No description available.

No description available.

No description available.

Recently, covering arrays have been the subject of considerable research attention as they hold both theoretical interest and practical importance due to their applications to testing. In this thesis, we perform the first comprehensive study of a generalization of covering arrays called variable strength covering arrays, where we dictate the interactions to be covered in the array by modeling them as facets of an abstract simplicial complex. We outline the necessary background in the theory of hypergraphs, combinatorial testing, and design theory that is relevant to the study of variable strength covering arrays. We then approach questions that arise in variable strength covering arrays in a number of ways. We demonstrate their connections to hypergraph homomorphisms, and explore the properties of a particular family of abstract simplicial complexes, the qualitative independence hypergraphs. These hypergraphs are tightly linked to variable strength covering arrays, and we determine and identify several of their important properties and subhypergraphs. We give a detailed study of constructions for variable strength covering arrays, and provide several operations and divide-and-conquer techniques that can be used in building them. In addition, we give a construction using linear feedback shift registers from primitive polynomials of degree 3 over arbitrary finite fields to find variable strength covering arrays, which we extend to strength-3 covering arrays whose sizes are smaller than many of the best known sizes of covering arrays. We then give an algorithm for creating variable strength covering arrays over arbitrary abstract simplicial complexes, which builds the arrays one row at a time, using a density concept to guarantee that the size of the resultant array is asymptotic in the logarithm of the number of facets in the abstact simplicial complex. This algorithm is of immediate practical importance, as it can be used to create test suites for combinatorial testing. Finally, we use the Lovasz Local Lemma to nonconstructively determine upper bounds on the sizes of arrays for a number of different families of hypergraphs. We lay out a framework that can be used for many hypergraphs, and then discuss possible strategies that can be taken in asymmetric problems.

Recently, covering arrays have been the subject of considerable research attention as they hold both theoretical interest and practical importance due to their applications to testing. In this thesis, we perform the first comprehensive study of a generalization of covering arrays called variable strength covering arrays, where we dictate the interactions to be covered in the array by modeling them as facets of an abstract simplicial complex. We outline the necessary background in the theory of hypergraphs, combinatorial testing, and design theory that is relevant to the study of variable strength covering arrays. We then approach questions that arise in variable strength covering arrays in a number of ways. We demonstrate their connections to hypergraph homomorphisms, and explore the properties of a particular family of abstract simplicial complexes, the qualitative independence hypergraphs. These hypergraphs are tightly linked to variable strength covering arrays, and we determine and identify several of their important properties and subhypergraphs. We give a detailed study of constructions for variable strength covering arrays, and provide several operations and divide-and-conquer techniques that can be used in building them. In addition, we give a construction using linear feedback shift registers from primitive polynomials of degree 3 over arbitrary finite fields to find variable strength covering arrays, which we extend to strength-3 covering arrays whose sizes are smaller than many of the best known sizes of covering arrays. We then give an algorithm for creating variable strength covering arrays over arbitrary abstract simplicial complexes, which builds the arrays one row at a time, using a density concept to guarantee that the size of the resultant array is asymptotic in the logarithm of the number of facets in the abstact simplicial complex. This algorithm is of immediate practical importance, as it can be used to create test suites for combinatorial testing. Finally, we use the Lovasz Local Lemma to nonconstructively determine upper bounds on the sizes of arrays for a number of different families of hypergraphs. We lay out a framework that can be used for many hypergraphs, and then discuss possible strategies that can be taken in asymmetric problems.

Recently, covering arrays have been the subject of considerable research attention as they hold both theoretical interest and practical importance due to their applications to testing. In this thesis, we perform the first comprehensive study of a generalization of covering arrays called variable strength covering arrays, where we dictate the interactions to be covered in the array by modeling them as facets of an abstract simplicial complex. We outline the necessary background in the theory of hypergraphs, combinatorial testing, and design theory that is relevant to the study of variable strength covering arrays. We then approach questions that arise in variable strength covering arrays in a number of ways. We demonstrate their connections to hypergraph homomorphisms, and explore the properties of a particular family of abstract simplicial complexes, the qualitative independence hypergraphs. These hypergraphs are tightly linked to variable strength covering arrays, and we determine and identify several of their important properties and subhypergraphs. We give a detailed study of constructions for variable strength covering arrays, and provide several operations and divide-and-conquer techniques that can be used in building them. In addition, we give a construction using linear feedback shift registers from primitive polynomials of degree 3 over arbitrary finite fields to find variable strength covering arrays, which we extend to strength-3 covering arrays whose sizes are smaller than many of the best known sizes of covering arrays. We then give an algorithm for creating variable strength covering arrays over arbitrary abstract simplicial complexes, which builds the arrays one row at a time, using a density concept to guarantee that the size of the resultant array is asymptotic in the logarithm of the number of facets in the abstact simplicial complex. This algorithm is of immediate practical importance, as it can be used to create test suites for combinatorial testing. Finally, we use the Lovasz Local Lemma to nonconstructively determine upper bounds on the sizes of arrays for a number of different families of hypergraphs. We lay out a framework that can be used for many hypergraphs, and then discuss possible strategies that can be taken in asymmetric problems.

<p>A metaheuristic is a generic algorithmic template that, once properly instantiated, can be used for finding high quality solutions of combinatorial optimization problems. For obtaining a fully functioning algorithm, a metaheuristic needs to be configured: typically some modules need to be instantiated and some parameters need to be tuned. For the sake of precision, we use the expression <em>parametric tuning</em> for referring to the tuning of numerical parameters, either continuous or discrete but in any case ordinal. On the other hand, we use the expression <em>structural tuning</em> for referring to the problem of defining which modules should be included and, in general, to the problem of tuning parameters that are either boolean or categorical. Finally, with <em>tuning</em> we refer to the composite <em>structural and parametric tuning</em>.</p> <p>Tuning metaheuristics is a very sensitive issue both in practical applications and in academic studies. Nevertheless, a precise definition of the tuning problem is missing in the literature. In this thesis, we argue that the problem of tuning a metaheuristic can be profitably described and solved as a machine learning problem.</p> <p>Indeed, looking at the problem of tuning metaheuristics from a machine learning perspective, we are in the position of giving a formal statement of the tuning problem and to propose an algorithm, called F-Race, for tackling the problem itself. Moreover, always from this standpoint, we are able to highlight and discuss some catches and faults in the current research methodology in the metaheuristics field, and to propose some guidelines.</p> <p>The thesis contains experimental results on the use of F-Race and some examples of practical applications. Among others, we present a feasibility study carried out by the German-based software company <em>SAP</em>, that concerned the possible use of F-Race for tuning a commercial computer program for vehicle routing and scheduling problems. Moreover, we discuss the successful use of F-Race for tuning the best performing algorithm submitted to the <em>International Timetabling Competition</em> organized in 2003 by the <em>Metaheuristics Network</em> and sponsored by <em>PATAT</em>, the international series of conferences on the <em>Practice and Theory of Automated Timetabling</em>.</p>

<p>In affinity protein biotechnology the selective bindingbetween a chosen protein and an interacting biomolecule isutilized for a variety of applications including bioseparation,detection and therapy. Traditionally, affinity proteinsrecruited for such applications have been derived from naturalproteins or immunoglobulins generated via immunization routes.More recently, advances in the construction and handling oflarge collections of proteins(denoted libraries) generated invitro have opened up for new routes for the development ofaffinity proteins with desired properties.</p><p>In this study, phage display selection technology was usedfor the isolation of novel human CD28 (hCD28)-specific affinityproteins from a protein library constructed by combinatorialprotein engineering of a 58 aa protein domain (Z) derived fromstaphylococcal protein A (SPA). From selections using hCD28 asa target molecule, several hCD28-specific affinity proteins(denoted affibodies) could be identified and analysis of theisolated affibody variants revealed a high degree of sequencehomology between the different clones. The biosensor analysisshowed that all variants bound to hCD28 with micromolardissociation constants (KD) and no significant cross-reactivitytowards the structurally related T-cell receptor hCTLA-4 couldbe observed. The apparent binding affinity for hCD28 of one ofthe isolated affibodies was further improved through fusion toa human Fc fragment fusion partner, resulting in a homodimericversion of the affibody ligand showing avidity effects uponhCD28 binding. Further, a co-culture experiment involvingJurkat T-cells and CHO cell lines tranfected to express eitherhuman CD80 or LFA-3 on the cell surface showed that apreincubation of Jurkat cells with one of the affibody variantsresulted in a specific concentration-dependent inhibition ofthe CD80 induced IL-2 production. This indicates that thisaffibody binds to hCD28 and specifically interferes with theco-stimulation signal mediated via hCD28 and hCD80. ACD28-specific binding protein could have potential as an agentfor various immunotherapy applications. In a second study, anaffinity protein-based strategy was investigated forsite-specific anchoring of proteins onto cellulose for woodfiber engineering purposes. Here, affinity proteins derivedfrom different sources were used for the assembly of acellulosome-like complex for specific and reversible anchoringof affinity domain-tagged reporter proteins to acellulose-anchored fusion protein. A fusion protein between acellulose binding module (Cel6A CBM1) derived from the fungalTrichoderma reesei and a five-domain staphylococcal protein A(SPA) moiety was constructed to serve as a platform for thedocking of reporter proteins produced as fusion to two copiesof a SPA-binding affibody affinity protein (denoted ZSPA-1),selected by phage display technology from a Z domain basedprotein library. In a series of experiments, involving repeatedwashing and low pH elutions, affinity tagged Enhanced GreenFluorescent Protein (EGFP) and Fusarium solani pisi lipasecutinase reporter proteins were both found to be specificallydirected from solution to a region of a cellulose-based filterpaper where the SPA-CBM fusion protein previously had beenpositioned. This showed that the cellulose-anchored SPA-Cel6ACBM1 fusion protein had been stably anchored to the surfacewith retained binding activity and that the interaction betweenSPA and the ZSPA-1 affibody domain was selective.</p><p>phage display, combinatorial, selection, CD28, cellulosome,cellulose, affibody</p>

When defining a structure to fulfill a set of axioms that are similar to those prescribed by Euclid, one must select a set of points and then define what is meant by a line and what is meant by a circle. When properly defined these labels will have properties which are similar to their counterparts in the (complex) plane, the lines and circles which Euclid undoubtedly had in mind. In this manner, the geometer may employ his intuition from the complex plane to prove theorems about other systems. Most "finite geometries" have clearly defined notions of points and lines but fail to define circles. The two notable exceptions are the circles in a finite affine plane and the circles in a Mobius plane. Using the geometry of Euclid as motivation, we strive to develop structures with both lines and circles. The only successful example other than the complex plane is the affine plane over a finite field, where all of Euclid's geometry holds except for any assertions involving order or continuity. To complement the prolific work concerning finite geometries and their lines, we provide a general definition of a circle, or more correctly, of a collection of circles and present some preliminary results concerning the construction of such structures. Our definition includes the circles of an affine plane over a finite field and the circles in a Mobius plane as special cases. We develop a necessary and sufficient condition for circularity, present computational techniques for determining circularity and give varying constructions. We devote a chapter to the use of circular designs in coding theory. It is proven that these structures are not useful in the theory of error-correcting codes, since more efficient codes are known, for example the Reed-Muller codes. However, the theory developed in the earlier chapters does have applications to Cryptology. We present five encryption methods utilizing circular structures.

The goal of this dissertation is to understand the market-based mechanisms that enable shippers to allocate lanes in an efficient way for truckload (TL) transportation procurement despite the self-interest of carriers. To understand the market-based mechanisms, we focus on proposing some novel models and mechanisms to enhance the use of combinatorial auction for TL transportation procurement. In this dissertation, our approach to gaining the understanding consists of three parts: 1. We develop a carrier optimal bid generation model for carriers (bidders) to discover the best sets of lanes to bid for at a given round. The optimal bid generation model simultaneously generates alternative tours and selects the most profitable package bid for the carrier under a myopic strategy, which has never been considered before. The simultaneous tour generation and selection significantly lessen the computational complexities of a carrier's optimization problem since it is unnecessary for the carrier to calculate the values for all possible packages. 2. We present an iterative combinatorial auction design that integrates the optimization problems for both the shipper and the bidders where the approximate dual prices derived from the result of a winner determination solution are used by the bidders in identifying profitable lanes. The auctions also allow the bidders to submit exclusive-OR (XOR) bids and are able to deal with some common business considerations. The extension of the concept of active bids enables this mechanism to effectively mitigate the exposure problem, the threshold problem, and the free-riding problem. Furthermore, both the shippers and the carriers are better off compared to multi-round auctions that do not integrate the shippers' and carriers' optimizations. 3. We extend a deterministic winner determination model to a two-stage stochastic winner determination model for TL transportation procurement under shipment volume uncertainty. We demonstrate that the value of the stochastic solution is always at least as good as one obtained by a deterministic model based on using expected shipment volumes. The sWDP model is to the best of our knowledge the first winner determination formulation of any kind that explicitly incorporates demand uncertainty.