The accumulation of high-throughput genomic and proteomic data allows for the reconstruction of the increasingly large and complex metabolic networks. In order to analyze the accumulated data and reconstructed networks, it is critical to identify network patterns and evolutionary relations between metabolic networks. But even finding similar networks becomes computationally challenging. The dissertation addresses these challenges with discrete optimization and the corresponding algorithmic techniques. Based on the property of the gene duplication and function sharing in biological network,we have formulated the network alignment problem which asks the optimal vertex-to-vertex mapping allowing path contraction, vertex deletion, and vertex insertions. We have proposed the first polynomial time algorithm for aligning an acyclic metabolic pattern pathway with an arbitrary metabolic network. We also have proposed a polynomial-time algorithm for patterns with small treewidth and implemented it for series-parallel patterns which are commonly found among metabolic networks. We have developed the metabolic network alignment tool for free public use. We have performed pairwise mapping of all pathways among five organisms and found a set of statistically significant pathway similarities. We also have applied the network alignment to identifying inconsistency, inferring missing enzymes, and finding potential candidates.

Comparing protein sequences is an essential procedure that has many applications in the field of bioinformatics. The recent advances in computational capabilities and algorithm design, simplified the comparison procedure of protein sequences from several databases. Various algorithms have emerged using state of the art approaches to match protein sequences based on structural and functional properties of the amino acids. The matching involves structural alignment, and this alignment may be global; comprising of the whole length of the protein, or local; comprising of the sub-sequences of the proteins. Families of related proteins are found by clustering sequence alignments. The frequency distributions of the amino acids within these different clusters define the sequence profile. The best alignment algorithm uses these profiles. In this thesis, we have studied different profile alignment algorithms where the cost function for comparing two profiles is changed. These are compared to the FFAS3 (Fold and Function Assignment) algorithm.

This thesis examines the challenges and strategies to IT-Business alignment from the perspective of IT managers. The increasing importance of Information technology (IT) to organizations in areas such as joint  research and development (R&D), Open innovation, and the ever-changing business environment means that organizations need to reassess their IT and business strategies so as to remain competitive. This implies that organizations in general and business and IT professionals in particular would have to work together more often than before in strategic planning. This is not easy because these professionals with diverse viewpoints may understand IT and business quite differently. Using a qualitative research design in the form of semi-structure interviews with open-ended questions, findings indicate that communication, partnership, governance, and skills are major challenges and strategies to alignment. This study contributes to ongoing research in IT-Business alignment by indicating that challenges to aligning business and IT strategies such as communication should not be narrowly thought of to exist just between IT and business professionals, it is equally a main concern among IT professionals.

The purpose of this study was to analyze kinetic and kinematic data of individuals with unilateral transtibial limb loss and the effect different alignments have on the individual’s gait while they walk over uneven terrain. Individuals with lower limb loss are currently having their prostheses dynamically aligned to ensure a satisfactory walking gait on level ground with smooth surfaces, usually in the clinician's office or hallway. This study was looking to determine whether or not current prosthesis alignment procedures are adequate for determining a satisfactory walking gait on non-level and non-smooth terrains as well level smooth surfaces. An effective and efficient walking pattern is necessary to prevent degenerative conditions within the bones, muscles or other tissues of the body, due to compensations of the gait pattern. Sometimes, individuals are able to mask any compensations if their safety is unaffected by their surroundings and they are able to maintain a gait that appears normal or optimal. However, if terrains used on a daily basis present a sense of insecurity, gait compensations could be more problematic to the individual and they need to be addressed and corrected as best they can. This study determined that while there were some changes in gait on the uneven surface, due to the number of subjects it is unclear whether the changes are significant. The individuals showed a decrease in walking speed and step length and an increase in step width. There were also changes in the peak axial force.

This thesis is a study about wether first year students in Swedish senior high schools understand the learning intentions and the matter of the subject of history specified in GY 11 introduced in July 2011. The overall question that this master tries to answer is: Do the students understand what and why they are studying history? Three classes studying the first history course in the new system answered a survey regarding five of the specified learning intentions for the course and their overall opinion of grades and level of knowledge and intentions. By measuring the level of understanding and the students’ general opinion the conclusion is following. The students understand the majority of the intention mentioned in GY11 although in the areas of ”historical consciousness” (historiemedvetande) and ”source criticism” (källkritik) the survey shows that the students’ understanding is poor. They also think that is is important to clarify the learning intentions, not only in history but in other subjects in school as well. If that is done the students think both that their grades would be higher and their knowledge would be greater. Even though the students understand the importance of their knowledge in history they have trouble specifying why. They do however point out that if the intention of the subject is made clear, their interest of the subject would increase, and that itself would lead to a higher level of knowledge and understanding.

Sequence alignment has become one of the most common tasks in bioinformatics. Most of the existing sequence alignment methods use general scoring schemes. But these alignments are sometimes not completely relevant because they do not necessarily provide the desired information. It would be extremely difficult, if not impossible, to include any possible objective into an algorithm. Our goal is to allow a working biologist to augment a given alignment with additional information based on their knowledge and objectives.<p></p>In this thesis, we will formally define constraints and compatible constraint sets for an alignment which require some positions of the sequences to be aligned together. Using this approach, one can align some specific segments such as domains within protein sequences by inputting constraints (the positions of the segments on the sequences), and the algorithm will automatically find an optimal alignment in which the segments are aligned together.<p></p>A necessary prerequisite of calculating an alignment is that the constraints inputted be compatible with each other, and we will develop algorithms to check this condition for both pairwise and multiple sequence alignments. The algorithms are based on a depth-first search on a graph that is converted from the constraints and the alignment. We then develop algorithms to perform pairwise and multiple sequence alignments satisfying these compatible constraints.<p></p>Using straightforward dynamic programming for pairwise sequence alignment satisfying a compatible constraint set, an optimal alignment corresponds to a path going through the dynamic programming matrix, and as we are only using single-position constraints, a constraint can be represented as a point on the matrix, so a compatible constraint set is a set of points. We try to determine a new path, rather than the original path, that achieves the highest score which goes through all the compatible constraint set points. The path is a concatenation of sub-paths, so that only the scores in the sub-matrices need to be calculated. This means the time required to get the new path decreases as the number of constraints increases, and it also varies as the positions of the points change. It can be further reduced by using the information from the original alignment, which can offer a significant speed gain.<p></p>We then use exact and progressive algorithms to find multiple sequence alignments satisfying a compatible constraint set, which are extensions of pairwise sequence alignments. With exact algorithms for three sequences, where constraints are represented as lines, we discuss a method to force the optimal path to cross the constraint lines. And with progressive algorithms, we use a set of pairwise alignments satisfying compatible constraints to construct multiple sequence alignments progressively. Because they are more complex, we leave some extensions as future work.

The outsourcing of elements of supply chain processes is now an integral component of the operationalization of a firm s competitive business strategy. While the purported goal of outsourcing is usually to derive a competitive advantage in the marketplace, it is not clear whether the outsourcing decisions made by firms are always strategically aligned with their overall competitive strategy. To shed light on this important issue, this research study empirically examines the performance impact of the alignment (congruence) between a firm s competitive priorities (cost, flexibility, innovativeness, quality, and time) and the drivers of its outsourcing decisions. First, we develop and validate a survey instrument used to collect data for this study from manufacturing firms operating in the United States. Next, we use structural equation modeling to examine the impact of alignment between individual competitive priorities and related groups of outsourcing drivers. This analysis finds a significant positive relationship between outsourcing alignment and performance for a number of competitive priorities. Finally, we use cluster analysis to develop a taxonomy of manufacturing strategies which are tested to determine the relationship between the alignment of outsourcing decisions and performance. The taxonomic investigation identifies three unique clusters of firms based on their competitive priorities and then determines alignment between each cluster strategy and outsourcing to be significantly associated with better performance. To the best of our knowledge, there are no studies in the literature that address the issue of strategic congruence between the outsourcing drivers and competitive priorities of a firm, and the impact of such congruence on firm performance.

Sequence alignment is a basic but powerful technique in molecular biology. Macromolecular sequences (DNA, RNA and protein sequences) can be aligned based on some criteria. The goal of sequence alignment is to find the similarity and the difference of input sequences. With various purposes, there are different algorithms In this thesis, we present a new algorithm which aligns sequences with consideration of secondary structures. Traditionally, a sequence alignment algorithm considers only the primary structure, which is the amino acid chain. When we make use of the information of protein secondary structure such as alpha helix, beta sheet etc, the sensitivity of pairwise alignment can be improved.

The fiber alignment shifts induced by the post-weld-shift (PWS) in laser-welded TO(Transistor outline)-Can type laser module packages is studied experimentally and numerically. The PWS induced fiber alignment shifts were quantitatively determined by four geometrical parameters: the lateral shift(r), the position angle(£\), the tilt angle(£Z), and the swing angle(£c). The measured coupling powers in laser module packages before welding, after welding, and after a compensation clearly confirmed with the measured fiber alignment shifts determined by the dominant parameters of the r and £\ that the fiber shifts due to the PWS could be realigned back closer to their original optimum position after applying a welding compensation, and hence the coupling powers loss due to the PWS could be regained. The measured coupling efficiency after laser welding was from 68% to 95%, and the overall coupling efficiency after the PWS compensation was from 77% to 97%. The increased coupling efficiency after this PWS compensation was from 2% to16%. A coupled thermal-elasto-plasticity model of finite-element method (FEM) analysis was performed to evaluate the effects of PWS on fiber alignment shifts in laser module packages. The measured fiber alignment shifts determined by the dominant parameters of the r and £\ were in good agreement with the numerical calculation of the FEM analysis. In this study, the combination of the experimental and numerical results have significantly provided a practical design guideline for fabricating reliable laser-welded TO-Can type laser module packages with a high yield and high performance for use in low-cost lightwave transmission systems. A novel measurement and compensation technique employing a high-magnification camera with image capturing system (HMCICS) to probe the post-weld-shift (PWS) induced fiber alignment shifts in high-performance butterfly-type laser module packages is investigated. The results show that the direction and magnitude of the fiber alignment shifts induced by the PWS in laser-welded butterfly-type laser module packaging can be quantitatively determined and then compensated. The measured coupling powers in laser module packages after welding and compensation clearly confirmed the measured fiber alignment shifts determined by the translational and rotational parameters that the fiber shifts due to the PWS could be realigned back closer to their original optimum position after applying a welding compensation, and hence the coupling powers loss due to the PWS could be regained. The measured coupling efficiency after laser welding was from 63% to 79%, and the overall coupling efficiency after the PWS compensation was from 69% to 89%. The increased coupling efficiency after this PWS compensation was from 3% to 10%. In comparison with previous studies of the PWS compensation by a qualitatively estimated technique in butterfly-type laser module packages, this novel HMCICS technique has significantly provided an important tool for quantitative measurement and compensation to the effect of the PWS on the fiber alignment shifts in laser module packages. Therefore, the reliable butterfly-type laser modules with a high yield and a high performance used in lightwave transmission systems can be developed and fabricated.

Phase key, which uses optical encoding techniques for system security, plays an important role in optical storage, optical communication, and optical display. It employs a random phase generator with a volume hologram for optical encoding. The advantages of using phase keys for optical communication is: (1) it is hard to be duplicated and (2) it requires sensitively alignment to decode the desired signal. Thus, it ensures security of the optical system. However, the adjunctive challenge of using a phase key is the difficulty of alignment by users. In this paper, we propose a method for optical alignment of the phase key in a random phase encoded volume holographic storage system. In this method, a holographic correlator is applied to help the optical alignment of the phase key. It has been shown that the desired signal from the random phase encoded volume holographic storage system can be retrieved easily with high security.