<p>For the vast majority of proteins no experimental information about the three-dimensional structure is known, but only its sequence. Therefore, the easiest way to obtain some understanding of the structure and function of these proteins is by relating them to well studied proteins. This can be done by searching for homologous proteins. It is easy to identify a homologous sequence if the sequence identity is above 30%. However, if the sequence identity drops below 30% then more sophisticated methods have to be used. These methods often use evolutionary information about the sequences, which makes it possible to identify homologous sequences with a low sequence identity.</p><p>In order to build a three--dimensional model from the sequence based on a protein structure the two sequences have to be aligned. Here the aligned residues serve as a first approximation of the structure.</p><p>This thesis focuses on the development of fold recognition and alignment methods based on evolutionary information. The use of evolutionary information for both query and target proteins was shown to improve both recognition and alignments. In a benchmark of profile--profile methods it was shown that the probabilistic methods were best, although the difference between several of the methods was quite small once optimal gap-penalties were used. An artificial neural network based alignment method ProfNet was shown to be at least as good as the best profile--profile method, and by adding information from a self-organising map and predicted secondary structure we were able to further improve ProfNet.</p>

<p>This report is a case study with the aim of examining the link between business strategy and the strategy of projects. The field of project management in strategy of projects and their link to the strategy of parent company has yet to be explored. The existing body of literature presents the alignment of project to strategy in two main views which are that projects should have a similar strategy with the parent or that projects should be independent in strategy and follow its own approach. Researchers acknowledge that the limited theoretical frameworks in this stream suffer from the lack of empirical research. Thus this research is based on the question “What is the relation between company’s business strategy and project’s strategy in innovation projects following the position driven alignment approach?” The researchers utilize the position-driven alignment framework as propositioned by Artto, Kujala, Dietrich and Martinsuo (2007). The factors of stakeholder complexity and project autonomy are examined to explore the relationship between the parent strategy and the project strategy. The study conducted is a single case study design on an IT Platform in a large insurance company. Analysis from the data reveal interesting results; that i) The obedience of the project creates risk on the parent strategy, ii) parent strategy changes as the project progresses and that iii) the perception of importance of the project by the parent influences the project autonomy. Further evidence through empirical research is suggested on the other project positions in this framework.</p>

<p>Query composition is an often complicated and cumbersome task for persons performing a literature search. This thesis is part of a project which aims to present possible queries to the user in form of natural language expressions. The thesis presents methods of ontology slice generation. Slices are parts of ontologies connecting two concepts along all possible paths between them. Those slices hence represent all relevant queries connecting the concepts and the paths can in a later step be translated into natural language expressions. Methods of slice alignment, connecting slices that originate from different ontologies, are also presented. The thesis concludes with some example scenarios and comparisons to related work.</p>

La connaissance de la structure tridimensionnelle (3D) des protéines est une information capitale. Néanmoins, le nombre de protéines dont la structure 3D a été déterminée expérimentalement est cent fois plus faible que le nombre de protéines connues aujourd'hui. Cet écart ne pourra pas être comblé, car les techniques expérimentales de détermination de structure (diffraction de rayons X et résonance magnétique nucléaire) sont coûteuses et lentes (un an de travail en moyenne pour une seule protéine). Un moyen d'obtenir plus rapidement la structure 3D de protéines est de la prédire par des moyens bioinformatiques. La technique de prédiction la plus précise actuellement est la modélisation par homologie. Celle-ci est basée sur la similitude de structure entre deux protéines de séquences similaires. L'étape critique de cette méthode est l'étape d'alignement entre la séquence à modéliser et une séquence similaire de structure connue. Notre travail a consisté tout d'abord en la conception d'une nouvelle méthode d'alignement pairé très fiable. Cette méthode a ensuite été incluse dans un système automatique de modélisation par homologie: la bonne qualité des structures prédites par le système trouve en partie son origine dans le programme d'alignement utilisé. Enfin, nous avons appliqué notre système de modélisation automatique à la modélisation de toutes les protéines déduites du génome d'une bactérie pathogène étudiée dans notre unité de recherche: Brucella melitensis. Cela nous a conduit à créer une banque de données structurales et fonctionnelles consacrée au génome de cette bactérie. Cette banque de données est devenue un outil de travail indispensable pour plusieurs équipes de recherche européennes qui étudient Brucella melitensis.

This thesis explores the development of parallel treebanks, collections of language data consisting of texts and their translations, with syntactic annotation and alignment, linking words, phrases, and sentences to show translation equivalence. We describe the semi-manual annotation of the SMULTRON parallel treebank, consisting of 1,000 sentences in English, German and Swedish. This description is the starting point for answering the first of two questions in this thesis. What issues need to be considered to achieve a high-quality, consistent,parallel treebank? The units of annotation and the choice of annotation schemes are crucial for quality, and some automated processing is necessary to increase the size. Automatic quality checks and evaluation are essential, but manual quality control is still needed to achieve high quality. Additionally, we explore improving the automatically created annotation for one language, using information available from the annotation of the other languages. This leads us to the second of the two questions in this thesis. Can we improve automatic annotation by projecting information available in the other languages? Experiments with automatic alignment, which is projected from two language pairs, L1–L2 and L1–L3, onto the third pair, L2–L3, show an improvement in precision, in particular if the projected alignment is intersected with the system alignment. We also construct a test collection for experiments on annotation projection to resolve prepositional phrase attachment ambiguities. While majority vote projection improves the annotation, compared to the basic automatic annotation, using linguistic clues to correct the annotation before majority vote projection is even better, although more laborious. However, some structural errors cannot be corrected by projection at all, as different languages have different wording, and thus different structures. / I denna doktorsavhandling utforskas skapandet av parallella trädbanker. Dessa är språkliga data som består av texter och deras översättningar, som har märkts upp med syntaktisk information samt länkar mellan ord, fraser och meningar som motsvarar varandra i översättningarna. Vi beskriver den delvis manuella uppmärkningen av den parallella trädbanken SMULTRON, med 1.000 engelska, tyska och svenska meningar. Denna beskrivning är utgångspunkt för att besvara den första av två frågor i avhandlingen. Vilka frågor måste beaktas för att skapa en högkvalitativ parallell trädbank? De enheter som märks upp samt valet av uppmärkningssystemet är viktiga för kvaliteten, och en viss andel automatisk bearbetning är nödvändig för att utöka storleken. Automatiska kvalitetskontroller och automatisk utvärdering är av vikt, men viss manuell granskning är nödvändig för att uppnå hög kvalitet. Vidare utforskar vi att använda information som finns i uppmärkningen, för att förbättra den automatiskt skapade uppmärkningen för ett annat språk. Detta leder oss till den andra av de två frågorna i avhandlingen. Kan vi förbättra automatisk uppmärkning genom att överföra information som finns i de andra språken? Experimenten visar att automatisk länkning som överförs från två språkpar, L1–L2 och L1–L3, till det tredje språkparet, L2–L3, får förbättrad precision, framför allt för skärningspunkten mellan den överförda länkningen och den automatiska länkningen. Vi skapar även en testsamling för experiment med överföring av uppmärkning för att lösa upp strukturella flertydigheter hos prepositionsfraser. Överföring enligt majoritetsprincipen förbättrar uppmärkningen, jämfört med den grundläggande automatiska uppmärkningen, men att använda språkliga ledtrådar för att korrigera uppmärkningen innan majoritetsöverföring är ännu bättre, om än mer arbetskrävande. Vissa felaktiga strukturer kan dock inte korrigeras med hjälp av överföring, eftersom de olika språken använder olika formuleringar, och därmed har olika strukturer.

For the vast majority of proteins no experimental information about the three-dimensional structure is known, but only its sequence. Therefore, the easiest way to obtain some understanding of the structure and function of these proteins is by relating them to well studied proteins. This can be done by searching for homologous proteins. It is easy to identify a homologous sequence if the sequence identity is above 30%. However, if the sequence identity drops below 30% then more sophisticated methods have to be used. These methods often use evolutionary information about the sequences, which makes it possible to identify homologous sequences with a low sequence identity. In order to build a three--dimensional model from the sequence based on a protein structure the two sequences have to be aligned. Here the aligned residues serve as a first approximation of the structure. This thesis focuses on the development of fold recognition and alignment methods based on evolutionary information. The use of evolutionary information for both query and target proteins was shown to improve both recognition and alignments. In a benchmark of profile--profile methods it was shown that the probabilistic methods were best, although the difference between several of the methods was quite small once optimal gap-penalties were used. An artificial neural network based alignment method ProfNet was shown to be at least as good as the best profile--profile method, and by adding information from a self-organising map and predicted secondary structure we were able to further improve ProfNet.

Cellulose whiskers (CWs) obtained from naturally occuring cellulose are nano-inclusions which show a lot of promise as mechanical reinforcements in polymers. Typically, a relatively high content is added to realize improvement in effective mechanical behavior. This enhancement in modulus is usually followed by a modest increase in strength but generally the ductility and toughness decrease. Our approach is to use small concentrations of CWs so as not to detrimentally affect processability, toughness and ductility. By aligning the small concentrations, we target the same kind of improvement in modulus and strength as reported in the literature, but at much smaller volume contents. In this work, we investigate the effect of AC electric field on the alignment of dispersed nanoscale CW in a polymer. Polyvinyl acetate (PVAc) is used as the model polymer because of the good interaction between CWs and PVAc. A low concentration of 0.4wt% was used for the study. Two dispersion methods, namely basic and modified, were developed. The basic method led to micron scale dispersion. Using the modified method, CWs were individually dispersed in PVAc with average lengths and diameters of 260 nm and 8 nm respectively yielding an aspect ratio of approximately 30. The behavior of CWs (alignment and chain formation) under an applied electric field was found to be a function of applied electric field magnitude, frequency and duration. Following alignment, the CW/PVAc nanocomposites are thermally dried in the presence of electric field to maintain the aligned microstructure. Improvements in dielectric constant and mechanical properties were observed for the aligned cases as compared to random case and pure PVAc. The optimal electric field magnitude, frequency and duration for the alignment and chain formation were found to be 200Vpp/mm, 50 KHz for duration of 20 minutes for the microcomposite and 250Vpp/mm, 10KHz for a duration of 1hr for the nanocomposite. At 0.4wt% concentration, 21% increase in dielectric constant for the optimal nanocomposite case. Above Tg, a 680% improvement in elastic modulus at 0.4wt% concentration for the optimal nanocomposite case. The reason for the significant reinforcement is attributed to alignment (rotation and chain formation) and chain-chain interaction (3D network formation and hydrogen bonding).

Several surveys indicate that corporate leaders still consider the aligning of IT and business functions as a top management issue. The aim of this thesis is to illustrate how coordination emerges between IT and business departments and how formal structures intended to coordinate are influenced by human action. To deepen the understanding of this phenomenon we seek to analyze IT/business coordination from a perspective based on practice theory. A field study was conducted where observations and informal interviews were carried out at the IT department of a global company. The empirical analysis indicate that coordination problems between IT and business departments is in part affected by embedded factors such as different goals and perspectives on how IT is to be used in the organization or how to design IT related processes. Our findings suggest that social interaction plays an important role for coordination. It can enhance existing formal structures or create new structures, which improve the possibilities to coordinate between IT and business departments. Our findings also show how formal structures such as cross-functional roles can constitute conditions to initiate social interaction. The results can be used as indicators for how to enhance coordination between IT and business departments.

Due to increasing numbers of non-coding RNA (ncRNA) being discovered recently, there is interest in identifying homologs of a given structured RNA sequence. Exhaustive homology searching for structured RNA molecules using covariance models is infeasible on genome-length sequences. Hence, heuristic methods are employed, but they largely ignore structural information in the query. We present a novel method, which uses secondary structure information, to perform homology searches for a structured RNA molecule. We define the concept of a <em>pair seed</em> and theoretically model alignments of random and related paired regions to compute expected sensitivity and specificity. We show that our method gives theoretical gains in sensitivity and specificity compared to a BLAST-based heuristic approach. We provide experimental verification of this gain. <br /><br /> We also show that pair seeds can be effectively combined with the spaced seeds approach to nucleotide homology search. The hybrid search method has theoretical specificity superior to that of the BLAST seed. We provide experimental evaluation of our hypotheses. Finally, we note that our method is easily modified to process pseudo-knotted regions in the query, something outside the scope of covariance model based methods.

Dental records have been widely used as tools in forensic identification. With the vast volume of cases that need to be investigated by forensic odontologists, a move towards a computer-aided dental identification system is necessary. We propose a computer-aided framework for efficient matching of dental x-rays for human identification purposes. Given a dental x-ray with a marked region of interest (ROI), we search the database of x-rays (presumed to be taken from known individuals) to retrieve a closest match. In this work we use a slightly extended Weighted Sum of Squared Differences (SSD) cost function to express the degree of similarity/overlap between two dental radiographs. Unlike other iterative Least Squares methods that use local information for gradient-based optimization, our method finds the globally optimal translation. In 90% of the identification trials, our method ranked the correct match in the top 10% using a database of 571 images. Experiments indicate that matching dental records using the extended SSD cost function is a viable method for human dental identification.