<p>Due to the explosion of the amount of biomedical data, knowledge and tools that are often publicly available over the Web, a number of difficulties are experienced by biomedical researchers. For instance, it is difficult to find, retrieve and integrate information that is relevant to their research tasks. Ontologies and the vision of a Semantic Web for life sciences alleviate these difficulties. In recent years many biomedical ontologies have been developed and many of these ontologies contain overlapping information. To be able to use multiple ontologies they have to be aligned or merged. A number of systems have been developed for aligning and merging ontologies and various alignment strategies are used in these systems. However, there are no general methods to support building such tools, and there exist very few evaluations of these strategies. In this thesis we give an overview of the existing systems. We propose a general framework for aligning and merging ontologies. Most existing systems can be seen as instantiations of this framework. Further, we develop SAMBO (System for Aligning and Merging Biomedical Ontologies) according to this framework. We implement different alignment strategies and their combinations, and evaluate them in terms of quality and processing time within SAMBO. We also compare SAMBO with two other systems. The work in this thesis is a first step towards a general framework that can be used for comparative evaluations of alignment strategies and their combinations.</p> / Report code: LiU-Tek-Lic-2006:6.

In this work the first observation of new type of liquid crystals is presented. This is ionic self-assembly (ISA) liquid crystals formed by introduction of oppositely charged ions between different low molecular tectonic units. As practically all conventional liquid crystals consist of rigid core and alkyl chains the attention is focused to the simplest case where oppositely charged ions are placed between a rigid core and alkyl tails. The aim of this work is to investigate and understand liquid crystalline and alignment properties of these materials. It was found that ionic interactions within complexes play the main role. Presence of these interactions restricts transition to isotropic phase. In addition, these interactions hold the system (like network) allowing crystallization into a single domain from aligned LC state. Alignment of these simple ISA complexes was spontaneous on a glass substrate. <br><br> In order to show potentials for application perylenediimide and azobenzene containing ISA complexes have been investigated for correlations between phase behavior and their alignment properties. The best results of macroscopic alignment of perylenediimide-based ISA complexes have been obtained by zone-casting method. In the aligned films the columns of the complex align perpendicular to the phase-transition front. The obtained anisotropy (DR = 18) is thermally stable. The investigated photosensitive (azobenzene-based) ISA complexes show formation of columnar LC phases. It was demonstrated that photo alignment of such complexes was very effective (DR = 50 has been obtained). It was shown that photo-reorientation in the photosensitive ISA complexes is cooperative process. The size of domains has direct influence on efficiency of the photo-reorientation process. In the case of small domains the photo-alignment is the most effective. Under irradiation with linearly polarized light domains reorient in the plane of the film leading to macroscopic alignment of columns parallel to the light polarization and joining of small domains into big ones. <br><br> Finally, the additional distinguishable properties of the ISA liquid crystalline complexes should be noted: (I) the complexes do not solve in water but readily solve in organic solvents; (II) the complexes have good film-forming properties when cast or spin-coated from organic solvent; (III) alignment of the complexes depends on their structure and secondary interactions between tectonic units. / In dieser Arbeit wird erstmalig eine neue Klasse von Flüssigkristallen auf Basis ionischer Self-Assembly (ISA) Komplexe beschrieben. Während herkömmliche thermotrope Flüssigkristalle aus steifen, formanisotropen Molekülfragmenten und kovalent gebundenen Flügelgruppen (meist Alkylketten) bestehen, entstehen diese neuartigen supramolekularen Verbindungen durch die Komplexierung gegensätzlich geladener ionischer tektonischer Einheiten und Tenside. <br><br> Ziel der Arbeit war es, die flüssigkristallinen und insbesondere die Orientierungseigenschaften dieser neuen Materialien am Beispiel repräsentativer Modellverbindungen zu untersuchen. Es wurde nachgewiesen, dass die ionischen Wechselwirkungen die thermischen Eigenschaften der Verbindungen entscheidend beeinflussen. So behindern sie den Übergang in die isotrope Phase. Das System wird quasi durch ein Netzwerk ionischer Wechselwirkungen stabilisiert. Makroskopisch orientierte LC Zustände sind offensichtlich Ausgangspunkt für hochgeordnete flüssigkristalline Filme oder gar für die Kristallisation von Monodomänen. In speziellen Fällen erfolgt eine spontane Ausbildung von ISA Monodomänen bereits auf Glassubstraten. <br><br> Mit Hinblick auf potentielle Anwendungen wurden Perylendiimid und Azobenzen enthaltene ISA Komplexe insbesondere hinsichtlich von Zusammenhängen zwischen Phasenverhalten und Orientierungseigenschaften untersucht. Die zone-casting Methode erwies sich als besonders geeignet für die makroskopische Orientierung perylendiimidbasierter ISA Komplexe. In orientierten Filmen richten sich die Kolumnen des Komplexes senkrecht zur Phasenübergangsfront aus. Das dabei erreichte dichroitische Verhältnis (DR=18) ist thermisch stabil. Die untersuchten Azobenzen basierten ISA Komplexe weisen kolumnare LC Phasen auf. Durch Photoalignment mittels linear polarisierten Lichts werden Komplexe sehr effektiv senkrecht bzw. die Columnen der Komplexe parallel zur Polarisation des Lichtes orientiert, wobei sehr hohe DR bis zu 50 erreicht wurden. Weiterhin wurde gezeigt, dass die Photo-Reorientierung photosensitiver ISA Komplexe kooperativ erfolgt. Die Größe der Domänen hat dabei einen entscheidenden Einfluß auf die Effektivität des Photo-Reorientierungsprozesses. So ist der Prozess im Fall kleiner Domänen effektiver. Durch die Bestrahlung mit linear polarisiertem Licht werden die Domänen in der Filmebene reorientiert, was zu einer makroskopischen Ausrichtung der Kolumnen parallel zur Lichtpolarisation und zu einer Vereinigung kleiner Domänen führt.

Vertical alignment liquid crystal display has the advantages of wide view angle, high contrast and good response time. Today vertical alignment liquid crystal display get flourishing development, and Multi-Domain Vertical Alignment (MVA) technology is progressive. In this report we would find an alignment materiel which could be fabricated easily, low cost and good E-O characteristic. The use of dimenthysiloxane (PDMS) in fabrication of microfluidic channels technology in biotechnology has the advantages of characteristics foregoing. In this study PDMS was used as LC vertical alignment materiel. We used the MVA structure and ASV structure to align LC direction because PDMS cannot be rubbed. In experiment we found that PDMS exhibited different surface energies when it was baked in different temperature. The results of measuring the pre-tilt angle in the different surface energy conditions are similar. ASV LC samples were fabricated using PDMS alignment layer. MVA LC cells were made using high viscosity PDMS. We found the characteristic of paper white at CIE chromaticity diagram in the ASV LC sample without any color filter and color correction technology.

RNA molecules form complex higher-order structures which are essential to perform their biological activities. The accurate prediction of an RNA secondary structure and other higher-order structural constraints will significantly enhance the understanding of RNA molecules and help interpret their functions. Covariation analysis is the predominant computational method to accurately predict the base pairs in the secondary structure of RNAs. I developed a novel and powerful covariation method, Phylogenetic Events Count (PEC) method, to determine the positional covariation. The application of the PEC method onto a bacterial 16S rRNA sequence alignment proves that it is more sensitive and accurate than other mutual information based method in the identification of base-pairs and other structural constraints of the RNA structure. The analysis also discoveries a new type of structural constraint – neighbor effect, between sets of nucleotides that are in proximity in the three dimensional RNA structure with weaker but significant covariation with one another. Utilizing these covariation methods, a proposed secondary structure model of an entire HIV-1 genome RNA is evaluated. The results reveal that vast majority of the predicted base pairs in the proposed HIV-1 secondary structure model do not have covariation, thus lack the support from comparative analysis. Generating the most accurate multiple sequence alignment is fundamental and essential of performing high-quality comparative analysis. The rapid determination of nucleic acid sequences dramatically increases the number of available sequences. Thus developing the accurate and rapid alignment program for these RNA sequences has become a vital and challenging task to decipher the maximum amount of information from the data. A template-based RNA sequence alignment system, CRWAlign-2, is developed to accurately align new sequences to an existing reference sequence alignment based on primary and secondary structural similarity. A comparison of CRWAlign-2 with eight alternative widely-used alignment programs reveals that CRWAlign-2 outperforms other programs in aligning new sequences with higher accuracy. In addition to aligning sequences accurately, CRWAlign-2 also creates secondary structure models for each sequence to be aligned, which provides very useful information for the comparative analysis of RNA sequences and structures. The CRWAlign-2 program also provides opportunities for multiple areas including the identification of chimeric 16S rRNA sequences generated in microbiome sequencing projects. / text

Transfer Alignment is the process of simultaneously initializing and calibrating a weapon inertial navigation system (INS) using data from host aircraft&rsquo / s navigation system. In general, this process is accomplished by calculating the difference of navigation solutions between aircraft and weapon INSs to form observations which are then used in a Kalman filter to generate desired estimates. Numerous techniques about the problem of transfer alignment exist in the literature. In this thesis, those techniques that can be applied in the presence of elastic motion of aircraft wing were analyzed. Several transfer alignment algorithms each of which process different measurement types were designed and implemented. In order to evaluate the performance of implemented algorithms under realistic conditions, a transfer alignment simulation environment was developed. Using this simulation environment, the advantages and disadvantages of each algorithm were analyzed and the dependence of transfer alignment performance on Kalman filter system model, aircraft maneuvers and alignment duration were investigated.

Thesis (M.Sc.). / Written for the Dept. of Biology. Title from title page of PDF (viewed 2008/12/07). Includes bibliographical references.

abstract: Genomic and proteomic sequences, which are in the form of deoxyribonucleic acid (DNA) and amino acids respectively, play a vital role in the structure, function and diversity of every living cell. As a result, various genomic and proteomic sequence processing methods have been proposed from diverse disciplines, including biology, chemistry, physics, computer science and electrical engineering. In particular, signal processing techniques were applied to the problems of sequence querying and alignment, that compare and classify regions of similarity in the sequences based on their composition. However, although current approaches obtain results that can be attributed to key biological properties, they require pre-processing and lack robustness to sequence repetitions. In addition, these approaches do not provide much support for efficiently querying sub-sequences, a process that is essential for tracking localized database matches. In this work, a query-based alignment method for biological sequences that maps sequences to time-domain waveforms before processing the waveforms for alignment in the time-frequency plane is first proposed. The mapping uses waveforms, such as time-domain Gaussian functions, with unique sequence representations in the time-frequency plane. The proposed alignment method employs a robust querying algorithm that utilizes a time-frequency signal expansion whose basis function is matched to the basic waveform in the mapped sequences. The resulting WAVEQuery approach is demonstrated for both DNA and protein sequences using the matching pursuit decomposition as the signal basis expansion. The alignment localization of WAVEQuery is specifically evaluated over repetitive database segments, and operable in real-time without pre-processing. It is demonstrated that WAVEQuery significantly outperforms the biological sequence alignment method BLAST for queries with repetitive segments for DNA sequences. A generalized version of the WAVEQuery approach with the metaplectic transform is also described for protein sequence structure prediction. For protein alignment, it is often necessary to not only compare the one-dimensional (1-D) primary sequence structure but also the secondary and tertiary three-dimensional (3-D) space structures. This is done after considering the conformations in the 3-D space due to the degrees of freedom of these structures. As a result, a novel directionality based 3-D waveform mapping for the 3-D protein structures is also proposed and it is used to compare protein structures using a matched filter approach. By incorporating a 3-D time axis, a highly-localized Gaussian-windowed chirp waveform is defined, and the amino acid information is mapped to the chirp parameters that are then directly used to obtain directionality in the 3-D space. This mapping is unique in that additional characteristic protein information such as hydrophobicity, that relates the sequence with the structure, can be added as another representation parameter. The additional parameter helps tracking similarities over local segments of the structure, this enabling classification of distantly related proteins which have partial structural similarities. This approach is successfully tested for pairwise alignments over full length structures, alignments over multiple structures to form a phylogenetic trees, and also alignments over local segments. Also, basic classification over protein structural classes using directional descriptors for the protein structure is performed. / Dissertation/Thesis / Ph.D. Electrical Engineering 2011

Este trabalho investiga técnicas de extração de termos multipalavra a partir de corpora comparáveis, que são conjuntos de textos em duas (ou mais) línguas sobre o mesmo domínio. A extração de termos, especialmente termos multipalavra é muito importante para auxiliar a criação de terminologias, ontologias e o aperfeiçoamento de tradutores automáticos. Neste trabalho utilizamos um corpus comparável português/inglês e queremos encontrar termos e seus equivalentes em ambas as línguas. Para isso começamos com a extração dos termos separadamente em cada língua, utilizando padrões morfossintáticos para identificar os n-gramas (sequências de n palavras) mais prováveis de serem termos importantes para o domínio. A partir dos termos de cada língua, utilizamos o contexto, isto é, as palavras que ocorrem no entorno dos termos para comparar os termos das diferentes línguas e encontrar os equivalentes bilíngues. Tínhamos como objetivos principais neste trabalho fazer a identificação monolíngue de termos, aplicar as técnicas de alinhamento para o português e avaliar os diferentes parâmetros de tamanho e tipo (PoS utilizados) de janela para a extração de contexto. Esse é o primeiro trabalho a aplicar essa metodologia para o Português e apesar da falta de alguns recursos léxicos e computacionais (como dicionários bilíngues e parsers) para essa língua, conseguimos alcançar resultados comparáveis com o estado da arte para trabalhos em Francês/Inglês. / This work investigates techniques for multiword term extraction from comparable corpora, which are sets of texts in two (or more) languages about the same topic. Term extraction, specially multiword terms is very important to help the creation of terminologies, ontologies and the improvement of machine translation. In this work we use a comparable corpora Portuguese/ English and want to find terms and their equivalents in both languages. To do this we start with separate term extraction for each language. Using morphossintatic patterns to identify n-grams (sequences of n words) most likely to be important terms of the domain. From the terms of each language, we use their context, i. e., the words that occurr around the term to compare the terms of different languages and to find the bilingual equivalents. We had as main goals in this work identificate monolingual terms, apply alignment techniques for Portuguese and evaluate the different parameters of size and type (used PoS) of window to the context extraction. This is the first work to apply this methodology to Portuguese and in spite of the lack of lexical and computational resources (like bilingual dictionaries and parsers) for this language, we achieved results comparable to state of the art in French/English.

Este trabalho investiga técnicas de extração de termos multipalavra a partir de corpora comparáveis, que são conjuntos de textos em duas (ou mais) línguas sobre o mesmo domínio. A extração de termos, especialmente termos multipalavra é muito importante para auxiliar a criação de terminologias, ontologias e o aperfeiçoamento de tradutores automáticos. Neste trabalho utilizamos um corpus comparável português/inglês e queremos encontrar termos e seus equivalentes em ambas as línguas. Para isso começamos com a extração dos termos separadamente em cada língua, utilizando padrões morfossintáticos para identificar os n-gramas (sequências de n palavras) mais prováveis de serem termos importantes para o domínio. A partir dos termos de cada língua, utilizamos o contexto, isto é, as palavras que ocorrem no entorno dos termos para comparar os termos das diferentes línguas e encontrar os equivalentes bilíngues. Tínhamos como objetivos principais neste trabalho fazer a identificação monolíngue de termos, aplicar as técnicas de alinhamento para o português e avaliar os diferentes parâmetros de tamanho e tipo (PoS utilizados) de janela para a extração de contexto. Esse é o primeiro trabalho a aplicar essa metodologia para o Português e apesar da falta de alguns recursos léxicos e computacionais (como dicionários bilíngues e parsers) para essa língua, conseguimos alcançar resultados comparáveis com o estado da arte para trabalhos em Francês/Inglês. / This work investigates techniques for multiword term extraction from comparable corpora, which are sets of texts in two (or more) languages about the same topic. Term extraction, specially multiword terms is very important to help the creation of terminologies, ontologies and the improvement of machine translation. In this work we use a comparable corpora Portuguese/ English and want to find terms and their equivalents in both languages. To do this we start with separate term extraction for each language. Using morphossintatic patterns to identify n-grams (sequences of n words) most likely to be important terms of the domain. From the terms of each language, we use their context, i. e., the words that occurr around the term to compare the terms of different languages and to find the bilingual equivalents. We had as main goals in this work identificate monolingual terms, apply alignment techniques for Portuguese and evaluate the different parameters of size and type (used PoS) of window to the context extraction. This is the first work to apply this methodology to Portuguese and in spite of the lack of lexical and computational resources (like bilingual dictionaries and parsers) for this language, we achieved results comparable to state of the art in French/English.

Este trabalho investiga técnicas de extração de termos multipalavra a partir de corpora comparáveis, que são conjuntos de textos em duas (ou mais) línguas sobre o mesmo domínio. A extração de termos, especialmente termos multipalavra é muito importante para auxiliar a criação de terminologias, ontologias e o aperfeiçoamento de tradutores automáticos. Neste trabalho utilizamos um corpus comparável português/inglês e queremos encontrar termos e seus equivalentes em ambas as línguas. Para isso começamos com a extração dos termos separadamente em cada língua, utilizando padrões morfossintáticos para identificar os n-gramas (sequências de n palavras) mais prováveis de serem termos importantes para o domínio. A partir dos termos de cada língua, utilizamos o contexto, isto é, as palavras que ocorrem no entorno dos termos para comparar os termos das diferentes línguas e encontrar os equivalentes bilíngues. Tínhamos como objetivos principais neste trabalho fazer a identificação monolíngue de termos, aplicar as técnicas de alinhamento para o português e avaliar os diferentes parâmetros de tamanho e tipo (PoS utilizados) de janela para a extração de contexto. Esse é o primeiro trabalho a aplicar essa metodologia para o Português e apesar da falta de alguns recursos léxicos e computacionais (como dicionários bilíngues e parsers) para essa língua, conseguimos alcançar resultados comparáveis com o estado da arte para trabalhos em Francês/Inglês. / This work investigates techniques for multiword term extraction from comparable corpora, which are sets of texts in two (or more) languages about the same topic. Term extraction, specially multiword terms is very important to help the creation of terminologies, ontologies and the improvement of machine translation. In this work we use a comparable corpora Portuguese/ English and want to find terms and their equivalents in both languages. To do this we start with separate term extraction for each language. Using morphossintatic patterns to identify n-grams (sequences of n words) most likely to be important terms of the domain. From the terms of each language, we use their context, i. e., the words that occurr around the term to compare the terms of different languages and to find the bilingual equivalents. We had as main goals in this work identificate monolingual terms, apply alignment techniques for Portuguese and evaluate the different parameters of size and type (used PoS) of window to the context extraction. This is the first work to apply this methodology to Portuguese and in spite of the lack of lexical and computational resources (like bilingual dictionaries and parsers) for this language, we achieved results comparable to state of the art in French/English.