments demonstrate that B virus does not down-­‐ regulate MHC I expression as effectively as HSV-­‐1, leading us to hypothesize that B virus in-­‐ fected cells are resistant to NK cell activity. We examined the expression of MHC I chain related genes (MICA/ MICB), which are activation ligands to NKG2D receptors on NK cells. Our results show that there is no significant difference in MICA and MICB expression between HSV-­‐1 and B virus infected cells. Furthermore, we tested for the up-­‐regulation of cytokines and chemokines responsible for NK cell activation and migration. Our results indicate a significant up-­‐regulation of IFN-­‐α from PBMCs co-­‐cultured with HSV-­‐1 infected cells, which plays an important role in activating NK cells. NK cells within these PBMCs up-­‐regulate perforin release indicative of NK cell activity. PBMCs co-­‐cultured with B virus infected cells do not up-­‐regulate any cytokines or chemokines responsible for NK cell activity. As a result the NK cells within these PBMCs do not significantly up-­‐regulate perforin release. These results demonstrate that B virus employs a novel immune evasion mechanism to subvert NK cell activity.

In this thesis, it is proposed to get the high definition color images by using super &ndash / resolution algorithms. Resolution enhancement of RGB, HSV and YIQ color domain images is presented. In this study, three solution methods are presented to improve the resolution of HSV color domain images. These solution methods are suggested to beat the color artifacts on super resolution image and decrease the computational complexity in HSV domain applications. PSNR values are measured and compared with the results of other two color domain experiments. In RGB color space, super &ndash / resolution algorithms are applied three color channels (R, G, B) separately and PSNR values are measured. In YIQ color domain, only Y channel is processed with super resolution algorithms because Y channel is luminance component of the image and it is the most important channel to improve the resolution of the image in YIQ color domain. Also, the third solution method suggested for HSV color domain offers applying super resolution algorithm to only value channel. Hence, value channel carry brightness data of the image. The results are compared with the YIQ color domain experiments. During the experiments, four different super resolution algorithms are used that are Direct Addition, MAP, POCS and IBP. Although, these methods are widely used reconstruction of monochrome images, here they are used for resolution enhancement of color images. Color super resolution performances of these algorithms are tested.

Pour compléter leur cycle de vie, les virus interagissent avec de nombreux facteurs de la cellule-hôte. Le virus Herpès simplex de type 1 (HSV-1) ne fait pas exception. Une récente étude protéomique du virus effectuée par notre laboratoire a permis d’identifier 49protéines cellulaires potentiellement incorporées dans les virions matures d’HSV-1 [1]. Étant donné que certaines de ces protéines peuvent jouer des rôles importants au cours du cycle de vie du virus, elles constituent des cibles de choix pour identifier et caractériser de nouvelles interactions hôte-pathogène dans le contexte d’HSV-1. D’ailleurs le laboratoire a été effectué un criblage aux petits ARN d’interférence qui a démontré qu'au moins 15 des protéines incorporées sont impliqués dans le cycle de réplication de HSV-1 en culture cellulaire (Annexe 1). Des nombreuses études rapportent l'incorporation des protéines de l'hôte dans les virions matures mais très peu abordent l'importance de la fraction des protéines cellulaires incorporée dans les virions pour le cycle virale. Pour vérifier ça, nous avons déplété ces protéines des virions matures extracellulaires en utilisant des petits ARN d’interférence. Par la suite, nous avons utilisé ces virus déplétés pour réinfecter des cellules déplétées ou normales. Cette méthode nous a permis d'identifier pour la première fois 8 protéines (DDX3X, HSPA8, KRT10, MIF, Rab5A, Rab6A, Rab10 et 14-3-3ζ) dont l'absence dans les virions réduit la production virale d'au moins 50%. Pour mieux comprendre à quelle étape du cycle viral ces protéines sont nécessaires, nous avons aussi quantifié les virus intracellulaires, produits des cellules déplétées individuellement des quinze protéines cellulaires. Ainsi, nous avons trouvé que dans nos conditions 7 de ces 8 protéines cellulaires (DDX3X, HSPA8, KRT10, MIF, Rab5A, Rab6A et Rab10) semblent impliquées dans la production des virus intracellulaires, ce qui nous a stimulés à débuter une série de tests plus approfondis de l’entrée d’HSV-1. Les résultats préliminaires, démontrent l’implication dans l’entrée d’HSV-1 d’au moins 3 à 4 de ces protéines (HSPA8, KRT10, Rab5A et Rab10). / To complete their life cycle viruses interact with many factors of the host cell. Herpes simplex virus type 1 (HSV-1) is no exception. A recent proteomic study of the virus carried by our laboratory has identified up to 49 cellular proteins potentially incorporated into the mature virions of HSV-1[1]. Since some of these proteins may play important roles during the viral life cycle, they are interesting targets for identification and characterization of new host-pathogen interactions in the context of HSV-1. To target the proteins that are relevant to the viral life cycle of Herpes, the laboratory performed a screening with small interfering RNAs (siRNAs), which showed that at least 15 incorporated proteins are involved in the replication cycle of HSV- 1 in cell culture (Appendix 1). Numerous studies report the incorporation of host proteins in mature virions but few addresses the importance for the viral infectivity of the fractions of cellular proteins incorporated into the virions. To verify this, we depleted these proteins from the mature extracellular virions using siRNAs. Subsequently, we used these viruses to re-infect depleted or normal cells. This method allowed us to identify for the first time eight proteins (DDX3X, HSPA8, KRT10, MIF, Rab5A, Rab6A, Rab10 and 14-3-3ζ) whose absence in virions reduced viral production by at least 50%. As part of understanding at what stage of the life cycle these proteins are necessary for HSV-1, we tested the infectivity of intracellular depleted viruses. Thus, we found at least seven cellular proteins (DDX3X, HSPA8, KRT10, MIF, Rab5A, Rab6A and Rab10) to have a pronounced effect on the replication of herpes virus, which has stimulated us to begin a series of more in-depth tests of the entry of HSV-1. Preliminary results demonstrate the involvement in the entry of HSV-1 of at least three to four proteins (HSPA8, KRT10, Rab5A and Rab10).

Herpesviruses have co-speciated with several vertebrate and invertebrate animals throughout the history of evolution. In the immunocompetent human host, primary infection is usually benign, whereafter the virus is brought into life-long latency. Viral reactivation can however cause severe disease in immunocompromised, and rarely also in immunocompetent, patients. The overall aim of this thesis was to study the immunologic effects of cytomegalovirus (CMV) and herpes simplex type 1 (HSV-1) infection in neurocognitive disorders. CMV is known to promote T-cell differentiation towards a more effector-oriented phenotype, similar to what is seen in the elderly. We have addressed the frequency of CMV-specific CD8+ T-cells in Alzheimer's disease (AD). Furthermore, we have investigated whether AD patients present with a different CMV-specific immune profile, overall CD8 phenotype or inflammatory cytokine response to anti-CD3/CD28 beads, CMV pp65 and amyloid beta. Subjects with AD presented with a lower proportion of CMV-specific CD8+ T-cells compared to non-demented (ND) controls, but no differences in overall CD8 differentiation were seen. Overall, AD subjects presented with a more pro-inflammatory peripheral blood mononuclear cell (PBMC) phenotype. When PBMCs were challenged with CD3/CD28-stimulation, CMV seropositive AD subjects presented with more IFN-γ release than both CMV seronegative AD subjects and CMV seropositive ND controls. For effective screening of humoral herpesvirus immunity, both in research and in clinical practice, efficient immunoassays are needed. We have addressed the methodology of multiplex herpesvirus immunoassays and related bioinformatics and investigated antibody levels in AD patients and ND controls. Subjects with AD presented with lower levels of human herpesvirus 6 (HHV-6) IgG. However, there was no difference in HHV-6 DNA levels in PBMCs between the groups. Herpes simplex encephalitis (HSE) is a devastating disease, where antiviral treatment has greatly decreased mortality but not eliminated the associated long-term neurocognitive morbidity. We have investigated the correlation between N-Methyl-D-Aspartate Receptor (NMDAR) autoimmunity and recovery of neurocognitive functions after HSE. Approximately one quarter of all HSE cases developed NMDAR autoantibodies within 3 months after onset of disease. Antibody development was associated with an impaired neurocognitive recovery during the two year follow-up and could become an important therapy guiding factor in the future.

Herpes simplex virus type 1 (HSV-1) is a double stranded DNA virus that causes epithelial skin infections and persists through the life of the host by infecting neurons, where it can switch to a latent state to evade an immune response. In rare cases during primary infection or after reactivation, instead of undergoing lytic infection at the epithelial surface, it instead travels to the brain and causes herpes simplex virus encephalitis (HSVE) which can have a ≥70% mortality rate if untreated. As the virus takes over its host cell, it gains control of the host cell machinery and manipulates host gene expression in order to evade the immune system and to pool its resources into the replication of the virus. One aspect of the dysregulated gene expression involves microRNAs (miRNAs). MiRNAs are short, non-coding RNAs that bind to the 3' untranslated region (3'UTR) of messenger RNAs (mRNAs), leading to translational repression of the target. Dysregulated miRNAs are often down-regulated during infection as the virus takes over, but many miRNAs have also been found to be up-regulated as well1–5. The aim of this study is to observe the full cellular miRNA changes in the context of an acute viral encephalitic infection using HSV-1, and to further characterize selected up-regulated miRNAs to determine their function in the context of the disease state. Of particular note were miR-141 and miR-200c which showed anti-apoptotic effects on neuronal cell culture and did not impact cell viability during an over-expression of the miRNAs. MiR-141, miR-183 and miR-200a expression was enriched within specific areas of the brain during infection. In addition, the potential for miR-150 to bind to a bioinformatically predicted target site within the shared 3'UTR of the HSV-1 UL18, UL19 and UL20 genes was explored. Examining the changes in expression of this class of regulatory RNAs and investigating their potential functions may yield new insight into the relationship between host and virus during infection.

Deux différents types de vecteurs, les nanocapsules lipidiques (LNC) et les systèmes multimodulaires (MMS) ont été développés pour l'administration par voie systémique de deux types d'acides nucléiques, l'ADN et les petits ARN à interférence (siRNA). Ces vecteurs sont formulés à base de complexes d'acides nucléiques et de lipides cationiques (lipoplexes) qui ont été soit encapsulés au coeur des LNC, soit recouverts de stabilisateurs stériques afin de former des MMS. Une partie du travail a consisté à développer des vecteurs de siRNA et à les caractériser par des méthodes physico-chimiques. En fonction du lipide cationique utilisé, jusqu'à 65% de siRNA ont pu être encapsulés dans les LNC, en présentant des caractéristiques appropriées pour une administration par voie systémique. La seconde partie a consisté à approfondir la caractérisation des vecteurs d'ADN et à analyser leur profil de distribution en utilisant de l'imagerie par fluorescence in vivo. Chez la souris saine, les vecteurs d'ADN ont présenté des profils de biodistribution spécifiques à leur composition. Sur deux modèles tumoraux (gliome sous-cutané et mélanome), les vecteurs ayant un temps de circulation prolongé ont également montré une co-localisation intéressante avec les cellules tumorales. Afin de mettre en évidence l'efficacité de ces vecteurs, un plasmide codant pour la tymidine kinase du virus herpes simplex (HSV-tk) a été encapsulé et administré. Puis un traitement par le ganciclovir (GCV) basé sur l'approche par gène suicide a été effectué. Les premiers résultats sont concluants, montrant une baisse de croissance tumorale après quelques jours de traitement aussi bien dans le modèle de gliome que dans celui du mélanome. Ces résultats indiquent que ces outils sont prometteurs pour une variété d'applications en thérapie génique.