Leung Chin-lung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 133-164). / Abstracts in English and Chinese. / Abstract --- p.iv / 摘要 --- p.vi / List of abbreviation --- p.viii / Chapter Chapter 1 --- Hepatocellular Carcinoma --- p.1 / Chapter 1.1 --- A Health Burden --- p.1 / Chapter 1.2 --- Pathology --- p.3 / Chapter 1.3 --- Epidemiology --- p.7 / Chapter 1.3.1 --- Global HCC distribution --- p.7 / Chapter 1.3.2 --- Age and Gender --- p.10 / Chapter 1.4 --- Risk Factors of HCC --- p.12 / Chapter 1.4.1 --- Hepatitis B virus (HBV) --- p.13 / Chapter 1.4.1.1 --- Chronic HBV infection --- p.13 / Chapter 1.4.1.2 --- Role of HBV in hepatocarcinogenesis --- p.16 / Chapter 1.4.1.2 a) --- Direct Oncogenesis --- p.16 / Chapter 1.4.1.2 b) --- Indirect Oncogenesis --- p.17 / Chapter 1.4.2 --- Hepatitis C virus (HCV) --- p.23 / Chapter 1.4.2.1 --- Chronic HCV infection --- p.23 / Chapter 1.4.2.2 --- Role of HCV in hepatocarcinogenesis --- p.23 / Chapter 1.4.3 --- Chemicals as liver carcinogens --- p.27 / Chapter 1.4.3.1 --- Aflatoxin Bi (AFB1) --- p.28 / Chapter 1.4.3.2 --- Vinyl chloride --- p.29 / Chapter 1.4.3.3 --- Alcoholic beverages --- p.29 / Chapter 1.4.4 --- Inborn Errors in Metabolisms --- p.30 / Chapter 1.4.4.1 --- Hereditary tyrosinemia --- p.30 / Chapter 1.4.4.2 --- Hereditary haemochromatosis --- p.30 / Chapter 1.4.4.3 --- α1-antitrypsin deficiency --- p.31 / Chapter 1.4.5 --- Liver lesions --- p.32 / Chapter 1.5 --- Genetic alterations in HCC --- p.33 / Chapter Chapter 2 --- Rationale of the study --- p.39 / Chapter Chapter 3 --- LOH study on 8p in HCC --- p.48 / Chapter 3.1 --- Introduction --- p.48 / Chapter 3.1.1 --- "Knudson's ""two-hit"" model and LOH" --- p.48 / Chapter 3.1.2 --- Microsatellite DNA and LOH study --- p.49 / Chapter 3.2 --- Materials and Methods --- p.51 / Chapter 3.2.1 --- Patients and Specimens --- p.51 / Chapter 3.2.1.1 --- Genomic DNA extraction from liver tissues --- p.53 / Chapter 3.2.1.2 --- Genomic DNA extraction from buffy coat --- p.55 / Chapter 3.3 --- LOH study on 8p in HCC --- p.57 / Chapter 3.3.1 --- Microsatellite markers --- p.57 / Chapter 3.3.2 --- 5-end labeling --- p.60 / Chapter 3.3.3 --- Amplification of microsatellite DNA --- p.60 / Chapter 3.3.4 --- Denaturing polyacrylamide gel electrophoresis --- p.61 / Chapter 3.3.5 --- Detection of LOH --- p.62 / Chapter 3.4 --- Results --- p.63 / Chapter 3.4.1 --- LOH status of 52 HCC cases --- p.63 / Chapter 3.4.2 --- Clinicopathological correlation --- p.67 / Chapter 3.4.3 --- Delineation of common deletion region (CDR) --- p.67 / Chapter 3.4.4 --- Common deletion region of interest --- p.77 / Chapter Chapter 4 --- Study on LZTS1 --- p.83 / Chapter 4.1 --- Introduction 一 LZTS1 --- p.83 / Chapter 4.2 --- Mutation analysis of LZTS1 in HCC --- p.87 / Chapter 4.2.1 --- Materials and Methods --- p.87 / Chapter 4.2.1.1 --- Patients and HCC cell lines --- p.87 / Chapter 4.2.1.2 --- Genomic DNA extraction from HCC cell lines --- p.87 / Chapter 4.2.1.3 --- Amplification of exons of LZTS1 --- p.89 / Chapter 4.2.1.3a) --- Primer pairs --- p.89 / Chapter 4.2.1.3b) --- PCR conditions --- p.90 / Chapter 4.2.1.4 --- Purification of PCR products --- p.93 / Chapter 4.2.1.5 --- Cycle sequencing reaction --- p.94 / Chapter 4.2.1.6 --- Purification of cycle sequencing reaction product --- p.94 / Chapter 4.2.1.7 --- Sequence analysis by automated sequencer --- p.95 / Chapter 4.2.1.8 --- Search for sequence variants of LZTS1 --- p.96 / Chapter 4.2.2 --- Results --- p.97 / Chapter 4.3 --- Expression analysis of LZTS1 in HCC with preliminary results --- p.103 / Chapter 4.3.1 --- Materials and Methods --- p.103 / Chapter 4.3.1.1 --- Patients and Specimens --- p.103 / Chapter 4.3.1.2 --- Total RNA extraction --- p.103 / Chapter 4.3.1.3 --- Reverse transcription --- p.104 / Chapter 4.3.1.4 --- Semi-quantitative PCR --- p.105 / Chapter 4.3.1.4a) --- Primer pairs --- p.105 / Chapter 4.3.1.4b) --- PCR conditions --- p.106 / Chapter 4.3.2 --- Results --- p.109 / Chapter Chapter 5 --- Discussion --- p.111 / Chapter 5.1 --- LOH study on 8p in HCC --- p.111 / Chapter 5.2 --- Study on LZTS1 in HCC --- p.125 / Chapter 5.2.1 --- Mutation analysis of LZTS1 --- p.125 / Chapter 5.2.2 --- Expression analysis of LZTS1 --- p.129 / Chapter 5.3 --- Future Study --- p.132 / References --- p.133

by Angela Bik-Yu Hui. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1997. / Includes bibliographical references (leaves 119-133). / Acknowledgements / Table of Contents / List of Tables / List of Figures / Abstract / Chapter CHAPTER 1 --- LITERATURE REVIEW --- p.1 / Chapter I. --- Nasopharyngeal carcinoma --- p.1 / Chapter II. --- Etiology of NPC --- p.3 / Chapter II a. --- Geographical & Environmental factors --- p.3 / Chapter II b. --- Epstein-Barr virus Infection --- p.5 / Chapter II c. --- Genetic Factors --- p.8 / Chapter III. --- Cytogenetic Studies of NPC --- p.10 / Chapter III a. --- Traditional Cytogenetics --- p.10 / Chapter III b. --- Previous cytogenetic findings of NPC --- p.12 / Chapter III.c. --- Fluorescence in-situ hybridization --- p.15 / Chapter III.d. --- The new NPC cell line: Cell-666 --- p.18 / Chapter IV. --- Molecular Genetic Studies in NPC --- p.19 / Chapter IV a. --- Oncogenes --- p.20 / Chapter IV b. --- Tumor suppresser genes (TSGs) --- p.22 / Chapter IV c. --- Loss of Heterozygosity Studies --- p.29 / Chapter IV d. --- LOH on Chromosome 11 --- p.32 / Chapter IV e. --- ATM Gene --- p.35 / Chapter CHAPTER 2 --- OBJECTIVE OF STUDY --- p.38 / Chapter CHAPTER 3 --- MATERIALS AND METHODS --- p.41 / Chapter I： --- Study of loss of heterozygosity on chromosome 11 --- p.41 / Chapter I a. --- Patients and Specimens --- p.41 / Chapter I.b. --- DNA extraction --- p.45 / Chapter I c. --- Microsatellite Polymorphism Analysis --- p.47 / Chapter I d. --- Multiplex PCR analysis --- p.52 / Chapter II. --- Cytogenetic Studies --- p.54 / Chapter II a. --- Culture of cell-666 --- p.54 / Chapter II b. --- Cytogenetic Analysis --- p.56 / Chapter II c. --- Fluorescence in-situ hybridization (FISH) --- p.58 / Chapter II d. --- FISH analysis of other NPC cell lines) --- p.62 / Chapter CHAPTER 4 --- RESULTS --- p.63 / Chapter I: --- Study of loss of heterozygosity on chromosome 11 --- p.63 / Chapter I a. --- LOH analysis --- p.63 / Chapter I b. --- Regions with L OH --- p.73 / Chapter I c. --- Multiplex PCR analysis --- p.79 / Chapter II: --- Cytogenetic Study --- p.83 / Chapter II a. --- Cytogenetic analysis of cell-666 --- p.83 / Chapter II.b. --- Fluorescence in-situ Hybridization (FISH) --- p.91 / Chapter CHAPTER 5 --- DTSCUSSION --- p.102 / Chapter I. --- LOH of Chromosome 11 Studies --- p.102 / Chapter II. --- Comparison with LOH studies of other chromosomes --- p.110 / Chapter III. --- Cytogenetic Studies --- p.113 / REFERENCES --- p.119

Pair programming is a software development method which describes two programmers working together on the same computer, sharing one keyboard. This approach requires programmers to communicate frequently, which can lead the pair to experience certain benefits over solo programming, such as faster problem solving and a greater enjoyment of their work (Cockburn and Williams, 2001, Bryant et al., 2006). Many programmers approach their first pairing experience with scepticism, having doubts about their partner’s working habits and programming style, and about the additional communication aspects that this programming style entails (Williams et al., 2000). Despite a significant amount of research into pair programming of over 15 years, it is not evident what communication between the pair contributes to the task of pair programming. This work presents an analytic coding scheme which was derived from the observation of the communication of expert pairs working in industry. Over 35 hours of communication across 11 different pairs was analysed. This coding scheme was further refined to produce industry-inspired pair programming guidelines that assist novice pair programmers to improve their experience of pair communication. Findings indicate that introducing these guidelines to novice student pairs can have a positive impact on their perception of intra-pair communication, and on their perception of their partner’s contribution. Feedback received from expert pairs was used to add detail to the guidelines, which have been made publically available through an online resource.

This dissertation dicusses two topics; the cross section measurement of ϓ(1S) meson pair production [1] and simulation studies of High Granularity Calorimetry (HGCal). The first part of the dissertation is dedicated for the analysis of ϓ(1S) meson pair production and measurement of its cross section. The data for this analysis were collected by the CMS experiment at Large Hadron Collider (LHC) at a center-of-mass energy of 8 TeV and correspond to an integrated luminosity of 20.7 fb −1 . Simultaneous production of two ϓ(1S) mesons is observed for the first time with 38 events, corresponding to a local significance exceeding five standard deviations from the expected combinatorial background b-quark decays. Both ϓ(1S) candidates are fully reconstructed via their decays to μ + μ − . The fiducial acceptance of the detector is measured from the simulation and is defined by an absolute Υ(1S) rapidity smaller than 2.0. To minimize the model-dependence, the acceptance and efficiency corrections are calculated on an event-by-event basis using measured ϓ meson and muon momenta. The fiducial cross section of ϓ(1S) meson production, assuming both ϓ(1S) mesons decay isotropically, is measured to be 68.8 ± 12.7 (stat) ± 7.4 (syst) ± 2.8 (B) pb, where the third uncertainty comes from the uncertainty in the branching fraction of ϓ(1S) decays to μ + μ − . Different assumptions about ϓ productions imply modifications to the cross section ranging from −38% to +36%. Cross section measurement of ϓ pair production will provide better understanding of the parton vstructure of proton and enhance precision of existing particle production models. LHC is planning to increase luminosity and energy of colliding protons. Due to accumulated radiation damage and to improve detector performance CMS experiment is expected to undergo upgrade plans. Hadron calorimeter is among them, and it is planned to be replaced with better performance high granularity calorimetry (HGCal). HGCal needs to be integrated with existing components of CMS and its smooth functioning is essential. The second part of the dissertation describes simulation studies performed to validate readiness of HGCal for the Phase II upgrade.

Sustainable and renewable energy is an incredibly important area in today’s society and investigation into avenues to improve this wide ranging technology are underway in many different fields. Thermoelectric devices possess the ability for the direct solid-state interconversion of heat and electrical power, which not only allows for sustainable refrigeration but also waste heat recovery. One current restriction on the efficiency of thermoelectric devices is the disparity in thermoelectric performance of p-type and n-type materials. Furthermore, a key physical attribute shared by the majority of high performing thermoelectric materials is low thermal conductivity. Thus in this thesis three separate p-type material systems exhibiting low thermal conductivity will be discussed. The Cu-excessed quaternary chalcogenides, CuM2InTe4 (M = Zn, Cd), and ternary chalcogenide, CuSbS2, were investigated due to their intrinsically low thermal conductivity. Whereas, skutterudites typically have good electrical properties but do not exhibit an intrinsically low thermal conductivity. Nevertheless low thermal conductivity can be achieved by taking advantage of their unique crystal structure by filling large voids with loosely bound atoms that act as phonon scattering centers. Therefore double-filled Fe substituted skutterudites with nominal compositions Yb0.4In0.02Co3FeSb12 and Yb0.8In0.02Co2.5Fe1.5Sb12 were also investigated. The CuM2InTe4 (M = Zn, Cd) and skutterudite specimens were synthesized by direct reactions, whereas the CuSbS2 specimens were synthesized by mechanical alloying. Structural and stoichiometric compositions were analyzed by a combination of X-ray diffraction, Rietveld refinement and energy dispersive spectroscopy. High-temperature transport properties were measured for all specimens and will be discussed in detail. The Cu-excessed quaternary chalcogenides display intrinsically low thermal conductivity that appears to be unaffected by the change in electrical properties that is a result of differing stoichiometries. This may provide a possible route to furthering the enhancement of the thermoelectric properties of these materials. Similarly the CuSbS2 ternary chalcogenides display a very low thermal conductivity due to stereochemically active lone-pair electrons and would potentially allow an optimization of the power factor without a significant increase of the very low thermal conductivity, thus improving the figure of merit. For the case of p-type skutterudites, (Yb, In) double-filled skutterudites have a maximum ZT of 0.6, which is promising in the hunt for improved p-type materials. This fundamental investigation provides insight that can lead to a deeper understanding of all three material systems outlined in this thesis and provides a platform for new research in the quest for materials suitable for thermoelectric applications.

This thesis investigates the use of single Cooper-pair transistor (SCPT) for fast and sensitive detection of quasiparticle dynamics. This investigation is motivated by the possibility of quantum information processing using superconducting nanoscale circuits, such as the SCPT and the Cooper-pair-box (CPB). In the SCPT coherent charge transport can be temporarily halted due to quasiparticle tunnelling, known as quasiparticle poisoning. Quasiparticle poisoning can be reduced by the use of engineered island and lead gap energies. The thesis begins by reporting measurements of the superconducting gap in aluminium - aluminium-oxide - aluminium tunnel junctions, as a function of film thickness. We have observed an increase in the superconducting energy gap of aluminium with decreasing film thickness. This method is used to engineer the island and gap energies in a SCPT and consequently we observe reduced poisoning and a modification of the thresholds for finite bias transport processes. Radio-frequency reflectometry is used to perform high-bandwidth measurements of quasiparticle tunnelling in a gap engineered SCPT. A model for the radio-frequency (rf) operation of the SCPT is presented and shows close agreement with experiment. Thermal activation of the quasiparticle dynamics is investigated, and consequently, we are able to determine energetics of the poisoning and unpoisoning processes. This enables an effective quasiparticle temperature to be determined, allowing the poisoning to be parametrised. An investigation of the use of normal metal quasiparticle traps for suppression of quasiparticle poisoning in SCPT devices is performed. To date, there has been little quantitative information about the behaviour of quasiparticle traps even though they have been used extensively. The work presented serves to clarify the nature of quasiparticle trap performance. Finally the single-quasiparticle sensitivity of the SCPT is employed to directly probe a few quasiparticle gas in a small superconducting volume. The quasiparticle population is monitored both in the steady-state and under non-equilibrium conditions of injection. In the non-equilibrium regime the quasiparticle recombination time is accessed from the response of the SCPT to pulsed injection. Agreement to previous experimental studies of recombination times in aluminium is found.

<p>This thesis investigates how disparity estimation may be used to visualize an object on a 3D-screen. The first part looks into different methods of disparity estimation, and the second part examines different ways to visualize an object from one or several stereo pairs and a disparity map. Input to the system is one or several stereo pairs, and output is a sequence of images of the input scene but from more angles. This sequence of images can be shown on Setred AB's 3D-screen. The system has high real time demands and the goal is to do the disparity estimation and visualization in real time.</p><p>In the first part of the thesis, three different ways to calculate disparity maps are implemented and compared. The three methods are correlation-based, local structure-based and phase-based techniques. The correlation-based methods cannot satisfy the real-time demands due to the large number of 2D-convolutions required per pixel. The local structure-based methods have too much noise and cannot satisfy the quality requirements. Therefore, the best method by far is the phase-based method. This method has been implemented in Matlab and C and comparisons between the different implementations are presented.</p><p>The quality of the disparity maps is satisfying, but the real-time demands cannot yet be fulfilled. The future work is therefore to optimize the C code and move some functions to a GPU, because a GPU can perform calculations in parallel with the CPU. Another reason is that many of the calculations are related to resizing and warping, which are well-suited to implementation on a GPU.</p>

Supercapacitors are one of the most important electrochemical energy storage and conversion devices, however low ionic conductivity of solid state polymer electrolytes and the poor accessibility of the ions to the active sites in the porous electrode will cause low performance for all-solid-state supercapacitors and will limit their application. The objective of the dissertation is to improve the performance of all-solid-state supercapactor by improving electrolyte conductivity and solving accessibility problem of the ions to the active sites. The low ionic conductivity (10-8 S/cm) of poly(ethylene oxide) (PEO) limits its application as an electrolyte. Since PEO is a semicrystal polymer and the ion conduction take place mainly in the amorphous regions of the PEO/Lithium salt complex, improvements in the percentage of amorphous phase in PEO or increasing the charge carrier concentration and mobility could increase the ionic conductivity of PEO electrolyte. Hot pressing along with the additions of different lithium salts, inorganic fillers and plasticizers were applied to improve the ionic conductivity of PEO polymer electrolytes. Four electrode methods were used to evaluate the conductivity of PEO based polymer electrolytes. Results show that adding certain lithium salts, inorganic fillers, and plasticizers could improve the ionic conductivity of PEO electrolytes up 10-4 S/cm. Further hot pressing treatment could improve the ionic conductivity of PEO electrolytes up to 10-3 S/cm. The conductivity improvement after hot pressing treatment is elucidated as that the spherulite crystal phase is convert into the fringed micelle crystal phase or the amorphous phase of PEO electrolytes. PEO electrolytes were added into active carbon as a binder and an ion conductor, so as to provide electrodes with not only ion conduction, but also the accessibility of ion to the active sites of electrodes. The NaI/I2 mediator was added to improve the conductivity of PEO electrolyte and provide pseudocapacitance for all-solid-state supercapacitors. Impedance, cyclic voltammetry, and gavalnostatic charge/discharge measurements were conducted to evaluate the electrochemical performance of PEO polymer electrolytes based all-solid-state supercapacitors. Results demonstrate that the conductivity of PEO electrolyte could be improved to 0.1 S/cm with a mediator concentration of 50wt%. A high conductivity in the PEO electrolyte with mediator is an indication of a high electron exchange rate between the mediator and mediator. The high electron exchange rates at mediator carbon interface and between mediator and mediator are essential in order to obtain a high response rate and high power. This automatically solves the accessibility problem. With the addition of NaI/I2 mediator, the specific capacitance increased more than 30 folds, specific power increased almost 20 folds, and specific energy increased around 10 folds. Further addition of filler to the electrodes along with the mediator could double the specific capacitor and specific power of the all-solid-state supercapacitor. The stability of the corresponded supercapacitor is good within 2000 cycles.

Computer simulations play a profound and fundamental role inmodern theoretical physics, chemistry and materials science. Tounderstand the complex physics of metally liquids, metals,quasicrystals and metally glasses a working model imposing thelocal and global order is needed. Experiments and theory havepredicted the local order in liquid metals to beicosahedral. The current work has been done using molecular dynamicscomputer simulations of a monatomic system using a simplepair-potential for the interactions. Two new pair-potentialshas been developed, the Zetterling-1(Z1) and Zetterling-2(Z2)potentials. They are specifically modeled to impose icosahedralorder. The basis for the development of the potentials was theold Dzugutov potential which is known to freeze into adodecagonal quasicrystal. The new Zetterling potentials have alonger interaction range and a narrower first minimum. The morenarrow first minimum will enhance the local icosahedralordering and the longer interaction range was introduced toincorporate a second maximum in the potential mimicing theFriedel oscillations found in metallic systems. These Friedeloscillations are due to the singularity which arises at theFermi surface due to the screening of the positive charge bythe electron gas. Five papers are included in the study. The first two papersare studies of icosahedral clustering in the liquid andsupercooled liquid. The simulations in Paper I was done usingthe old Dzugutov potential while the new potentials were usedin Paper II using both molecular dynamics and the Basin Hoppingalgorithm presented in Chapter 5. Paper III considers theconcept of dynamical ergodicity in the context of thesuper-cooled liquid behaviour. The simulations were made usingthe old Dzugutov potential. Paper IVr eports a moleculardynamics simulation using the Dzugutov potential undersuper-cooling. A formation of icosahedrally structured domainswith distinctly slow diffusion which grows with cooling in alow-dimensional manner and percolate around Tc, the criticaltemperature of the mode-coupling theory. A sharp slowing downof the structural relaxation relative to diffusion is observed.It is concluded that this effect cannot be accounted for by thespatial variation in atomic mobility. The low-dimensionalclustering is discussed as a possible mechanism of fragility.Paper Vin vestigates the crystallization of a simple monatomicliquid model which utilizes the Zetterling-1 potential. Thesystem forms a thermodynamically stable solid phase exhibitingcubic symmetry. Its diffraction pattern is identified as thatof γ-brass, a tetrahedrally packed crystalline structurewith 52 atoms in the unit cell. <b>Keywords:</b>simple liquids, molecular dynamics, pairpotential, icosahedral cluster.

For any communication, the conveyed information must be carried by some physical system. If this system is a quantum system rather than a classical one, its behavior will be governed by the laws of quantum mechanics. Hence, the properties of quantum mechanics, such as superpositions and entanglement, are accessible, opening up new possibilities for transferring information. The exploration of these possibilities constitutes the field of quantum communication. The key ingredient in quantum communication is the qubit, a bit that can be in any superposition of 0 and 1, and that is carried by a quantum state. One possible physical realization of these quantum states is to use single photons. Hence, to explore the possibilities of optical quantum communication, photonic quantum states must be generated, transmitted, characterized, and detected with high precision. This thesis begins with the first of these steps: the implementation of single-photon sources generating photonic qubits. The sources are based on photon-pair generation in nonlinear crystals, and designed to be compatible with fiber optical communication systems. To ensure such a compatibility and to create a high-quality source, a theoretical analysis is made, optimizing the coupling of the photons into optical fibers. Based on the theoretical analysis, a heralded single-photon source and a two-crystal source of entangled photons-pairs are experimentally implemented. The source of entangled photons is further developed into a compact source with a narrow bandwidth compatible with standard telecommunication wavelength-division multiplexers, and even further developed to a more stable one-crystal source. The sources are to be used for quantum communication in general and quantum cryptography in particular. Specifically, a heralded single-photon source is implemented and then used for a full test of a decoy-state quantum cryptography protocol. / QC 20100914