The comparison methods for RNA or protein molecules are important basic tools in molecular biology. So far, most comparison methods are only applicable to the primary structures of biomolecules, such as the sequence alignment and comparison methods. The functions of biomolecules have close relationship with their structures. The recent methods for finding the structures of biomolecules are NMR spectroscopy, X-ray crystallography, and prediction with computational simulation. There are many biomolecules with known structures, but their functions are unknown. The RNA secondary structure alignment problem is to align two RNA molecules to get the structure similarity, where their secondary structures are given. In addition, it is also helpful to predict the functions of biomolecules and to classify them. In this thesis, we design a dynamic programming method for aligning two RNA secondary structures which do not contain any pseudoknot. The time complexity of our algorithm is O(N4), where N is the number of blocks contained in the given RNA sequences. We also apply our algorithm to the real biomolecules, the tRNAs of Homo sapiens mitochondrion, to evaluate the practicability our method. We take three tRNA genes, TRNG, TRNA and TRNV, to test the performance of our algorithm. From the view point of human eyes, in fact, the structure of TRNG is more similar to TRNA. Our algorithm also gets this result. Hence, our algorithm provides an effective method to measure the similarity of two RNA secondary structures.

A huge number of genomic information, including protein and DNA sequences, is generated by the human genome project. Deciphering these sequences and detecting local residue patterns of multiple sequences are very difficult. One of the ways to decipher these biological sequences is to detect local residue patterns from them. However, detecting unknown patterns from multiple sequences is still very difficult. In this thesis, we propose an algorithm, based on the Gibbs sampler method, for identifying local consensus patterns (motifs) in monomolecular sequences. We first designed an ACO (ant colony optimization) algorithm to find a good initial solution and a set of better candidate positions for revising the motif. Then the Gibbs sampler method is applied with these better candidate positions as the input. The required time for finding motifs using our algorithm is reduced drastically. It takes only 20 % of time of the Gibbs sampler method and it maintains the comparable quality.

The objective of this thesis is to reduce the training size for the Mandarin address inputting system and the Mandarin phrase recognition system. A set of two-word Mandarin phrases is developed by the balanced sieving and mixture training techniques. This greatly reduces the training data size for the systems. Hidden Markov model using both MFCC and LPCC features is proposed in this thesis. Speech-text alignment, frame overlapping and tone recognition are incorporated to increase the correct recognition rates. For the speaker-dependent case, any phrase in these two speech systems can be recognized within one second.

Controlling the orientation of liquid crystal molecules in LC displays is extremely important for optimizing device performance. The method most commonly used in industry today involves rubbing the surface of the polymer-coated glass substrates used in the displays with a velvet cloth to create microscopic grooves. Berreman theory states that the liquid crystal molecules then align along the direction of the grooves. Alternatively, some literature shows that the friction caused by rubbing aligns the polymer chains in the surface layer which then attract and align the liquid crystal molecules along the direction of the chains. Even now, it is still unclear exactly how the process of rubbing the surface causes the liquid crystal molecules to align in an orderly manner. This thesis describes a systematic study of the physical and chemical influence of the substrate on the alignment and orientation of liquid crystal molecules. We used Fourier Transform Infrared spectroscopy (FTIR) to identify surface chemistry, contact angle measurements to determine the surface energy, and atomic force microscopy (AFM) to observe the alignment of liquid crystal on the surfaces. In the course of this study, we have gained insight into how the physical and chemical properties of the surface affect the molecular arrangement in the solid-liquid interface. Our results can be applied not only to LCD technology, but more generally to biochips and biosensor devices.

<p>The ability to tackle NP-hard problems has been greatly extended by the introduction of Metaheuristics (see Blum & Roli (2003)) for a summary of most Metaheuristics, general problem-independent optimisation algorithms extending the hill-climbing local search approach to escape local minima. One of these algorithms is Iterated Local Search (ILS) (Lourenco et al., 2002; Stützle, 1999a, p. 25ff), a recent easy to implement but powerful algorithm with results comparable or superior to other state-of-the-art methods for many combinatorial optimisation problems, among them the Traveling Salesman (TSP) and Quadratic Assignment Problem (QAP). ILS iteratively samples local minima by modifying the current local minimum and restarting</p><p>a local search porcedure on this modified solution. This thesis will show how ILS can be implemented for MSA. After that, ILS will be evaluated and compared to other MSA algorithms by BAliBASE (Thomson et al., 1999), a set of manually refined alignments used in most recent publications of algorithms and in at least two MSA algorithm surveys. The runtime-behaviour will be evaluated using runtime-distributions.</p><p>The quality of alignments produced by ILS is at least as good as the best algorithms available and significantly superiour to previously published Metaheuristics for MSA, Tabu Search and Genetic Algorithm (SAGA). On the average, ILS performed best in five out of eight test cases, second for one test set and third for the remaining two. A drawback of all iterative methods for MSA is the long runtime needed to produce good alignments. ILS needs considerably less runtime than Tabu Search and SAGA, but can not compete with progressive or consistency based methods, e. g. ClustalW or T-COFFEE.</p>

<p>Enterprise resource planning (ERP) system which first emerged in the early 90’s, have become</p><p>so popular today that almost every large business corporation uses one. Recent years</p><p>have seen increased spending on this software application package, but sadly not all organizations</p><p>which invest in ERP systems have gotten back their money’s worth. There have</p><p>been many instances of unsuccessful ERP implementation attempts and in some cases total</p><p>failure. Researchers and scholars have long since studied these systems in a bid to provide</p><p>explanations for the complexity and failure of implementation attempts. This has led to the</p><p>establishment of critical success factors (CSF), which slightly vary with different authors</p><p>but have some strong common points. Prominent among these CSF’s is alignment between</p><p>business processes and ERP built-in processes.</p><p>This project therefore focuses on alignment issues that arise between the software package</p><p>and the organization’s business processes during ERP implementation efforts. The main</p><p>purpose of the work is to establish a set of ‘best practices’ that must be considered or executed</p><p>in order to secure a good alignment between the system and software package.</p><p>In order to achieve the main goal of this work, a case study approach has been used. The</p><p>case in question is a small manufacturing firm in Vetlanda called T-Emballage, which uses</p><p>an ERP system Jeeves. Mainly using scientific research techniques which comprise a deductive</p><p>approach and a mixed mode data collection method, some valuable conclusions are</p><p>drawn from the analysed data. The critical points that are worth considering during ERP</p><p>implementation, when trying to achieve alignment, arrived at in this study include: carrying</p><p>out a proper gap analysis, top management leading and following up, choosing software according</p><p>to needs, simplicity, flexibility, communication and liability of data.</p><p>This project further investigates the advantages and disadvantages of adapting or altering</p><p>the software package to fit the organization’s business processes and vice versa. Finally, the</p><p>work also tries to assess the alignment maturity level that has been attained in the organization</p><p>by applying the Luftman’s alignment maturity model.</p>

Background: Constructive alignment (CA) is a pedagogical approach that emphasizes the alignment between the intended learning outcomes (ILOs), teaching and learning activities (TLAs) and assessment tasks (ATs) as well as creation of a teaching/learning environment where students will be able to actively create their knowledge. Objectives: This paper aims at investigating the extent of constructively-aligned courses in Computer Engineering and Informatics department at Dalarna University, Sweden. This study is based on empirical observations of teacher’s perceptions of implementation of CA in their courses. Methods: Ten teachers (5 from each department) were asked to fill a paper-based questionnaire, which included a number of questions related to issues of implementing CA in courses. Results: Responses to the items of the questionnaire were mixed. Teachers clearly state the ILOs in their courses and try to align the TLAs and ATs to the ILOs. Computer Engineering teachers do not explicitly communicate the ILOs to the students as compared to Informatics teachers. In addition, Computer Engineering teachers stated that their students are less active in learning activities as compared to Informatics teachers. When asked about their subjective ratings of teaching methods all teachers stated that their current teaching is teacher-centered but they try to shift the focus of activity from them to the students. Conclusions: From teachers’ perspectives, the courses are partially constructively-aligned. Their courses are “aligned”, i.e. ILOs, TLAs and ATs are aligned to each other but they are not “constructive” since, according to them, there was a low student engagement in learning activities, especially in Computer Engineering department. / <p>Högskolepedagogik, högskolepedagogisk utbildning, BHU</p>

It is recognized that an iterative comparative analysis of large-scale homologous RNAs significantly promote the understanding of an RNA family. The Gutell lab is renowned for maintaining high quality RNA sequence alignments and accurately predicted RNA secondary structures using this approach. While the current available alignment and structure data are mainly obtained by trained domain experts with extensive manual effort, it is highly desired that this process is automated and replicable given the exponentially growing number of RNA sequence data and the amount of time required for expert training. In this thesis, we learn the processes involved in comparative analysis by manually aligning a non-coding RNA family, IVS sequences, with the supervision of Dr. Gutell. Each process is then simulated by mathematical objective functions and algorithms. We also evaluate the current available RNA analysis packages that aim each of the processes. Finally, a new RNA sequence alignment algorithm incorporating structure information that can be extended for different alignment tasks is proposed. / text

This paper considers the combination of interference alignment and distributed antenna systems to improve the rate performance of cell-edge users in the cellular downlink. Because the power resources of each antenna in distributed antenna systems are geographically separated, practical implementations of distributed antenna systems require consideration of per-antenna power constraints on the transmit antennas. For this reason, we consider interference alignment with two types of power constraints: per-antenna power inequality constraints and per-antenna power equality constraints. On one hand, we show that interference alignment with per-antenna power inequality constraints is arbitrarily feasible using a technique of antenna power back-off but suffers from a loss of performance that we quantify in the case of Rayleigh-fading. On the other hand, we show that interference alignment with per-antenna power equality constraints does not suffer from a systematic loss of performance but yet requires more antennas to be feasible. We develop algorithms for implementing interference alignment with both types of constraints and numerically validate the results of our analysis. Finally, we demonstrate using the 3rd Generation Partnership Project spatial channel model in a cellular setting that interference alignment with distributed antenna systems has better rate performance than interference alignment with centralized antenna systems throughout the entire cell, especially near the cell boundary. / text

The accurate prediction of an RNA secondary structure from its sequence will enhance the experimental design and interpretation for the increasing number of scientists that study RNA. While the computer programs that make these predictions have improved, additional improvements are necessary, in particular for larger RNAs. The first major section of this dissertation is concerned with improving the prediction accuracy of RNA secondary structures by generating new energetic parameters and evaluating a new RNA folding model. Statistical potentials for hairpin and internal loops produce significantly higher prediction accuracy when compared with nine other folding programs. While more improvements can be made to the energetic parameters used by secondary structure folding programs, I believe that a new approach is also necessary. I describe a RNA folding model that is predicated on a large body of computational and experimental work. This model includes energetics, contact distance, competition and a folding pathway. Each component of this folding model is evaluated and substantiated for its validity. The statistical potentials were created with comparative analysis. Comparative analysis requires the creation of highly accurate multiple RNA sequence alignments. The second major section of this dissertation is focused on my template-based sequence aligner, CRWAlign. Multiple sequence aligners generally run into problems when the pairwise sequence identity drops too low. By utilizing multiple dimensions of data to establish a profile for each position in a template alignment, CRWAlign is able to align new sequences with high accuracy even for pairs of sequence with low identity. / text