Or Man Wai. / "January 2002." / "glued" in title is superscript. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references. / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web.

Made available in DSpace on 2016-04-27T17:05:59Z (GMT). No. of bitstreams: 1 Vagner Uendel de Sa Medeiros.pdf: 1681184 bytes, checksum: 6838cfdf4c1b1e02f7c96d2ae71dd60c (MD5) Previous issue date: 2015-03-02 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / One of the problems faced by the visually impaired is the location of objects in an unfamiliar environment. Find a product in a store without assistance is almost impossible for a person with low vision. Therefore, in this research we developed a system to provide the location of products in the supermarket aisles and then allow reading the bar code or NFC tag on the product or on the shelf .To select from the options location or identification, the screen cell was divided into two parts such that the blind or visually impaired persons may choose between them. Hence, in this study used a smartphone with Android operating system. The system was developed using the MIT App Inventor 2. This interface is a web application with open source developed by Google and maintained by the Massachusetts Institute of Technology (MIT). The interface is divided into two parts, one devoted to the design and implementation for another logic. The program is based on the Scheme language, Google voice ID and bar code reader. The device was tested indoors simulating aisles and shelves of a supermarket measuring the time required to find and identify five products. The adoption by store and supermarket system developed for this research, facilitating the location and identification of products, should contribute to the independence and quality of life for people with visual limitations / Um dos problemas enfrentados pelos deficientes visuais é a localização de objetos em um ambiente desconhecido. Encontrar um produto numa loja, sem assistência é quase impossível para uma pessoa com baixa visão. Portanto,nessa pesquisa foi desenvolvido um sistema para proporcionar a localização de produtos nos corredores dos supermercados e a seguir permitir a leitura do código de barras ou da etiqueta NFC no produto ou na prateleira. Para selecionar entre as opções localização ou identificação, a tela do celular foi dividida em duas partes de tal modo que os deficientes visuais ou pessoas com baixa visão possam escolher entre elas . Para tanto, neste trabalho foi usado um smartphone com sistema operacional Android. O sistema foi desenvolvido utilizando o MIT App Inventor 2. Esta interface é uma aplicação web com código-fonte aberto desenvolvido pelo Google e mantido pelo Instituto de Tecnologia de Massachusetts (MIT). A interface é dividida em duas partes, uma para à concepção da aplicação dedicada e outra para a lógica. A programação é baseada na linguagem Scheme, identificador de voz Google e leitor de código de barras. O dispositivo foi testado em ambiente fechado simulando corredores e prateleiras de um supermercado mensurando o tempo necessário para encontrar e identificar cinco produtos.A adoção por loja e supermercados do sistema desenvolvido para essa pesquisa, facilitando a localização e identificação de produtos, devera contribuir para a independência e qualidade de vida das pessoas com limitações visuais

Chemical biology can be defined as the area of science where chemical tools are used to study biological systems. The simplest way this can be achieved is in the identification of compounds which inhibit or modulate a biological pathway and the consequences studied. However, novel tools are required to enable, for example, the development of assays to allow simpler screening of difficult targets such as membrane proteins and protein-protein interactions. A series of kisspeptin analogues were synthesised for the development of a screening platform compatible with G-protein coupled receptors and tagged one bead one compound (OBOC) combinatorial libraries. Fluorescently labelled kisspeptin showed good affinity for GPCR54 and an on-bead version of the peptide, with the required C-terminal amide presented away from the bead was prepared and used for testing possible screening methods. GPCR54 was expressed in a number of formats and a kisspeptin based OBOC library designed and synthesised. Investigation into the C-terminal RF-amide motif of Kisspeptin was also carried out in order to assess the importance of the carbonyl moiety. The corresponding peptide amine was synthesised and the compound biologically assessed. This led to the development of a novel acid labile benzofuranone (ALBA) linker for anchoring amines to a solid support. For the preparation of fluorescent kisspeptin ligands, a novel general synthetic route which gives direct access to single isomer functionalised rhodamine dyes from phthalides has been developed. This circumvents the arduous task of isomer separation usually associated with the synthesis of functionalised rhodamines. The route has been demonstrated with a range of linkage groups and rhodamine types. This rhodamine material was used as a reporter group in various multifunctional reagents synthesised using a trifunctional orthogonally protected backbone (TOBa), which was prepared on a solid support and enables rapid synthesis of trifunctional reagents. This resin takes advantage of protecting group orthogonality and the high yields of peptide bond formation. A series of trifunctional reagents for screening use were prepared using this resin. A proof of concept study was carried out involving the simultaneous labelling and immobilisation of a protein for applications in probing protein-protein interactions. Development of a trifunctional hydroxamic acid containing cross-linker was carried out which takes advantage of its reaction with boronic acids to enable reversible capture on solid support for enrichment of cross-linked peptides. A new benzophenone based heterobifunctional reagent was prepared for protein cross-linking and mass spectrometry analysis. This was shown to give complimentary reactivity to existing cross-linkers, allowing more structural information to be extracted from protein samples.

Knowledge of fish habitat use and connectivity is critical for understanding the structure and dynamics of fish populations and, therefore, necessary for the implementation of successful fisheries management strategies. Tagging is an effective means of providing such information, and the elemental composition contained within fish otoliths is increasingly being used as a natural tag. The chemical composition of otoliths reflects the incorporation of elements from different water bodies and can thus be used to understand the habitat use, movements, and life history patterns of fishes. To assess the applicability of otolith elemental composition as a tagging technique within the Tampa Bay estuary, Florida, laser ablation-inductively coupled-plasma mass spectrometry (LA-ICP-MS) was used to analyze the elemental composition of otoliths from two estuarine-dependent fish species, Snook (Centropomus undecimalis) and Red Drum (Sciaenops ocellatus). Otolith elemental fingerprints can be used to quantify the proportion of juveniles from different nurseries that survive to join the sub-adult and adult fisheries, thus, providing resource managers with quantitative criteria to prioritize the most productive areas for conservation and restoration. To evaluate the use of otolith elemental fingerprinting in the Tampa Bay estuary, the spatial and temporal scales of chemical variation in otoliths collected from throughout Tampa Bay were examined by performing permutation-based multivariate analyses of variance (MANOVA) on the elemental data at several spatial (individual tributary, two-region, and three-region) and temporal (annual and seasonal) scales. Canonical Analysis of Principal Coordinates (CAP) was used to generate classifiers based on the otolith elemental fingerprints of juvenile fish, and `leave-one-out' cross-validation procedures indicated that the greatest classification accuracy was obtained by using the two-region model (upper vs. lower Tampa Bay) for both species (for Snook F=45.8, p=0.001, CAP cross-validation success=76%; for Red Drum F=9.7, p=0.001, CAP cross-validation success=87%). For both species, all temporal analyses at the inter-annual scale indicated that otolith elemental fingerprints were significantly different across years (two-way MANOVA; p Several environmental factors which may have contributed to the regional differences in otolith chemistry were examined, including physico-chemical parameters (surface measurements of salinity, dissolved oxygen, pH, and temperature taken at the time of sample collection), surficial geologic stratigraphy, and land development. Weak, but significant correlations were identified between some elements and physico-chemical parameters; however, instantaneous measurements taken at the time of fish collection may not have provided an accurate representation of the overall conditions experienced by the fish during the period in which the otolith material used in analyses had been deposited (2 - 4 weeks). A significant correlation between latitude and otolith Sr/Ca was found, likely corresponding to an increasing ambient gradient that occurs from the upper to lower bay (for Red Drum F=77.1, p=0.001; for Snook F=69.2, p=0.001). The Land Development Intensity metric was negatively correlated with otolith Li/Ca and Sr/Ca. While surficial geologic inputs may have also contributed to the elemental composition of otoliths, the relationships revealed by redundancy analyses (RDA) were somewhat unclear or contradictory. Once the appropriate chemical characterization of the study area was identified (the two-region models for both species), elemental fingerprints from the core portions of sub-adult and adult otoliths were assigned to their most probable juvenile habitat region using a maximum likelihood estimator based on the posterior probabilities generated by CAP analyses (CAP-MLE). Application of the two-region model revealed that the majority of Red Drum (83%) was determined to have originated from juvenile habitats in the upper Tampa Bay region, while most Snook (60%) originated from juvenile habitats in the lower Tampa Bay region. The majority of sub-adult/adult Snook and Red Drum were collected from the same region in which they were determined to have originated (for Snook, 36 out of 55 = 65%; for Red Drum, 58 out of 78 = 74%), indicating some level of site fidelity to juvenile habitat areas. The use of otolith elemental profiling to reconstruct specific environmental and physiological experiences has the potential to provide unique insights regarding the life histories of Snook, a species with unpredictable spawning and movement characteristics. Otoliths from Snook maintained in captivity at the Mote Aquaculture Park (MAP) were analyzed to elucidate the degree to which various factors, including otolith growth (macrostructure features), spawning events, handling stress, and salinity influence otolith chemistry. Cross-correlation analyses of otolith elemental profiles and quantified macrostructure features (including annuli and checks) demonstrated that interpretations of elemental patterns should not be confounded by changes associated with otolith crystallography. An elemental marker for known spawning events was not identified (ANOVA spawners vs. non-spawners, p>0.05); however, because the physiological costs and alterations in blood chemistry associated with gonadal maturation (rather than the singular act of spawning) could affect otolith chemistry, additional studies which more thoroughly track maturation stages may be able to identify a suite of elements that can be used to discern the reproductive histories of Snook. Significantly elevated Zn:Ca (ANOVA: F=5.64, p=0.012) and decreased Fe:Ca (ANOVA: F=25.02, p Continuous life history Ba:Ca and Sr:Ca profiles of 56 wild Snook collected from throughout Tampa Bay revealed significant plasticity in the types of juvenile habitats settled, as well as in the timing of ontogenetic movements from these habitats. Of the profiles examined, 55% exhibited otolith core signatures characterized by an opposing Sr:Ca and Ba:Ca pattern, followed by an inverted pattern, providing an indicator of the movement of larvae from high salinity, pre-settlement environments into mesohaline, tidally-influenced juvenile habitats. In contrast, nearly half (45%) the Sr:Ca and Ba:Ca profiles indicated settlement in higher salinity environments, suggesting a high degree of habitat plasticity for juveniles of this species. For fish that settled into mesohaline habitats, decreases in Ba:Ca and/or increases in Sr:Ca over the first several years of life signaled the ontogenetic transition out of the juvenile habitat, with the timing of emergence ranging from within the first year to age-3. Because conditions during early life may propagate into divergent behaviors in subsequent life stages, information on the experiences of early life and juvenile stages could help to inform whether the occupation of different juvenile habitat types, or the precocious or delayed emergence from those habitats, explain the peculiar spawning and movement habits that occur in this species.

This thesis principally addresses some problems in genetic programming (GP) and grammar-guided genetic programming (GGGP) arising from the lack of operators able to make small and bounded changes on both genotype and phenotype space. It proposes a new and flexible representation for genetic programming, using a state-of-the-art formalism from natural language processing, Tree Adjoining Grammars (TAGs). It demonstrates that the new TAG-based representation possesses two important properties: non-fixed arity and locality. The former facilitates the design of new operators, including some which are bio-inspired, and others able to make small and bounded changes. The latter ensures that bounded changes in genotype space are reflected in bounded changes in phenotype space. With these two properties, the thesis shows how some well-known difficulties in standard GP and GGGP tree-based representations can be solved in the new representation. These difficulties have been previously attributed to the treebased nature of the representations; since TAG representation is also tree-based, it has enabled a more precise delineation of the causes of the difficulties. Building on the new representation, a new grammar guided GP system known as TAG3P has been developed, and shown to be competitive with other GP and GGGP systems. A new schema theorem, explaining the behaviour of TAG3P on syntactically constrained domains, is derived. Finally, the thesis proposes a new method for understanding performance differences between GP representations requiring different ways to bound the search space, eliminating the effects of the bounds through multi-objective approaches.

In the field of Music Data Mining, Mood and Topic information has been considered as a high level metadata. The extraction of mood and topic information is difficult but is regarded as very valuable. The immense growth of Web 2.0 resulted in Social Tags being a direct interaction with users (humans) and their feedback through tags can help in classification and retrieval of music. One of the major shortcomings of the approaches that have been employed so far is the improper filtering of social tags. This thesis delves into the topic of information extraction from songs’ tags and lyrics. The main focus is on removing all erroneous and unwanted tags with help of other features. The hierarchical clustering method is applied to create clusters of tags. The clusters are based on semantic information any given pair of tags share. The lyrics features are utilized by employing CLOPE clustering method to form lyrics clusters, and Naïve Bayes method to compute probability values that aid in classification process. The outputs from classification are finally used to estimate the accuracy of a tag belonging to the song. The results obtained from the experiments all point towards the success of the method proposed and can be utilized by other research projects in the similar field.

This thesis covers the process from expression of a heterologous gene in Escherichia coli to structure determination of a protein by nuclear magnetic resonance (NMR) spectroscopy. The first part concerns structural genomics-related parallel screening studies on the effect of fusion tags (in particular the His tag) on protein solubility and the use of fusion tags in fast, parallel purification protocols intended for initial biophysical characterization of human proteins produced in E. coli. It was found that for most proteins the His tag has a negative influence on protein solubility. This influence appears to be more pronounced for our C-terminal His tag than for the N-terminal His tags used in this study. Moreover, high ratios of soluble per total protein do not always guarantee a high yield of soluble protein after purification, as different vector - target protein combinations result in large differences in host cell growth rates. Protein purification protocols for different fusion tags were developed that make it possible to express, purify and study structural properties of low concentration samples of 15N-labeled proteins in one or two days. The second part of this thesis describes the assignment and solution structure determination of ribosomal protein L18 of Thermus thermophilus. The protein is a mixed α/β structure with two α-helices on one side of a four-stranded β-sheet. Comparison to RNA-bound L18 showed that the protein to a large extent adopts identical structures in free and bound states, with exception of the loop regions and the flexible N-terminus. Keywords: protein production, protein solubility, fusion tags, nuclear magnetic resonance, structure determination, ribosomal protein

When users are searching for documents, they must sift through a collection of potentially relevant documents assessing, categorizing and prioritizing them based on the current task at hand, a process we refer to as document triage. Since users' time is precious, as much information as possible should be presented to them to aid the process of document triage. This thesis presents a simple visualization and a set of features that can help users in identifying information of interest. As a part of this thesis, the System Layer of the Visual Knowledge Builder (VKB) was developed as a tab strip container. Each of the tabs presents a different type of information about Web Documents. The types of information currently included in VKB are: a summary of the Web Document, keywords based on users' interests provided by the Interest Profile Manager (IPM), popular keywords from a social bookmarking site, metadata about the Web Document, a list of outgoing links of the Web Document, and the history of the Web Document. We performed a heuristic evaluation to assess the usefulness of the new visualization and features. During the evaluation, participants were asked to rate the usefulness of each of the new web document features over a scale of 1 to 7, where a value of 1 indicated strong disagreement, and 7 indicated strong agreement. Our results indicate that the document summary, the keywords from IPM, popular tags, and the history of the Web Document are expected to be most useful during the process of document triage.

In the multidisciplinary design process, design documents are used to help support a team's design and mediate any misunderstandings that occur. Current methods of organizing such design documents are either difficult to keep up to date physically with their digital versions, or inhibit distributed users access to important comparative information. Digital tag and content thumbnail-based document organization is presented as a possible alternative. The effects of tag-based document organization on the manner in which collocated and distributed design teams categorize, review and search design documents and resolve design misunderstandings were compared to the effects of traditional physical (the pin up walls of project rooms)&digital (shared digital file folders) document organization. Student participant design teams were assembled. These teams were observed organizing a provided set of design documents and develop a design solution as a team using either tag-based or traditional physical or digital document organization. Team members were given retrieval tests to compare search times between methods of document organization. User feedback on organization preferences were collected and used to develop a conceptual prototype of a document organization interface supportive of the multidisciplinary design process. Though the quantitative results did no clearly favor tag-based organization, observational results and user comments were in support of the capabilities tag-based organization provides.

<p>This thesis covers the process from expression of a heterologous gene in Escherichia coli to structure determination of a protein by nuclear magnetic resonance (NMR) spectroscopy. </p><p>The first part concerns structural genomics-related parallel screening studies on the effect of fusion tags (in particular the His tag) on protein solubility and the use of fusion tags in fast, parallel purification protocols intended for initial biophysical characterization of human proteins produced in E. coli. It was found that for most proteins the His tag has a negative influence on protein solubility. This influence appears to be more pronounced for our C-terminal His tag than for the N-terminal His tags used in this study. Moreover, high ratios of soluble per total protein do not always guarantee a high yield of soluble protein after purification, as different vector - target protein combinations result in large differences in host cell growth rates. Protein purification protocols for different fusion tags were developed that make it possible to express, purify and study structural properties of low concentration samples of 15N-labeled proteins in one or two days. </p><p>The second part of this thesis describes the assignment and solution structure determination of ribosomal protein L18 of Thermus thermophilus. The protein is a mixed α/β structure with two α-helices on one side of a four-stranded β-sheet. Comparison to RNA-bound L18 showed that the protein to a large extent adopts identical structures in free and bound states, with exception of the loop regions and the flexible N-terminus.</p><p><b>Keywords:</b> protein production, protein solubility, fusion tags, nuclear magnetic resonance, structure determination, ribosomal protein</p>