A técnica geofísica da eletrorresistividade adaptada para ambientes aquáticos, com a tecnologia que hoje temos à disposição, mostra-se bastante promissora e de grande produtividade tanto na coleta dos dados de campo como no reconhecimento de feições de interesse do substrato, possibilitando ainda a liberdade de se adquirir tais informações em perfis subaquáticos contínuos em quaisquer trechos navegáveis de rios e lagos e, eventualmente de mares. Neste contexto, esta dissertação abordou a aplicabilidade desta técnica, com a utilização de modernos equipamentos e acessórios adaptados para trabalhos em lâmina d\'água, onde foram executados e estudados os procedimentos de campo, processamentos e integração dos dados coletados, além da verificação da consistência dos resultados obtidos através da realização de linhas de estudos paralelas e também ortogonais. Os testes de aplicação da técnica foram realizados nas águas do rio São Francisco, mais precisamente em seu trecho que faz divisa dos estados da Bahia e Pernambuco, região nordeste do Brasil, local este que também tem sido objeto de estudos para o Projeto do Aproveitamento Hidrelétrico Riacho Seco, pertencentes à empresa Companhia Hidro Elétrica do São Francisco (CHESF), responsável por diversos estudos e desenvolvimentos desta região, notadamente dos recursos hídricos do baixo São Francisco. Os trabalhos de campo lançaram mão do uso de embarcação para transportar e arrastar, na superfície da água, um cabo multi-eletrodo de imageamento geoelétrico, especialmente desenvolvido para tais fins, bem como todos os equipamentos integrados a saber: equipamento GPS de navegação em ambientes aquáticos, eco-batímetro de dupla freqüência adaptado na embarcação, eletrorresistivímetro multicanal e notebook com software específico para o gerenciamento de todas as operações e dados. Os resultados mostraram que foi possível mapear a fisiografia do leito do rio bem como identificar e delimitar anomalias geofísicas compatíveis a prováveis ocorrências de depósitos de sedimentos assim como feições típicas de contatos litológicos e mesmo de estruturas do tipo alteração/fraturamento no interior dos materiais do subfundo do rio. / The electric tomography geophysical technique adapted for aquatic environment, with the modern technology available nowadays, reveals itself sufficiently promising and of great productivity both in the field data collection and in the recognition of aspects of interest of the substratum. It is possible to make the data acquiring in any navigable stretches of rivers, lakes and some seas. In this context, this paper approached the applicability of this technique, with the use of modern equipment and accessories for works in the water. The field procedures, the data processing and integration of the data collection are discussed considering the acquisition of a great amount of data both parallel and orthogonal to the river. The application tests of the technique were conducted in the river San Francisco, in the region of the border of the states of Bahia and Pernambuco, northeast region of Brazil. This area was selected because it has been subject of studies to install a hydroelectric plant (Riacho Seco), owned by the Companhia Hidro Elétrica do São Francisco (CHESF). To perform the field works a boat was used to carry and drag, in the surface of the water, a multi-electrode cable of electric tomography, especially developed for such purposes, as well as all the integrated equipment namely: GPS especially designed for navigation in aquatic environments, adapted fathometer of double frequency in the boat, multichannel eletrorresistivímeter and notebook with specific software that managed all the operations and data. The results had shown that it was possible to map the fisiography of the riverbed as well as identifying and delimiting geophysical anomalies compatible to the probable occurrences of deposits of sediments as well as typical lithologic contacts and structures like weathering and fractures in the underground materials in the bottom of the river.

Health care today harms too frequently and routinely fails to deliver its potential benefits. Significant evidence suggests that high quality primary care can positively affect health outcomes. I explored three related topics mentioned frequently in current United States health reform €“ Electronic Health Records (EHR), physician profiling and Medical Home. An investment in these areas is expected to significantly improve quality of care and efficiency; however, there is only a patchwork of evidence supporting such claims. To achieve EHR promises, my research employed a standardization lens to study the dynamics between EHR embedded structures and primary care processes. Using grounded theory, a standardization dynamics model was created describing the influencers, conditions and consequences of the process state. A matrix of two conditions, information exchange and patient complexity, identified four distinct pathways that require a different balance between standardization and flexibility. The value of such pathways is that they frame choices about how to use embedded IT structures to support effective delivery processes. Physician profiling is an emerging methodology used in health care quality improvement programs. Efforts to measure performance at the individual physician level face a number of challenges, including the need for sufficient sample size to support reliable measurement. A process for creating a physician profiling model was developed, and a model designed for a case study site. Results indicate that reliable physician profiling is possible across care domains using a hierarchical composite model. Patient-Centered Medical Home (PCMH) is a new care delivery approach for providing comprehensive primary care that seeks to strengthen the physician-patient relationship. This exploratory study utilizes Pearson correlation coefficients to test four hypotheses about relationships between two sources of data: (1) PPC-PCMH Survey results that measure adoption of PCMH structures and (2) patient experience data from Massachusetts Health Quality Partners (MHQP). The results showed that the PPC-PCMH structures of access and communication were negatively correlated with the related patient experience measure. This study contributes to the literature by addressing deficiencies in how EHR-enabled processes, physician profiling models and Medical Home constructs are measured, to support improved outcomes.

As the amount of information captured about users increased over the last decade, interest in personalized user interfaces has surged in the HCI and IS communities. Personalization is an effective means for accommodating for differences between individuals. The fundamental idea behind personalization rests on the notion that if a system can gather useful information about the user, generate a relevant user model and apply it appropriately, it would be possible to adapt the behavior of a system and its interface to the user at the individual level. Personal-ization of a user interface features can enhance usability. With recent technological advances, personalization can be achieved automatically and unobtrusively. A user interface can deploy a NeuroIS technology such as eye-tracking that learns from the user's visual behavior to provide users an experience most unique to them. The advantage of eye-tracking technology is that subjects cannot consciously manipulate their responses since they are not readily subject to manipulation. The objective of this dissertation is to develop a theoretical framework for user personalization during reading comprehension tasks based on two machine learning (ML) models. The proposed ML-based profiling process consists of user's age characterization and user's cognitive load detection, while the user reads text. To this end, detection of cognitive load through eye-movement features was investigated during different cognitive tasks (see Chapters 3, 4 and 6) with different task conditions. Furthermore, in separate studies (see Chapters 5 and 6) the relationship between user's eye-movements and their age population (e.g., younger and older generations) were carried out during a reading comprehension task. A Tobii X300 eye tracking device was used to record the eye movement data for all studies. Eye-movement data was acquired via Tobii eye tracking software, and then preprocessed and analyzed in R for the aforementioned studies. Machine learning techniques were used to build predictive models. The aggregated results of the studies indicate that machine learning accompanied with a NeuroIS tool like eye-tracking, can be used to model user characteristics like age and user mental states like cognitive load, automatically and implicitly with accuracy above chance (range of 70-92%). The results of this dissertation can be used in a more general framework to adaptively modify content to better serve the users mental and age needs. Text simplification and modification techniques might be developed to be used in various scenarios.

As the backbone of many computing environments today, it is important that process virtual machines be both performant and robust in mobile, personal desktop, and enterprise applications. This thesis focusses on code generation within these virtual machines, particularly addressing situations where redundant work is being performed. The goal is to exploit information sharing in order to improve the performance and robustness of virtual machines that are accelerated by native code generation. First, the thesis investigates the potential to share generated code between multiple threads in a dynamic binary translator used to perform instruction set simulation. This is done through a code generation design that allows native code to be executed by any simulated core and adding a mechanism to share native code regions between threads. This is shown to improve the average performance of multi-threaded benchmarks by 1.4x when simulating 128 cores on a quad-core host machine. Secondly, the ahead-of-time code generation system used for executing Android applications is improved through the use of profiling. The thesis investigates the potential for profiles produced by individual users of applications to be shared and merged together to produce a generic profile that still provides a lot of benefit for a new user who is then able to skip the expensive profiling phase. These profiles can not only be used for selective compilation to reduce code-size and installation time, but can also be used for focussed optimisation on vital code regions of an application in order to improve overall performance. With selective compilation applied to a set of popular Android applications, code-size can be reduced by 49.9% on average, while installation time can be reduced by 31.8%, with only an average 8.5% increase in the amount of sequential runtime required to execute the collected profiles. The thesis also shows that, among the tested users, the use of a crowd-sourced and merged profile does not significantly affect their estimated performance loss from selective compilation (0.90x-0.92x) in comparison to when they they perform selective compilation with their own unique profile (0.93x). Furthermore, by proposing a new, more powerful code generator for Android’s virtual machine, these same profiles can be used to perform focussed optimisation, which preliminary results show to increase runtime performance across a set of common Android benchmarks by 1.46x-10.83x. Finally, in such a situation where a new code generator is being added to a virtual machine, it is also important to test the code generator for correctness and robustness. The methods of execution of a virtual machine, such as interpreters and code generators, must share a set of semantics about how programs must be executed, and this can be exploited in order to improve testing. This is done through the application of domain-aware binary fuzzing and differential testing within Android’s virtual machine. The thesis highlights a series of actual code generation and verification bugs that were found in Android’s virtual machine using this testing methodology, as well as comparing the proposed approach to other state-of-the-art fuzzing techniques.

Studien syftar till att undersöka och analysera flera olika varumärkens möjligheter att samsas i en stor koncern, samt hur man på bästa sätt exponerar dessa varumärken i ett gemensamt showroom.The purpose of the study is to explore and analyze a variety of brands ability to combine in a large group and how to expose these brands the best in a combined showroom. / Program: Textil produktutveckling med entreprenörs- och affärsinriktning

Ng Yeung Lam. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 180-209). / Abstracts in English and Chinese. / acknowledgements --- p.i / abstract --- p.ii / abstract in chinese --- p.vi / table of contents --- p.ix / list of tables --- p.xiii / list of figures --- p.xi v / list of abbreviations --- p.xvi / Chapter 1 --- chapter1 introduction and literature review --- p.1 / Chapter 1.1 --- Introduction of brain tumors --- p.1 / Chapter 1.2 --- Oligodendroglial tumors (OTs) --- p.3 / Chapter 1.2.1 --- Oligodendroglioma (OD) and anaplastic oligodendroglioma (AOD) --- p.3 / Chapter 1.2.1.1 --- WHO's definition and grading --- p.3 / Chapter 1.2.1.2 --- "Incidence, age, sex distribution, tumor location and survival rate" --- p.3 / Chapter 1.2.1.3 --- Clinical presentation --- p.4 / Chapter 1.2.1.4 --- Macroscopy and histopathology --- p.4 / Chapter 1.2.1.5 --- Immunohistochemistry --- p.5 / Chapter 1.2.1.6 --- Treatment --- p.6 / Chapter 1.2.2 --- Oligoastrocytoma (OA) and anaplastic oligoastrocytoma (AOA) --- p.11 / Chapter 1.2.2.1 --- WHO's definition and grading --- p.11 / Chapter 1.2.2.2 --- "Incidence, age, sex distribution, tumor location and survival rate" --- p.12 / Chapter 1.2.2.3 --- Clinical features --- p.12 / Chapter 1.2.2.4 --- Macroscopy and histopathology --- p.12 / Chapter 1.3 --- Overview of Genetic and Epigenetic Aberrations of OTs --- p.14 / Chapter 1.3.1 --- Chromosomal and genetic aberrations in OTs --- p.14 / Chapter 1.3.2 --- Candidate regions and genes on 1 p --- p.15 / Chapter 1.3.3 --- Candidate regions and genes on 19q --- p.20 / Chapter 1.3.4 --- Other aberrations in WHO grade II OTs --- p.24 / Chapter 1.3.5 --- Progression-associated aberrations in ODs --- p.25 / Chapter 1.3.6 --- Chromosomal and genetic aberrations in OAs --- p.29 / Chapter 1.4 --- Correlation of genetic alterations with response to therapy and survival --- p.31 / Chapter 1.4.1 --- Response to PCV chemotherapy correlates with lp and combined lp/19q status in patients with AODs --- p.31 / Chapter 1.4.2 --- Survival of patients with AODs correlates with lp/19q status --- p.32 / Chapter 1.4.3 --- WHO grade II ODs behavior and lp/19q status --- p.32 / Chapter 1.4.4 --- Response to other therapies (temozolomide and radiotherapy) and lp/19q status in patients with ODs --- p.33 / Chapter 1.4.5 --- lp and 19q loss in OAs and diffuse astrocytomas --- p.34 / Chapter 1.5 --- Microarray-based expression profiling of OTs --- p.35 / Chapter 1.6 --- Description of p73 protein --- p.37 / Chapter 1.6.1 --- Introduction of p73 --- p.37 / Chapter 1.6.2 --- p73: gene structure and splicing variants --- p.37 / Chapter 1.6.3 --- Signaling in p73 --- p.40 / Chapter 1.6.4 --- Regulation ofp73 protein stability and transcriptional activity --- p.43 / Chapter 1.6.4.1 --- Regulation by DNA damage --- p.43 / Chapter 1.6.4.2 --- Regulation by oncogenes --- p.44 / Chapter 1.6.4.3 --- Interaction with viral proteins --- p.44 / Chapter 1.6.5 --- Role of p73 in the nervous system --- p.45 / Chapter 1.6.6 --- p73 in cancer --- p.45 / Chapter 1.6.6.1 --- p73 knockout mice --- p.45 / Chapter 1.6.6.2 --- Alteration of p73 expression in human cancers --- p.46 / Chapter 1.6.7 --- p73 and chemosensitivity --- p.50 / Chapter CHAPTER2 --- AIMS OF STUDY --- p.51 / Chapter CHAPTER3 --- MATERIALS AND METHODS --- p.53 / Chapter 3.1 --- Tumor and blood samples --- p.53 / Chapter 3.2 --- Cell culture --- p.53 / Chapter 3.3 --- DNA extraction from frozen tissues and blood samples --- p.54 / Chapter 3.4 --- Detection of allelic loss of chromosome lp --- p.58 / Chapter 3.4.1 --- LOH analysis --- p.58 / Chapter 3.4.2 --- Fluorescence in situ Hybridization (FISH) analysis on Paraffin and Frozen Sections --- p.60 / Chapter 3.6 --- DNA sequencing analysis --- p.62 / Chapter 3.7 --- Analysis of Methylation --- p.63 / Chapter 3.7.1 --- Bisulfite sequencing --- p.63 / Chapter 3.7.2 --- Methylation-specific polymerase chain reaction (MSP) --- p.66 / Chapter 3.8 --- Northern Blot analysis --- p.68 / Chapter 3.9 --- RNA isolation and cDNA preparation --- p.70 / Chapter 3.10 --- Laser microdissection and RNA extraction from microdissected tumor cells --- p.71 / Chapter 3.10.1 --- Conventional RT-PCR --- p.71 / Chapter 3.11 --- Primer design for TP73 and its isoforms --- p.74 / Chapter 3.12 --- Real-time RT-PCR --- p.77 / Chapter 3.12.1 --- Real-time RT-PCR for TP73 and its isoforms --- p.78 / Chapter 3.12.2 --- Real-time RT-PCR for KIAA0495 --- p.79 / Chapter 3.13 --- Statistical analyses --- p.81 / Chapter CHAPTER4 --- RESULTS --- p.82 / Chapter 4.1 --- Genes annotated in the minimally deleted regions --- p.82 / Chapter 4.2 --- Expression analyses of TP73 and its isoforms in ODs by quantitative real-time RT-PCR --- p.85 / Chapter 4.3 --- Methylation analysis of TP73 in ODs by methylation sensitive PCR (MSP) --- p.97 / Chapter 4.4 --- A rapid screen of candidate genes for aberrant expression in microdissected tumors --- p.100 / Chapter 4.5 --- Quantitative real-time RT-PCR of KIAA0495 gene --- p.103 / Chapter 4.6 --- Mutation analysis of KIAA0495 gene --- p.110 / Chapter 4.7 --- Methylation analysis of KIAA0495 in ODs by bisulfite sequencing…… --- p.112 / Chapter 4.8 --- Detection of allelic loss of lp by LOH analysis and interphase FISH --- p.121 / Chapter 4.9 --- Two-hit inactivation of KIAA0495 gene in ODs --- p.126 / Chapter 4.10 --- Tissue distribution of KIAA0495 gene --- p.130 / Chapter 4.11 --- Bioinformatics of KIAA0495 --- p.133 / Chapter CHAPTER5 --- DISCUSSION --- p.146 / Chapter 5.1 --- Expression analysis of TP73 and its isoforms in ODs by isoform-specific RT-PCR --- p.148 / Chapter 5.2 --- Methylation status ofTP73 in ODs --- p.153 / Chapter 5.3 --- A rapid screening of candidate genes for aberrant expressionin microdissected tumors --- p.156 / Chapter 5.4 --- Expression pattern of KIAA0495 mRNA in a large cohort of ODs --- p.157 / Chapter 5.5 --- No somatic mutation in coding region of KIAA0495 --- p.158 / Chapter 5.6 --- Methylation status of putative promoter region of KIAA0495 in ODs --- p.159 / Chapter 5.7 --- Status of chromosome lp in ODs --- p.161 / Chapter 5.8 --- Two-hit inactivation of KIAA0495 gene in ODs by promoter hypermethylation and allelic loss of lp --- p.162 / Chapter 5.9 --- Evaluation of expression of KIAA0495 gene as a marker for the response to chemotherapy and prognostic marker in patients with OTs --- p.164 / Chapter 5.10 --- Tissue distribution of KIAA0495 --- p.166 / Chapter 5.11 --- "KIAA0495 cDNA sequence, protein sequence and potential functional features" --- p.167 / Chapter 5.12 --- Candidate tumor suppressor genes on lp in other type of tumors with loss of lp --- p.171 / Chapter CHAPTER6 --- CONCLUSIONS --- p.174 / Chapter CHAPTER7 --- FUTURE STUDIES --- p.177 / Chapter CHAPTER8 --- REFERENCES --- p.180

Memória Transacional tem se demonstrado um paradigma promissor na implementação de aplicações concorrentes sob memória compartilhada que busquem evitar um modelo de sincronização baseado em locks. Em vez de sujeitar a execução a um acesso exclusivo com base no valor de um lock que é compartilhado por threads concorrentes, uma aplicação sob Memória Transacional tenta executar seções críticas de modo otimista, desfazendo as modificações no caso de um conflito de acesso à memória. Entretanto, apesar de a abordagem baseada em locks ter adquirido um número significativo de ferramentas automatizadas para a depuração, profiling e otimização automatizados (por ser uma das técnicas de sincronização mais antigas e mais bem pesquisadas), o campo da Memória Transacional ainda é comparativamente recente, e programadores frequentemente precisam adaptar manualmente suas aplicações transacionais ao encontrar problemas de eficiência. Este trabalho propõe um sistema no qual o profiling de código em uma implementação de Memória Transacional simulada é utilizado para caracterizar uma aplicação transacional, formando a base para uma parametrização automatizada do respectivo sistema especulativo para uma execução eficiente do código em questão. Também é proposta uma abordagem de escalonamento de threads guiado por profiling em uma implementação de Memória Transacional baseada em software, usando dados coletados pelo profiler para prever a probabilidade de conflitos e determinar que thread escalonar com base nesta previsão. São apresentados os resultados de experimentos sob ambas as abordagens. / Transactional Memory has shown itself to be a promising paradigm for the implementation of shared-memory concurrent applications that eschew a lock-based model of data synchronization. Rather than conditioning exclusive access on the value of a lock that is shared across concurrent threads, Transactional Memory attempts to execute critical sections optimistically, rolling back the modifications in the event of a data access conflict. However, while the lock-based approach has acquired a significant body of debugging, profiling and automated optimization tools (as one of the oldest and most researched synchronization techniques), the field of Transactional Memory is still comparably recent, and programmers are usually tasked with an unguided manual tuning of their transactional applications when facing efficiency problems. We propose a system in which code profiling in a simulated hardware implementation of Transactional Memory is used to characterize a transactional application, which forms the basis for the automated tuning of the underlying speculative system for the efficient execution of that particular application. We also propose a profile-guided approach to the scheduling of threads in a software-based implementation of Transactional Memory, using collected data to predict the likelihood of conflicts and determine what thread to schedule based on this prediction. We present the results achieved under both designs.

Mitochondria are a key organelle within human cells, with functions ranging from ATP synthesis to apoptosis. Changes in mitochondrial function are associated with many diseases, as well as 'natural' processes like ageing. Mitochondria have a unique evolutionary origin, as the result of an endosymbiotic relationship between a bacterium and an archaeal cell. Therefore, the phylogenetic history of the mitochondrial proteome is also unique within the total human proteome. A new description of the genes encoding the human mitochondrial proteome - IMPI (Integrated Mitochondrial Protein Index) 2017 - provided an opportunity for exploration of mitochondrial proteome history and the application of this knowledge to the understanding of gene function, disease and ageing. To facilitate the exploration of the mitochondrial proteome, I created a manually curated dataset of 190,097 predicted orthologues of the 1,550 IMPI 2017 human genes across 359 species, using reciprocal best hit analysis as the basis for orthologue prediction. I used this to explore gene history and the potential for phylogenetic profiling to predict the function of uncharacterised genes. This inspired the use of phylogenetic profiling within two phyla of animals, to link presence and absence of metabolic genes to the function of mitochondrial transporters. Potential transport substrates were predicted for two groups of uncharacterised mitochondrial carriers. I also used the dataset to identify features of genes associated with monogenetic disease, as well as differences between recessive and dominant disease genes. A similar orthologue identification method was used to explore the total sequenced viral proteome for potential orthologues of mitochondrial proteins. This showed that a range of mitochondrial proteins are shared with viruses, potentially facilitating the co-opting of mitochondrial function during viral infection of eukaryotic cells. I then used orthology to explore the conservation of residues linked to protein acetylation and identify a link with lifespan in warm-blooded vertebrates. In conclusion, I have used orthology to further the understanding of human mitochondrial proteome history and developed applications of this information. For example, phylogenetic features of disease genes are being used as part of a wider pipeline to predict mitochondrial disease genes. Furthermore, predicted substrates of the SLC25A14/30 mitochondrial carriers are being tested. My dataset provides further opportunities to explore the evolution and function of the mitochondrion.

Yu, Pui Man. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 68-78). / Abstracts in English and Chinese. / Acknowledgements --- p.iv / Abstract --- p.v / Table of Contents --- p.ix / List of Figures --- p.xii / List of Tables --- p.xiv / List of Abbreviations --- p.xv / Chapter Chapter 1. --- General Introduction --- p.1 / Chapter Chapter 2. --- Literature Review --- p.5 / Chapter 2.1 --- The importance of terpenoids --- p.5 / Chapter 2.2 --- The difficulties in synthesizing terpenoids --- p.8 / Chapter 2.3 --- Structure and classification of terpenoids --- p.9 / Chapter 2.4 --- MVA and MEP pathways of terpenoid biosynthesis in higher plants --- p.12 / Chapter 2.4.1 --- The MVA pathway --- p.16 / Chapter 2.4.2 --- The MEP pathway --- p.18 / Chapter 2.5 --- The crosstalk between MVA and MEP routes --- p.20 / Chapter 2.6 --- The farnesyl diphosphate is a key enzyme in terpenoid biosynthetic pathway --- p.20 / Chapter 2.7 --- The glutaredoxin system --- p.22 / Chapter Chapter 3. --- Materials and Methods --- p.25 / Chapter 3.1 --- Plant materials and growth condition --- p.25 / Chapter 3.2 --- DNA extraction and screening of fps mutants --- p.25 / Chapter 3.3 --- Validation of the fps mutant by semi-quantitative RT-PCR --- p.26 / Chapter 3.4 --- Semi-quantitative RT-PCR analysis of the fps mutants --- p.28 / Chapter 3.5 --- Genechip analysis of fps mutants --- p.29 / Chapter 3.6 --- Enzyme assays --- p.29 / Chapter 3.7 --- Triterpene and sterol analysis of fps mutants --- p.30 / Chapter 3.8 --- Preparation of carotenoid standards for carotenoid analysis --- p.31 / Chapter 3.9 --- Carotenoids analysis of fps mutants by HPLC --- p.31 / Chapter 3.10 --- Subcellular localization of FPS 1 and FPS2 by transient expression --- p.33 / Chapter Chapter 4. --- Results --- p.36 / Chapter 4.1 --- Screening of fpsl and fps2 homozygous mutants --- p.36 / Chapter 4.2 --- Validation of fps mutants by RT-PCR and enzyme activity assay --- p.36 / Chapter 4.3 --- Genechip analysis of two fps mutants --- p.40 / Chapter 4.3.1 --- Quality control and normalization of microarray sample --- p.40 / Chapter 4.3.2 --- Normalization and identification of differentially expressed genes --- p.42 / Chapter 4.3.3 --- GO annotation of differentially expressed genes in fps mutants --- p.43 / Chapter 4.3.4 --- Genes participate in stress and defense response were differentially expressed in both fpsl and fps2 mutants --- p.48 / Chapter 4.3.5 --- Genes in the plastidial pathway were down-regulated --- p.51 / Chapter 4.4 --- Effects of FPS mutations on pathway enzymes --- p.53 / Chapter 4.5 --- Effects of fps mutants on terpenoids and sterol metabolism --- p.55 / Chapter 4.6 --- Comparison on carotenoids and chlorophyll contents --- p.55 / Chapter 4.7 --- Subcellular localization of FPS 1 and FPS2 --- p.61 / Chapter Chapter 5. --- Discussion --- p.62 / Chapter Chapter 6. --- Conclusion --- p.67 / Reference --- p.68 / Appendices --- p.79 / Appendix A. Primers designed for homozygous mutant screening for fps mutants --- p.79 / "Appendix B. Primer pairs designed for fps ORF, common sequence and fpsl specific region" --- p.80 / Appendix C. Primer pairs designed for studying expression level of the downstream genes of FPS --- p.81 / Appendix D. Annotations of differentially expressed genes in fpsl mutant --- p.82 / Appendix E. Annotations of differentially expressed genes in fps2 mutant --- p.84 / Appendix F. Log fold changes of terpenoid pathway genes involved in FPS mutants --- p.94

Qi, Yan. / Thesis submitted in: December 2008. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 63-79). / Abstracts in English and Chinese. / ACKNOWLEDGEMENTS --- p.III / ABSTRACT --- p.IV / TABLE OF CONTENTS --- p.VII / LIST OF ABBREVIATIONS --- p.XI / Chapter CHAPTER 1. --- LITERATURE REVIEW --- p.1 / Chapter 1.1 --- the Plant of Artemisia annua L --- p.1 / Chapter 1.2 --- The disease of malaria --- p.3 / Chapter 1.2.1 --- The life cycle of Plasmodium parasites --- p.4 / Chapter 1.2.2 --- The Artemisinin-based combination therapies (ACTs) for the treatment of malaria --- p.5 / Chapter 1.3 --- Artemisinin --- p.8 / Chapter 1.3.1 --- The content and distribution of artemisinin --- p.8 / Chapter 1.3.2 --- The mechanism of artemisinin action --- p.9 / Chapter 1.3.2.1 --- The proposed non-specific mechanisms of action --- p.10 / Chapter 1.3.2.2 --- The proposed parasite-specific mechanisms of action --- p.11 / Chapter 1.3.3 --- The biosynthesis of artemisnin in vivo --- p.12 / Chapter 1.3.4 --- The biosynthesis of artemisinin in vitro --- p.16 / Chapter 1.4 --- Trichomes --- p.18 / Chapter 1.4.1 --- Non-glandular trichomes --- p.19 / Chapter 1.4.2 --- Glandular trichome --- p.20 / Chapter 1.4.3 --- Trichomes of Artemisia annua L --- p.21 / Chapter 1.5 --- DNA Sequencing Methods --- p.24 / Chapter 1.5.1 --- The basic principle of pyrosequencing --- p.25 / Chapter 1.5.2 --- 454 pyrosequencing and its application --- p.27 / Chapter CHAPTER 2. --- MATERIALS AND METHODS --- p.32 / Chapter 2.1 --- Chemicals --- p.32 / Chapter 2.2 --- Plant materials --- p.32 / Chapter 2.3 --- Preparation of the cDNA sample for 454 sequencing --- p.33 / Chapter 2.3.1 --- Scanning electron microscopy --- p.33 / Chapter 2.3.2 --- Isolation of glandular trichomes --- p.34 / Chapter 2.3.3 --- cDNA synthesis and normalization --- p.34 / Chapter 2.4 --- 454-EST SEQUENCING AND PROCESSING --- p.36 / Chapter 2.5 --- Analysis of 454 sequencing data --- p.37 / Chapter 2.6 --- Establishment of regeneration system of A. annua L --- p.37 / Chapter 2.6.1 --- Shoots induction from leaf discs --- p.37 / Chapter 2.6.2 --- The sensitivity of the explants to Kanamycin --- p.38 / Chapter 2.6.3 --- Rooting of the regenerated seedlings --- p.38 / Chapter CHAPTER 3. --- RESULTS AND DISCUSSION --- p.40 / Chapter 3.1 --- Glandular trichome isolation and cDNA preparation --- p.40 / Chapter 3.1.1 --- The distribution of glandular trichomes on A. annua --- p.40 / Chapter 3.1.2 --- The isolation of glandular trichomes --- p.42 / Chapter 3.1.3 --- The preparation of ds cDNA for 454 sequencing --- p.43 / Chapter 3.2 --- Pre-process of 454 pyrosequencing data --- p.44 / Chapter 3.3 --- Functional annotation of the 454-EST data --- p.47 / Chapter 3.4 --- Comparison of two sequencing runs --- p.49 / Chapter 3.5 --- Analysis of the 454 ESTs involved in secondary metabolisms --- p.50 / Chapter 3.6 --- Selection of the candidate genes --- p.55 / Chapter 3.7 --- Establishment of regeneration system of A. annua L --- p.57 / Chapter 3.7.1 --- Shoots induction from leaf discs --- p.57 / Chapter 3.7.2 --- Roots induction from shoots --- p.57 / Chapter 3.7.3 --- Sensitivity of A. annua to Kan --- p.59 / Chapter CHAPTER 4. --- CONCLUSION --- p.61 / REFERENCES --- p.63