Les Thrombopénies Induites par l’Héparine (TIH) sont une complication sévère des traitements par l’héparine dues à des IgG qui ciblent le facteur plaquettaire 4 modifié par l’héparine (FP4/H) et induisent une activation cellulaire via FcγRIIA, conduisant à des complications thrombotiques. Nous avons caractérisé 5B9, IgG1 monoclonale chimérique anti-FP4/H mimant parfaitement les anticorps de TIH et qui est donc un excellent outil pour étudier la physiopathologie des TIH. La pathogénicité des anticorps (Ac) de TIH implique leur fixation aux FcγR. Nous avons montré que le clivage de la région charnière des IgG de TIH par IdeS inhibe ces interactions IgG-FcγR et supprime la pathogénicité des Ac. Nous avons aussi construit un Antibody-Drug Conjugate (ADC) antithrombotique, en bioconjuguant le tirofiban (inhibiteur de l’agrégation plaquettaire) et 5B9 déglycosylé grâce à un linker clivable par la thrombine, protéase générée en excès lors d’une TIH. / Heparin Induced Thrombocytopenia (HIT) is a rare but severe complication of heparin treatments. HIT is due to IgG antibodies specific to platelet factor 4 modified by heparin (PF4/H), which activate blood cells, (especially platelets) after binding to FcγRIIA, this process explaining frequent thrombotic complications. We characterized 5B9, a chimeric IgG1 targeting PF4/H and which fully mimics human HIT antibodies. Therefore, 5B9 is a perfect tool for studying the physiopathology of HIT. IgG antibodies to PF4/H are pathogenic by interacting with FcγR. In this regard, we showed that cleavage by IdeS, a bacterial protease, of the hinge of anti-PF4/H IgG, fully suppressed their pathogenicity. Furthermore, we designed an antithrombotic Antibody-Drug Conjugate that combined tirofiban, a GPIIbIIIa inhibitor with deglycosylated 5B9 using a thrombin cleavable linker.

Over the last 25 years, interior-point methods (IPMs) have emerged as a viable class of algorithms for solving various forms of conic optimization problems. Most IPMs use a modified Newton method to determine the search direction at each iteration. The system of equations corresponding to the modified Newton system can often be reduced to the so-called normal equation, a system of equations whose matrix ADA' is positive definite, yet often ill-conditioned. In this thesis, we first investigate the theoretical properties of the maximum weight basis (MWB) preconditioner, and show that when applied to a matrix of the form ADA', where D is positive definite and diagonal, the MWB preconditioner yields a preconditioned matrix whose condition number is uniformly bounded by a constant depending only on A. Next, we incorporate the results regarding the MWB preconditioner into infeasible, long-step, primal-dual, path-following algorithms for linear programming (LP) and convex quadratic programming (CQP). In both LP and CQP, we show that the number of iterative solver iterations of the algorithms can be uniformly bounded by n and a condition number of A, while the algorithmic iterations of the IPMs can be polynomially bounded by n and the logarithm of the desired accuracy. We also expand the scope of the LP and CQP algorithms to incorporate a family of preconditioners, of which MWB is a member, to determine an approximate solution to the normal equation. For the remainder of the thesis, we develop a new preconditioning strategy for solving systems of equations whose associated matrix is positive definite but ill-conditioned. Our so-called adaptive preconditioning strategy allows one to change the preconditioner during the course of the conjugate gradient (CG) algorithm by post-multiplying the current preconditioner by a simple matrix, consisting of the identity matrix plus a rank-one update. Our resulting algorithm, the Adaptive Preconditioned CG (APCG) algorithm, is shown to have polynomial convergence properties. Numerical tests are conducted to compare a variant of the APCG algorithm with the CG algorithm on various matrices.

This work aims to investigate some applications of the conjugate duality for scalar and vector optimization problems to the construction of gap functions for variational inequalities and equilibrium problems. The basic idea of the approach is to reformulate variational inequalities and equilibrium problems into optimization problems depending on a fixed variable, which allows us to apply duality results from optimization problems. Based on some perturbations, first we consider the conjugate duality for scalar optimization. As applications, duality investigations for the convex partially separable optimization problem are discussed. Afterwards, we concentrate our attention on some applications of conjugate duality for convex optimization problems in finite and infinite-dimensional spaces to the construction of a gap function for variational inequalities and equilibrium problems. To verify the properties in the definition of a gap function weak and strong duality are used. The remainder of this thesis deals with the extension of this approach to vector variational inequalities and vector equilibrium problems. By using the perturbation functions in analogy to the scalar case, different dual problems for vector optimization and duality assertions for these problems are derived. This study allows us to propose some set-valued gap functions for the vector variational inequality. Finally, by applying the Fenchel duality on the basis of weak orderings, some variational principles for vector equilibrium problems are investigated.

<p>Multifunctional enzymes have alternative functions or activities, known as “moonlighting” or “promiscuous”, which are often hidden behind a native enzyme activity and therefore only visible under special environmental conditions. In this thesis, the active-site of Pseudozyma (formerly Candida) antarctica lipase B was explored for a promiscuous conjugate addition activity. Pseudozyma antarctica lipase B is a lipase industrially used for hydrolysis or transacylation reactions. This enzyme contains a catalytic triad, Ser105-His224-Asp187, where a nucleophilic attack from Ser105 on carboxylic acid/ester substrates cause the formation of an acyl enzyme. For conjugate addition activity in Pseudozyma antarctica lipase B, replacement of Ser105 was assumed necessary to prevent competing hemiacetal formation. However, experiments revealed conjugate addition activity in both wild-type enzyme and the Ser105Ala variant. Enzyme-catalyzed conjugate additions were performed by adding sec-amine, thiols or 1,3-dicarbonyl compounds to various α,β-unsaturated carbonyl compounds in both water or organic solvent. The reactions followed Michaelis-Menten kinetics and the native ping pong bi bi reaction mechanism of Pseudozyma antarctica lipase B for hydrolysis/transacylation was rerouted to a novel ordered bi uni reaction mechanism for conjugate addition (Paper I, II, III). The lipase hydrolysis activity was suppressed more than 1000 times by the replacement of the nucleophilic Ser105 to Ala (Paper III).</p>

Shape optimization is an important step in many design processes. With the growing use of Computer Aided Engineering in the design chain, it has become very important to develop robust and efficient shape optimization algorithms. The field of Computer Aided Optimal Shape Design has grown substantially over the recent past. In the early days of its development, the method based on small shape perturbation to probe the parameter space and identify an optimal shape was routinely used. This method is nothing but an educated trial and error method. A key development in the pursuit of good shape optimization algorithms has been the advent of the adjoint method to compute the shape sensitivities more formally and efficiently. While undoubtedly, very attractive, this method relies on very sophisticated and advanced mathematical tools which are an impediment to its wider use in the engineering community. It that spirit, it is the purpose of this thesis to propose a new shape optimization algorithm based on more intuitive engineering principles and numerical procedures. In this thesis, the new shape optimization procedure which is proposed is based on the generation of a body-fitted mesh. This process maps the physical domain into a regular computational domain. Based on simple arguments relating to the use of the chain rule in the mapped domain, it is shown that an explicit expression for the shape sensitivity can be derived. This enables the computation of the shape sensitivity in one single solve, a performance analogous to the adjoint method, the current state-of-the art. The discretization is based on the Finite Difference method, a method chosen for its simplicity and ease of implementation. This algorithm is applied to the Laplace equation in the context of heat transfer problems and potential flows. The applicability of the proposed algorithm is demonstrated on a number of benchmark problems which clearly confirm the validity of the sensitivity analysis, the most important aspect of any shape optimization problem. This thesis also explores the relative merits of different minimization algorithms and proposes a technique to “fix” meshes when inverted element arises as part of the optimization process. While the problems treated are still elementary when compared to complex multiphysics engineering problems, the new methodology presented in this thesis could apply in principle to arbitrary Partial Differential Equations.

Conjugated linoleic acid (CLA) exhibits multiple biological and molecular activities that have made it the subject of considerable nutrition-related research. Numerous studies support broad acting anti-tumor effects including anti-inflammatory, anti-proliferation, and pro-apoptosis in a variety of model systems. CLA’s ability to influence multiple tumor promoting pathways, without toxicity, may prove valuable in the chemoprevention of breast cancer. The overall objective of this dissertation research was to investigate the potential of CLA in the chemoprevention of breast cancer in a subgroup of women at risk of developing estrogen receptor (ER) negative disease. Overexpression of either the ERBB2 oncogene or the epidermal growth factor receptor (EGFR) is a common event in ER negative breast cancer. To respond to this association, the stated research objective was pursued in relevant model systems. The primary hypothesis was that CLA would downregulate the ERBB2 receptor in vitro and inhibit mammary tumorigenesis in vivo. The t10c12 CLA isomer significantly reduced ERBB2 protein expression in the ERBB2 overexpressing cell line SKBr3. This was accompanied by a decrease in NFκB nuclear localization, cyclooxygenase-2 (COX2)-derived prostaglandin (PG) E2 production, increased apoptosis, and inhibition of proliferation. In contrast to the in vitro data, however 1% dietary CLA had pro-tumor effects in the PyV-mT transgenic mouse model, Mammary gland whole mounts indicated a significant loss of adipose in the CLA-treated group compared to controls that was confirmed by the downregulation of adipocyte-specific genes including PPARγ and adiponectin. CLA’s effect on the adipose was supported by decreases in fatty acid synthase at the protein and mRNA level. cDNA microarray revealed significant downregulation of cytoskeletal and adhesion-related genes in the CLA-treated group. These data suggest CLA’s combined effect on the adipose and epithelial architecture may have promoted tumor growth in this model While the large body of evidence supporting an anti-tumor effect of CLA can not be discounted, the studies herein demonstrate the complexity of its action that may not be captured in simple model systems. Reports of adverse effects of mixed isomers or the t10c12 purified isomer lend caution to supplementation that is supported by our in vivo data.

We present a new method for regularization of ill-conditioned problems that extends the traditional trust-region approach. Ill-conditioned problems arise, for example, in image restoration or mathematical processing of medical data, and involve matrices that are very ill-conditioned. The method makes use of the L-curve and L-curve maximum curvature criterion as a strategy recently proposed to find a good regularization parameter. We describe the method and show its application to an image restoration problem. We also provide a MATLAB code for the algorithm. Finally, a comparison to the CGLS approach is given and analyzed, and future research directions are proposed.

Nonwoven-fabrics have been in use since 1930s. Their advantages over other web fonnation methods like knitting and weaving have attracted many industries such as aerospace, automotive, sports, geotextiles, composites, battery separators etc. to explore and increase their usage. During nonwoven manufacturing, most of the laid loose webs have an insufficient strength as fonned, and require an additional bonding procedure in order to provide the produced nonwoven with its intended properties. To achieve the desired properties of the nonwoven web, the bonding process is therefore, the most important part during production. The thennal bonding through air is one of the modem techniques which is incrementally improved to increase the yield of manufactured nonwoven properties. The system has a disadvantage which is, that the production capacity and energy efficiency is very low. The entitled research aims an industrial optimisation of the thermal bonding through air by entailing a strategic approach and encompassing the whole process chain of the thennal bonding process. The comprehensive and flexible optimisation opportunities provided by the CFD has been used to aid in the control and optimisation of the thermal bonding process and machinery. To optimise the process and product quality, the complex system composing of several components and various physical phenomena occurring during processing is simulated using a hierarchical methodology. More specifically a hierarchical decomposition procedure to recast the original multi scale problem as a sequence of three scale decoupled macro-, meso-, and micro scale subproblems is exploited. The methodology is applied in conjunction with the validation of experiments on through-air bonding product lines. 2D and 3D computational fluid dynamics (CFD) models based on the continuum modelling approach and the theory of porous media coupled with the theory of mixtures are developed to treat the flow behavior, heat transfer, phase change and air moisture transport within the whole through-air bonding system. The model is concluded to be an economic computational tool hence providing rapid process optimisation and valuable infonnation early in the process, which can replace costly experiments and ensure product consistency under variable process and climate conditions. 2D and 3D hybrid modelling considering parametric discrete and continuum parts is also perfonned using conjugate heat transfer analyses. The approach precisely permits the optimisation of the machine component design and the associated optimisation of consistent process and product properties.

This thesis is concerned with the asymmetric conjugate addition reactions of a range of chiral nucloeophiles. Chapter 1 introduces the conjugate addition reaction as a valuable carbon-carbon and carbon-heteroatom bond forming reaction in organic chemistry, and explores the asymmet- ric conjugate addition of a range of chiral and achiral carbon and nitrogen nucleophiles to a range of acceptors. Chapter 2 explores the use of the N-benzyl-N-(α-methylbenzyl)amino group as a chi- ral auxiliary, by employing the attempted conjugate additions of both N-benzyl-N-(α- methylbenzyl)hydrazine and N -benzyl-N -(α-methylbenzyl)hydroxylamine as chiral ammo- nia and water equivalents respectively. Chapter 3 describes the asymmetric and stereoselective preparation of a range of 4,4- disubstituted isoxazolidin-5-ones from the conjugate addition of lithium (S)-N-tert-butyl- dimethylsilyloxy-N -(α-methylbenzyl)amide. The isoxazolidin-5-ones are then globally de- protected via hydrogenolysis, giving rise to the corresponding β^2,2,3-amino acids. Chapter 4 focuses on the development of a protocol to effect the conjugate addition of a chiral aniline equivalent. The scope of the reaction is delineated by varying both the nu- cleophile and the α,β-unsaturated ester. Finally, cyclisation of the β-N-arylamino esters to the corresponding tetrahydroquinolines is explored, and an application to the synthesis of the natural product (−)-angustureine is presented. Chapter 5 contains full experimental procedures and characterisation data for all com- pounds synthesised in Chapters 2, 3 and 4.

<p>Medium-sized cyclic ethers are challenging synthetic targets due to enthalpic and entropic barriers. Methods for the stereoselective synthesis of &#945;,&#945;&#900;-disubstituted medium-sized cyclic ethers began to appear with the discovery of naturally-occurring, ladder-shaped polycyclic ethers, such as brevetoxin B, and monocyclic ethers, such as (+)-laurencin. Despite the progress made in this field, limitations remain including competing formation of smaller ring sizes and scarcity of catalytic methods. Our aim has been to develop stereoselective syntheses for 7- and 8-membered cyclic ethers which have potential for application in natural product synthesis. The C-O bond disconnection was selected for the methods described within because cyclization and stereoinduction could be achieved simultaneously. In the case of 7-membered cyclic ethers, an organocatalytic oxa-conjugate addition reaction promoted by the gem-disubstituent (Thorpe&#8722;Ingold) effect has been developed to stereoselectively provide &#945;,&#945;&#8242;-trans-oxepanes. A gold(I)-catalyzed alkoxylation reaction has also allowed access to &#945;,&#945;&#8242;-cis-oxocenes. This method has been probed for feasibility in the stereoselective synthesis of (+)-intricenyne, an 8-membered cyclic ether belonging to the C15 nonterpenoid acetogenin natural product class. These methods have the potential to become general and efficient routes to highly functionalized oxepanes and oxocenes.</p> / Dissertation