Diabetic symmetrical polyneuropathy is the most common secondary complication of diabetes, with no effective treatment, apart from maintaining tight glycemic control. It is therefore essential to understand the mechanisms underlying the pathogenesis of the disease in order to develop new therapeutic strategies. Biochemical and structural changes are observed in the extracellular matrix (ECM) of the peripheral nerve in diabetes: including increased endoneurial collagen; reduplication of basement membranes around endoneurial capillaries; a thickening of basal lamina; and accumulation of advanced glycation end-products (AGEs). In normal nerves, ischaemic or other damage to distal axons provokes a regenerative response; in diabetes this is abortive and failure of axonal regeneration is a hallmark of clinical and experimental diabetic neuropathy. Matrix metalloproteinases (MMPs) are a large family of zinc-dependent proteolytic enzymes that cleave the protein components of the ECM. MMP-2 and MMP-9 play a central role in Wallerian degeneration and regeneration following nerve injury. This thesis investigates whether MMP-2 and -9 expression and/or activity were altered in the peripheral nerve in diabetes, and could contribute to regenerative failure in diabetic neuropathy. Using an experimental model of diabetes, we have demonstrated that MMP-2, but not MMP-9, is upregulated at gene, protein and activity levels in the rat sciatic nerve 8 weeks post-streptozotocin (STZ). This upregulation was not maintained at later time-points of diabetes. In vitro sciatic nerve cryoculture studies showed that peripheral nerve from STZ-diabetic rats was less supportive for neurite outgrowth from dissociated adult rat sensory neurons than nerve obtained from age-matched control rats. Cyrocultures were pre-treated with either MMP-2 or chondroitinase ABC, remodelling the peripheral nerve ECM, via the removal of inhibitory chondroitin sulfate proteoglycans from the sciatic nerve, and significantly enhanced its ability to support axonal regeneration, and partially restored the diabetes-associated regenerative deficit. However, exogenous MMP-2 or MMP-9 did not directly affect neurite outgrowth of dissociated adult rat sensory neurons. Finally, we assessed the neuroprotective effects of the AGE inhibitors LR90 and pyridoxamine in experimental diabetes, using a number of electrophysiological, behavioural and biochemical endpoints. These inhibitors were effective at preventing the development of some of the functional deficits observed in STZ-diabetes. Sensory nerve conduction velocity deficits and lipid peroxidation in the sciatic nerve were prevented by both LR90 and pyridoxamine. These agents have potential for the treatment of diabetic neuropathy.

Matrix metalloproteinases (MMPs) play a significant role in degrading the extracellular matrix in cancer development and metastasis. Overexpression of matrix metalloproteinases in tumour tissues relative to normal tissues has been exploited as a target for peptide-based therapeutics, to improve therapeutic index of currently used agents. The stability of MMP-activated prodrugs in normal tissue or organs is a significant challenge for their success in the clinic. In an in vitro study, the stability of twenty six prodrugs was studied in mouse liver, kidney, lung and tumour homogenates using HPLC and LC/MS. Selected agents were studied in vivo. Each prodrug has a characteristic amino acid sequence with dominant FITC N-terminal end cap. All prodrugs were conjugated to a colchicine derivative (ICT 2552) which is a vascular disrupting agent causing tumour vasculature shutdown and consequently, tumour necrosis. ICT 3146, ICT 3019, ICT 3120 and ICT 3115 prodrugs showed significant stability in normal tissues and considerable activation in certain tumour tissues compared to the lead compound ICT 2588. Also, the selectivity of promising prodrugs to the MMP family was confirmed by using leupeptin (serine, cysteine and threonine protease inhibitor), pepstatin A (aspartate protease inhibitor), phosphoramidon (nepralysin inhibitor), ilomastat (metalloproteinase inhibitor) and BML-P115 (matrix metalloproteinase inhibitor). Moreover, members of the MMP family responsible for cleaving the selected prodrugs were identified using recombinant MMP enzymes. Furthermore, a LC/MS-MS method was developed to specifically detect and quantify MMP-16 protein expression in H460 tumour. MMP- 16 was responsible for the cleavage of ICT 3146 and ICT 3115. Therefore, MMPactivated prodrugs could be a useful therapeutic approach to avoid off-site toxicities of currently used anti-tumour agents.

Clustering techniques play an important role in exploratory pattern analysis, unsupervised pattern recognition and image segmentation applications. Clustering algorithms are computationally intensive in nature. This thesis proposes new parallel algorithms for Single Link and Complete Link hierarchical clustering. The parallel algorithms have been mapped on a SIMD machine model with a linear interconnection network. The model consists of a linear array of N (number of patterns to be clustered) processing elements (PEs), interfaced to a host machine and the interconnection network provides inter-PE and PE-to-host/host-to-PE communication. For single link clustering, each PE maintains a sorted list of its first logN nearest neighbors and the host maintains a heap of the root elements of all the PEs. The determination of the smallest entry in the distance matrix and update of the distance matrix is achieved in O(logN) time. In the case of complete link clustering, each PE maintains a heap data structure of the inter pattern distances. This significantly reduces the computation time for the determination of the smallest entry in the distance matrix during each iteration, from O(N2) to O(N), as the root element in each PE gives its nearest neighbor. The proposed algorithms are faster and simpler than previously known algorithms for hierarchical clustering. For clustering a data set with N patterns, using N PEs, the computation time for the single link clustering algorithm is shown to be O(NlogN) and the time complexity for the complete link clustering algorithm is shown to be O(N2). The parallel algorithms have been verified through simulations on the Intel iPSC/2 parallel machine.

Large silencers used in the power generation industry usually have a very large cross section at the inlet and outlet. Higher-order modes will populate the inlet and outlet even at very low frequencies. Although the silencer itself is often modeled by a three-dimensional analysis tool such as the boundary element method (BEM) or finite element method (FEM), a direct computation of the transmission loss (TL) from the BEM or FEM model can be challenging without incorporating certain forms of modal expansion. A so-called “impedance-to-scattering matrix method” is proposed to extract the modes at the inlet and outlet from the BEM impedance matrix based on the point collocation method. The BEM impedance matrix relates the sound pressures at the inlet and outlet to the corresponding particle velocities, while the scattering matrix relates the modes at the inlet and outlet. Normally there are more boundary elements than the total number of modes at the inlet and outlet, and a least-squares procedure is used to condense the element-based impedance matrix to the mode-based scattering matrix. The TL computation will follow if a certain form of the incident wave is assumed and the outlet is non-reflective. Several commonly used inlet/outlet configurations are considered in this dissertation, which include axisymmetric, non-axisymmetric circular, and rectangular inlet/outlet shapes. In addition to the single inlet and outlet silencers, large multi-inlet and multi-outlet silencers are also investigated. Besides the collocation-based impedance-to-scattering matrix method, an integral-based impedance-to-scattering matrix method based on the reciprocal identity is also proposed for large silencer analysis. Although it may be more time-consuming to perform the additional numerical integration, an integral-based method is free of any uncertainties associated with collocation points. The computational efficiency, accuracy and stability are compared between two proposed methods. One bonus effect of producing the scattering matrix is that it can also be used to combine subsystems in series connection. The Redheffer’s star product is introduced to combine scattering matrices of subsystems. In the design stage, rapid assessment of the silencer performance is always preferred. However, the existing analytical approaches are only suitable for simple dissipative silencers such as straight lined ducts. A two-dimensional first-mode semi-analytical solution is developed to quickly evaluate the performance of tuned dissipative silencers below the cut-off frequency. The semi-analytical solution can also serve as a validation tool for the BEM.

L'objectif de ce travail est de développer et d'évaluer des approches méthodologiques pour la prédiction de séquences cis-régulatrices. Ces approches ont été intégrées dans la suite logicielle RSAT (Regulatory Sequences Analysis Tools). Ces séquences jouent un rôle important dans la régulation de l'expression des gènes. Cette régulation, au niveau transcriptionnel, s'effectue à travers la reconnaissance spécifique entre les facteurs de transcription et leurs sites de fixation (TFBS) au niveau de l'ADN. Nous avons développé et évalué une série d'outils bioinformatiques qui utilisent les matrices position-poids pour prédire les TFBS ainsi que les modules cis-régulateurs (CRM). Nos outils présentent l'avantage d'intégrer les différentes approches déjà proposées par d'autres auteurs tout en proposant des fonctionnalités innovantes. Nous proposons notamment une nouvelle approche pour la prédiction de CRM basé sur la détection de régions significativement enrichies en TFBS. Nous les avons appelés les CRER (pour Cis-Regulatory Elements Enriched Regions). Un autre aspect essentiel de toute notre approche réside dans le fait que nous proposons des mesures statistiques rigoureuses pour estimer théoriquement et empiriquement le risque associé aux différentes prédictions. Les méthodes de prédictions de séquences cis-regulatrices prédisent en effet un taux de fausses prédictions généralement élevé. Nous intégrons un calcul des P-valeurs associées à toutes les prédictions. Nous proposons ainsi une mesure fiable de la probabilité de faux positifs. Nous avons appliqué nos outils pour une évaluation systématique de l'effet du modèle de background sur la précision des prédictions à partir de la base de données de TRANSFAC. Nos résultats suggèrent une grande variabilité pour les modèles qui optimisent la précision des prédictions. Il faut choisir le modèle de background au cas par cas selon la matrice considérée. Nous avons ensuite évalué la qualité des matrices de tous les facteurs de transcription de drosophile de la base de données ORegAnno, c'est à dire leur pouvoir de discrimination entre les TFBS et les séquences génomiques. Nous avons ainsi collecté des matrices des facteurs de transcription de drosophile de bonne qualité. A partir des matrices de drosophile que nous avons collectées, nous avons entamé une analyse préliminaire multi-genome de prédictions de TFBS et de CRM dans la région de lʼenhancer dorsocentral (DCE) du complexe achaete-scute de drosophile. Les gènes de ce complexe jouent un rôle important dans la détermination des cellules système nerveux périphérique de drosophile. Il a été prouvé expérimentalement qu'il existe un lien direct entre le phénotype du système nerveux périphérique et les séquences cis-régulateurs des gènes de ce complexe. Les outils que nous avons développés durant ce projet peuvent s'appliquer à la prédiction des séquences de régulation dans les génomes de tous les organismes.

Husqvarna is a Swedish company producing products for forestry, park and gardens. Due to harder competition they wish to increase efficacy in production. This can be achieved by shorter lead-times in the complex process of making casting molds. Activities within this process have certain relations and dependencies between each other that can be analyzed by using a Dependence Structure Matrix. The Dependence Structure Matrix is a tool that can improve efficiency by rearranging activities according to how they are dependent of each other. The purpose is to make a Dependence Structure Matrix of activities that Husqvarna can use to analyze dependencies within the process of cast molding. The DSM Matrix will propose restructured activities of the process which can be evaluated to determine if greater efficacy can be reached. To determine the activities within the process of making cast molds a workshop at Husqvarna for the people involved was conducted. A matrix has been constructed based on the information of activities and their dependencies. This information has then been analyzed by the software Multiplan. The process of making casting molds could be analyzed by the DSM/DMM approach. A new order of how to carry out activities is the outcome of the analysis. The result can be analyzed by Husqvarna in order to determine if greater efficacy can be reached.

The capacitor test process at ABB Capacitors in Ludvika must be improved to meet future demands for high voltage products. To find a solution to how to improve the test process, an investigation was performed to establish which parts of the process are used and how they operate. Several parts which can improves the process were identified. One of them was selected to be improved in correlation with the subject, mechanical engineering. Four concepts were generated and decision matrixes were used to systematically select the best concept. By improving the process several benefits has been added to the process. More units are able to be tested and lead time is reduced. As the lead time is reduced the cost for each unit is reduced, workers will work less hours for the same amount of tested units, future work to further improve the process is also identified. The selected concept was concept 1, the sway stop concept. This concept is used to reduce the sway of the capacitors as they have entered the test facility, the box. By improving this part of the test process a time saving of 20 seconds per unit can be achieved, equivalent to 7% time reduction. This can be compared to an additional 1400 units each year.

Development of the secondary palate (SP) is a complex event despite the small area it encompasses. Problems with SP development can lead to a cleft palate, which is one of the most common birth disorders. The matrix metalloproteinases (MMPs) are required for proper SP development, but a functional role for any one of them remains unknown. MMP-25 is a candidate MMP to have a functional role in SP formation as genetic scans of the DNA of human cleft palate patients indicate a common mutation at a region upstream of the Mmp-25 gene. The purpose of this thesis is to investigate gene expression of Mmp-25 in the developing mouse SP, whether it has a functional role in mouse SP development and begin to identify factors potentially upstream of Mmp-25 expression.<p> Mmp-25 mRNA and protein is found at all SP developmental stages in mice with highest expression at embryonic day (E) 13.5 when analyzed by quantitative real-time PCR and western blotting. Immunohistochemistry localizes MMP-25 protein primarily to the plasma membranes of palate shelf epithelial cells with secondary expression in apical mesenchymal cells. Mmp-25 knockdown with siRNA in palatal cultures resulted in a significant decrease in palate shelf fusion and persistence of the medial edge epithelium in vitro. Mmp-25 mRNA and protein levels are significantly decreased in vitro when cultured palate shelves are incubated in growth medium with 5 ìg/ml of a TGFâ3-neutralizing antibody. Mmp-25 gene expression is highest at E12.5 and E13.5, which corresponds to increasing palate shelf growth downward alongside the tongue. Immunohistochemistry localized MMP-25 protein expression predominantly in the epithelium of the palate shelves, but also in areas of the mesenchyme that were immediately adjacent to the epithelium and apical in location. Knockdown of Mmp-25 expression resulted in palate shelf fusion being impaired and significant medial edge epithelium remaining in contacted areas. Bioneutralization of TGFâ3 resulted in a significant decrease in Mmp-25 gene expression. These data suggest a functional role for MMP-25 in mouse SP development by removing extra-cellular matrix barriers to increased palate shelf growth and place its expression downstream of TGF-â3 signaling. This is the first research to present a role for a single MMP in mouse SP development.

Complex products are comprised of a large number of tightly integrated components, assemblies and systems resulting in extensive logical and physical interdependences between the constituent parts. Thus a change to one item of a system is highly likely to lead to a change to another item, which in turn can propagate further. The aim of this research therefore is to investigate dependency models that can be used to identify the impact and trace thepropagation of changes in different information domains, such as requirements, physical product architecture or organisation. Cont/d.

Development of the secondary palate (SP) is a complex event despite the small area it encompasses. Problems with SP development can lead to a cleft palate, which is one of the most common birth disorders. The matrix metalloproteinases (MMPs) are required for proper SP development, but a functional role for any one of them remains unknown. MMP-25 is a candidate MMP to have a functional role in SP formation as genetic scans of the DNA of human cleft palate patients indicate a common mutation at a region upstream of the Mmp-25 gene. The purpose of this thesis is to investigate gene expression of Mmp-25 in the developing mouse SP, whether it has a functional role in mouse SP development and begin to identify factors potentially upstream of Mmp-25 expression.<p> Mmp-25 mRNA and protein is found at all SP developmental stages in mice with highest expression at embryonic day (E) 13.5 when analyzed by quantitative real-time PCR and western blotting. Immunohistochemistry localizes MMP-25 protein primarily to the plasma membranes of palate shelf epithelial cells with secondary expression in apical mesenchymal cells. Mmp-25 knockdown with siRNA in palatal cultures resulted in a significant decrease in palate shelf fusion and persistence of the medial edge epithelium in vitro. Mmp-25 mRNA and protein levels are significantly decreased in vitro when cultured palate shelves are incubated in growth medium with 5 ìg/ml of a TGFâ3-neutralizing antibody. Mmp-25 gene expression is highest at E12.5 and E13.5, which corresponds to increasing palate shelf growth downward alongside the tongue. Immunohistochemistry localized MMP-25 protein expression predominantly in the epithelium of the palate shelves, but also in areas of the mesenchyme that were immediately adjacent to the epithelium and apical in location. Knockdown of Mmp-25 expression resulted in palate shelf fusion being impaired and significant medial edge epithelium remaining in contacted areas. Bioneutralization of TGFâ3 resulted in a significant decrease in Mmp-25 gene expression. These data suggest a functional role for MMP-25 in mouse SP development by removing extra-cellular matrix barriers to increased palate shelf growth and place its expression downstream of TGF-â3 signaling. This is the first research to present a role for a single MMP in mouse SP development.