Reliable biomarkers of axonal damage are urgently needed in neurological diseases. Neurofilaments (Nf) are specific structural elements of neurons composed of at least three subunits: Nf light chain (NfL), Nf medium and Nf heavy chain (NfH). This PhD aimed to characterise NfL levels and their correlation with clinical features in patients with neurological diseases with a different rate of progression and following and under different treatment regimes. An important aim was also to develop a bioassay for NfL measurements in blood. Cerebrospinal fluid (CSF) NfL levels discriminated patients with a clinically isolated syndrome (CIS) (p=0.001) or multiple sclerosis (MS) (p=0.035) from healthy controls more efficiently, and was more sensitive to change after natalizumab therapy (p<0.0001) than CSF NfH (p=0.002). Further, CSF NfL levels decreased in fingolimodtreated MS patients (p=0.001), but not in those receiving placebo (p=0.433). Based on these findings, a sensitive method for the detection of NfL in serum was developed and validated. Patients with neurological diseases had higher serum NfL values than controls. In acute spinal cord injury (SCI), serum NfL levels correlated with injury severity and long-term motor outcome, and Minocycline treatment was associated with decreased NfL levels in complete SCI patients compared to placebo. Finally, I found that serum NfL levels were higher in CIS patients than in healthy controls but did not predict conversion to clinically definite MS (CDMS). Independent predictors of CDMS were instead oligoclonal bands, number of T2 lesions and age at CIS. Lower 25-OHvitamin D levels were associated with CDMS in univariate analysis, but this was attenuated in the multivariate model. In conclusion, NfL proved to be an analytically stable protein which is an important prerequisite for biomarkers. The role of NfL quantification as a surrogate measure of neuroaxonal damage is corroborated by my findings and further supports the usefulness of NfL as a putative biomarker of axonal damage in various neurological diseases.

by Sui-Pan Yam. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1998. / Includes bibliographical references. / Abstract also in Chinese. / Acknowledgements --- p.V / Abstract --- p.VI / Chapter Chapter 1 --- Introduction --- p.1-1 / Chapter 1.1) --- Tunable Multi-Wavelength Optical Sources --- p.1 -1 / Chapter 1.2) --- All-Optical Switching --- p.1 -3 / Chapter 1.2.1) --- Nonlinear Effect / Chapter 1.2.2) --- Special Design of the Laser Structure / Chapter 1.2.3) --- Self-Injection Seeding of Fabry-Perot Laser Diode / Chapter 1.3) --- About This Project --- p.1-6 / Chapter Chapter 2 --- Basic Theory --- p.2-1 / Chapter 2.1) --- Mechanism of Gain-Switching --- p.2-1 / Chapter 2.1.1) --- General Description / Chapter 2.1.2) --- "Optical Pulsewidth, Spectra, and Frequency Chirping of Gain-Switched Pulses" / Chapter 2.2) --- Mechanism of Self-Injection Seeding --- p.2-8 / Chapter 2.2.1) --- General Description / Chapter 2.2.2) --- Dynamics of Single-Mode Formation / Chapter 2.2.3) --- Frequency Evolution of the Laser Diode for Cavity Mode Selection / Chapter 2.2.4) --- Turn-On Delay Time Jitter (TOJ) / Chapter 2.3) --- Mechanism of Injection Seeding --- p.2-17 / Chapter 2.3.1) --- General Description / Chapter 2.3.2) --- The Model of Weak Injection / Chapter 2.3.3) --- The Model of Strong Injection / Chapter Chapter 3 --- Single- and Multi-wavelength Optical Pulses Generated by a Diffraction Grating --- p.3-1 / Chapter 3.1) --- Introduction --- p.3-1 / Chapter 3.2) --- Basic Principle --- p.3-2 / Chapter 3.3) --- Experimental Setup --- p.3-5 / Chapter 3.4) --- Results and Discussion --- p.3-7 / Chapter 3.4.1) --- Spectral Characteristics Analysis / Chapter 3.4.2) --- Individually Access of the Four-Wavelength Output / Chapter 3.4.3) --- The Optical Pulsewidth Characteristics / Chapter 3.4.4) --- Discussion / Chapter 3.5) --- Summary --- p.3-14 / Chapter Chapter 4 --- Using a Highly Dispersive Fiber for Tunable Multi-Wavelength Pulse Generation --- p.4-1 / Chapter 4.1) --- Introduction --- p.4-1 / Chapter 4.2) --- Basic Principle --- p.4-2 / Chapter 4.3) --- Experimental Setup --- p.4-5 / Chapter 4.4) --- Experimental Results --- p.4-7 / Chapter 4.4.1) --- Spectral and Temporal Characteristics / Chapter 4.4.2) --- Wavelength Tuning / Chapter 4.4.3) --- Individually Access of Two Wavelength Channels / Chapter 4.4.4) --- Multi-Wavelength Generation / Chapter 4.5) --- Summary --- p.4-13 / Chapter Chapter 5 --- Comparison of Two Self-Seeding Configurations --- p.5-1 / Chapter 5.1) --- Introduction --- p.5-1 / Chapter 5.2) --- Polarization Sensitivity --- p.5-1 / Chapter 5.3) --- Stability --- p.5-2 / Chapter 5.4) --- Tunability --- p.5-2 / Chapter 5.5) --- Simplification --- p.5-3 / Chapter 5.6) --- Summary of the advantages and disadvantages of Two Configurations --- p.5-4 / Chapter Chapter 6 --- All-Optical Wavelength Switching achieved by Self-Seeding and External Injection-Seeding --- p.6-1 / Chapter 6.1) --- Introduction --- p.6-1 / Chapter 6.2) --- Experimental Setup --- p.6-2 / Chapter 6.3) --- Results and Discussion --- p.6-4 / Chapter 6.3.1) --- Spectral Characteristics / Chapter 6.3.2) --- The Optical Pulsewidth / Chapter 6.3.3) --- The Optical Switching Behaviors / Chapter 6.3.4) --- The Detail Information of Switching / Chapter 6.3.5) --- Optical Power / Chapter 6.4) --- Summary --- p.6-10 / Chapter Chapter 7 --- A Novel Self-Injection Seeding Scheme --- p.7-1 / Chapter 7.1) --- Introduction --- p.7-1 / Chapter 7.2) --- Basic Principle --- p.7-2 / Chapter 7.3) --- Experimental Setup --- p.7-9 / Chapter 7.4) --- Results and Discussion --- p.7-11 / Chapter 7.4.1) --- Spectral and Temporal Characterizations of Two-Wavelength Switching / Chapter 7.4.2) --- Different Wavelength Selection / Chapter 7.4.3) --- Operation Frequency Against the Fiber Length / Chapter 7.4.4) --- Multi-Wavelength Generation / Chapter 7.5) --- Discussion --- p.7-20 / Chapter 7.6) --- Summary --- p.7-22 / Chapter Chapter 8 --- Comparison of Switching Methods --- p.8-1 / Chapter 8.1) --- Introduction --- p.8-1 / Chapter 8.2) --- Switching between Self-Seeding and Injection-Seeding --- p.8-1 / Chapter 8.3) --- Switching by Self-Seeding of a F-P Laser Diode --- p.8-2 / Chapter 8.4) --- Summary --- p.8-3 / Chapter Chapter 9 --- Conclusion --- p.9-1 / References / Figure Captions / Appendix 一 Equipment Descriptions / List of Accepted and Submitted Publications

Circadian clocks are biological signalling networks which have a period of ~24 hours under constant environmental conditions. They have been identified in a wide range of organisms, from cyanobacteria to mammals and through the temporal co-ordination of biological processes are believed to increase individual fitness. The mechanisms which generate these self-sustained rhythms, the pathways of entrainment and the target outputs of the clock are all areas of great interest to circadian biologists. The plant circadian clock is believed to comprise of interlocking feedback loops of transcription and translation. The morning MYB-transcription factors CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) bind to the promoter of TIMING OF CAB2 1 (TOC1) and repress its expression, as well as their own. As levels of CCA1 and LHY fall, TOC1 is expressed and activates the expression of its repressors. This is a simplified version of the known clock components and the current model contains this core loop as well as an interlocked morning and evening loop, which also incorporates some post-translational modification (Chapter 1). Understanding the plant circadian network and its entrainment are the topics of this thesis. The study has focused on two plant species, the land plant Arabidopsis thaliana and the picoeukaryotic marine algae Ostreococcus tauri. In both of these species light-mediated entrainment of the clock has been investigated (Chapter 8), as well as the core circadian mechanism. In A. thaliana the role of a circadian associated gene, EARLY FLOWERING 3 has been a particular focus for investigation, through both experimentation and mathematical models (Chapters 4 and 5). In O. tauri the responses to light signals have been tested, as have the circadian responses to pharmacological manipulation (Chapters 6, 7 and 8). The work presented identifies a role for ELF3 in the repression of circadian genes and also links it with the regulation of protein stability. Likewise, in O. tauri the regulation of protein stability is identified to be a key mechanism for sustaining circadian rhythms. As well as investigating the clock in plants, certain photoreceptors have been characterised in S. cerevisiae with the aim of linking them to a synthetic oscillator. Together the work presented in this thesis provides evidence for the circadian community to aid with the understanding of circadian rhythms in plants, and possibly other organisms.

Li, Kwan Ho = 多體量子系統問題 / 李君豪. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves [243]-246). / Text in English; abstracts in English and Chinese. / Li, Kwan Ho = Duo ti liang zi xi tong wen ti / Li Junhao. / Abstract --- p.i / Acknowledgment --- p.iv / Chapter I --- Computational Quantum Mechanics and Its Applications --- p.1 / Chapter 1 --- Theoretical Methodology of Electronic Structures --- p.2 / Chapter 1.1 --- The Schrodinger Equation --- p.3 / Chapter 1.2 --- Molecular Hamiltonian and Born-Oppenheimer Approximation --- p.4 / Chapter 1.3 --- The Variational Method --- p.7 / Chapter 1.3.1 --- Rayleigh-Ritz Variation Principle --- p.7 / Chapter 1.3.2 --- Linear Variation --- p.8 / Chapter 1.4 --- Many-Electron Wavfunction --- p.9 / Chapter 1.4.1 --- Hartree-product Wavefunction --- p.9 / Chapter 1.4.2 --- Slater Determinant and the Pauli Exclusion Principle --- p.11 / Chapter 1.5 --- The Expectation Value of Total Electronic Energy --- p.13 / Chapter 1.6 --- Derivation of the Hartree-Fock Equations --- p.16 / Chapter 1.7 --- Orbital Energies and the SCF Total Electronic Energy --- p.19 / Chapter 1.8 --- Koopmans' Theorem --- p.20 / Chapter 1.9 --- The LCAO expansion and Self-Consistent Field Calculation --- p.22 / Chapter 1.10 --- AO Basis Sets --- p.23 / Chapter 1.10.1 --- Slater-Type Orbitals --- p.24 / Chapter 1.10.2 --- Gaussian Functions --- p.24 / Chapter 1.11 --- Hartree-Fock Limit --- p.25 / Chapter 1.12 --- Electron Correlation --- p.26 / Chapter 1.12.1 --- Weakness in the Single Determinantal Wavefunction --- p.26 / Chapter 1.12.2 --- Configuration Interaction --- p.26 / Chapter 1.13 --- Density Functional Theory --- p.27 / Chapter 1.13.1 --- Early approximations --- p.28 / Chapter 1.13.2 --- Hohenberg-Kohn Theorems --- p.31 / Chapter 1.13.3 --- Kohn-Sham (KS) Method --- p.33 / Chapter 1.13.4 --- Exchange-Correlation Energy Functional and B3LYP --- p.36 / Chapter 2 --- Theoretical Investigation of Oxadiazole-Triphenylamine Based Compounds --- p.40 / Chapter 2.1 --- Organic Light Emitting Diode and Oxadiazole-Triphenylamine Based Com- pounds --- p.40 / Chapter 2.2 --- Methodology --- p.42 / Chapter 2.2.1 --- Theoretical Methodology --- p.42 / Chapter 2.2.2 --- Computational Methodology --- p.46 / Chapter 2.3 --- Computational Results --- p.47 / Chapter 2.3.1 --- Molecular Structure --- p.47 / Chapter 2.3.2 --- Electronic Structure --- p.79 / Chapter 2.4 --- Absorption and Emission Energy --- p.94 / Chapter 2.5 --- Reorganization Energy and Mobility --- p.95 / Chapter 2.6 --- Summary --- p.99 / Chapter 3 --- The Transport Properties of Oligoacenes --- p.102 / Chapter 3.1 --- Introduction --- p.102 / Chapter 3.2 --- Computational Details --- p.103 / Chapter 3.3 --- Results and Discussions --- p.103 / Chapter 3.3.1 --- Molecular Configuration --- p.103 / Chapter 3.3.2 --- Reorganization Energy --- p.106 / Chapter 3.3.3 --- Coupling Matrix Element --- p.107 / Chapter 3.4 --- Conclusion --- p.133 / Chapter 4 --- The Transport Properties in Rubrene Thin Film and Crystal --- p.135 / Chapter 4.1 --- Introduction --- p.135 / Chapter 4.2 --- Computational Details --- p.137 / Chapter 4.3 --- Results and Discussions --- p.137 / Chapter 4.3.1 --- Molecular Structure --- p.137 / Chapter 4.3.2 --- Frontier Orbitals --- p.144 / Chapter 4.3.3 --- Reorganization Energy --- p.147 / Chapter 4.3.4 --- Coupling Matrix Element and Mobility --- p.147 / Chapter 4.4 --- Conclusion --- p.175 / Chapter II --- Analytical Studies of Anisotropic Spin-1/2 Heisenberg Anti-ferromagnetic Linear Chains --- p.177 / Chapter 5 --- Coupled-Cluster Approximation for Two Anisotropic Spin-1/2 Heisenberg Antiferromagnetic Linear Chains with Inter-chain Anisotropic Ferromagnetic Interaction --- p.178 / Chapter 5.1 --- Introduction --- p.178 / Chapter 5.2 --- Approximation in the Coupled-Cluster Method --- p.179 / Chapter 5.3 --- Anisotropic spin-1/2 Heisenberg Antiferromagnetic Model in One Dimension --- p.183 / Chapter 5.3.1 --- The Zeroth Level --- p.185 / Chapter 5.3.2 --- The First Level --- p.186 / Chapter 5.3.3 --- The Second Level --- p.189 / Chapter 5.4 --- Two Anisotropic Spin-1/2 Heisenberg Antiferromagnetic Linear Chains with Inter-chain Anisotropic Ferromagnetic Interaction --- p.198 / Chapter 5.4.1 --- The Zeroth Level --- p.199 / Chapter 5.4.2 --- The First Level --- p.201 / Chapter 5.4.3 --- The Second Level --- p.206 / Chapter 5.5 --- Conclusion --- p.242 / Bibliography --- p.243

Electrospinning has been recognized as an efficient technique for the fabrication of polymer fibers. These electrospun fibers have many applications across a broad range of industries. In this research, optical transparent composites were successfully fabricated by embedding polyacrylonitrile (PAN) hollow nanofibers into poly (methyl methacrylate) (PMMA) matrix. The hollow PAN nanofibers were prepared by coaxial electrospinning. The PAN was used as the shell solution, and the mineral oil was used as the core solution. The resulting fibers were then etched with octane to remove the mineral oil from the core. The hollow PAN fibers were then homogeneously distributed in PMMA resins to fabricate the composite. The morphology, transmittance and mechanical properties of the PAN/PMMA composite were then characterized with an ESEM, TEM, tensile testing machine, UV-vis spectrometer and KD2 Pro Decagon device. The results indicated that the hollow nanofibers have relatively uniform size with one-dimensional texture at the walls. The embedded PAN hollow nanofibers significantly enhanced the tensile stress and the Young's modulus of the composite (increased by 58.3% and 50.4%, respectively), while having little influence on the light transmittance of the composite. The KD2 Pro device indicated that the thermal conductivity of the PMMA was marginally greater than the PAN/PMMA composite by 2%. This novel transparent composite could be used for transparent armor protection, window panes in vehicles and buildings, and airplane windshield etc.

A multi-scale approach was used to investigate the occurrence and physical characteristics of viral surrogates in water systems. This approach resulted in a methodology to quantify the dynamics and physical parameters of viral surrogates, including bacteriophages and nanoparticles. Physical parameters impacting the occurrence and survival of viruses can be incorporated into models that predict the levels of viral contamination in specific types of water. Multiple full-scale water systems (U.S., Italy and Australia) were tested including surface water, drinking water, stormwater and wastewater systems. Water quality parameters assessed included viral markers (TTV, polyomavirus, microviridae and adenovirus), bacteriophages (MS2 and ΦX-174), and coliforms (total coliforms and E. coli). In this study, the lack of correlations between adenovirus and that of bacterial indicators suggests that these bacterial indicators are not suitable as indicators of viral contamination. In the wastewater samples, microviridae were correlated to the adenovirus, polyomavirus, and TTV. While TTV may have some qualities which are consistent with an indicator such as physical similarity to enteric viruses and occurrence in populations worldwide, the use of TTV as an indicator may be limited as a result of the detection occurrence. The limitations of TTV may impede further analysis and other makers such as coliphages, and microviridae may be easier to study in the near future. Batch scale adsorption tests were conducted. Protein-coated latex nanospheres were used to model bacteriophages (MS2 and ΦX-174) and includes a comparison of the zeta potentials in lab water, and two artificial groundwaters with monovalent and divalent electrolytes. This research shows that protein-coated particles have higher average log10 removals than uncoated particles. Although, the method of fluorescently labeling nanoparticles may not provide consistent data at the nanoscale. The results show both that research on viruses at any scale can be difficult and that new methodologies are needed to analyze virus characteristics in water systems. A new dynamic light scattering methodology, area recorded generalized optical scattering (ARGOS) method, was developed for observing the dynamics of nanoparticles, including bacteriophages MS2 and ΦX-174. This method should be further utilized to predict virus fate and transport in environmental systems and through treatment processes. While the concentration of MS2 is higher than ΦX-174 as demonstrated by relative total intensity, the RMSD shows that the dynamics are greater and have more variation in ΦX-174 than MS2 and this may be a result of the hydrophobic nature of ΦX-174. Relationships such as these should be further explored, and may reflect relationships such as particle bonds or hydrophobicity.

"The simultaneous degradation of five organic contaminants: 1,4 dioxane, n-nitrosodimethylamine, tris-2-chloroethyl phosphate, gemfibrozil, and 17β estradiol, was investigated using a 1 L batch water-jacketed UV photoreactor utilizing titanium dioxide (TiO2) nanoparticles (Degussa P-25) as a photocatalyst. The primary objectives of this research were: (1) to experimentally assess the feasibility of heterogeneous photocatalysis as a promising alternative for the degradation of organic compounds in water; and (2) to model the chemical reactions by the application of two different approaches based on adsorption – surface reactions (Langmuir–Hinshelwood) and its simplification to a first order rate reaction. These objectives were motivated by the lack of information regarding simultaneous degradation of organic compounds in different categories as found in real aqueous matrices, and generation of specific intermediates that could eventually represent a potential risk to the environment. Contaminants were chosen based on their occurrence in water sources, their representativeness of individual sub-categories, and their importance as part of the CCL3 as potential contaminants to be regulated. Contaminant degradation was evaluated over time, and the TiO2 concentration and solution pH were varied under constant UV irradiation, oxygen delivery rate, mixing gradient, and temperature. 

 Specific accomplishments of this study were: (1) reaction kinetics data were obtained from the UV/TiO2 experiments and showed the potential that this UV/TiO2 process has for effectively removing different types of organic compounds from water; (2) a good fit was obtained between photocatalytic reaction kinetics models and the contaminant data using pseudo first-order and Langmuir-Hinshelwood (L-H) models; (3) results of the analytical methods developed in this study were validated by measurements performed by a certified laboratory; (4) the reaction kinetic parameters obtained in this study were normalized to electrical energy per order, reactor volume and surface area of the photocatalyst in order to provide rate constants with wider applicability for scale-up to more complex systems; and (5) degradation intermediates from the oxidation process and from interaction among compounds were identified and possible pathways for their formation suggested. This research has provided a better understanding of the photocatalytic process for the removal of organic contaminants from complex aqueous matrices."

Typescript (photocopy). / Digitized by Kansas Correctional Industries / Department: Animal Sciences and Industry.

Adapting the tools of optical microscopy to the large-scale dynamic systems encountered in the development of multicellular organisms provides a path toward understanding the physical processes necessary for complex life to form and function. Obtaining quantitatively meaningful results from such systems has been challenging due to difficulty spanning the spatial and temporal scales representative of the whole, while also observing the many individual members from which complex and collective behavior emerges. A three-dimensional imaging technique known as light sheet fluorescence microscopy provides a number of significant benefits for surmounting these challenges and studying developmental systems. A thin plane of fluorescence excitation light is produced such that it coincides with the focal plane of an imaging system, providing rapid acquisition of optically sectioned images that can be used to construct a three-dimensional rendition of a sample. I discuss the implementation of this technique for use in larva of the model vertebrate Danio rerio (zebrafish). The nature of light sheet imaging makes it especially well suited to the study of large systems while maintaining good spatial resolution and minimizing damage to the specimen from excessive exposure to excitation light. I show the results from a comparative study that demonstrates the ability to image certain developmental processes non-destructively, while in contrast confocal microscopy results in abnormal growth due to phototoxicity. I develop the application of light sheet microscopy to the study of a previously inaccessible system: the bacterial colonization of a host organism. Using the technique, we are able to obtain a survey of the intestinal tract of a larval zebrafish and observe the location of microbes as they grow and establish a stable population in an initially germ free fish. Finally, I describe a new technique to measure the fluid viscosity of this intestinal environment in vivo using magnetically driven particles. By imaging such particles as they are oscillated in a frequency chirped field, it is possible to calculate properties such as the viscosity of the material in which they are embedded. Here I provide the first known measurement of intestinal mucus rheology in vivo. This dissertation includes previously published co-authored material.

Understanding and identifying critical protein-protein interactions is just one of the key outcomes in biological research. It can help to confirm key cellular interactions, which in some fields, such as cancer research, can result in a greater understanding of disease pathogenesis, elucidate mechanisms of therapeutic resistance and aid in the development of new specific targets, leading to new methods of prevention and treatment. Time-correlated single photon counting fluorescence lifetime imaging microscopy is just one of the tools used to carry out this line of research. Here we demonstrate a direct interaction between two proteins involved in gene regulation and expression; p21 and FMN2. Furthermore, we also show the capability of this system to measure chromatin compaction in three dimensions. However, fluorescence lifetime imaging has some drawbacks, acquisition times on such a system can range from the tens of seconds to minutes, which is often too long to comprehensively measure many biological events. But microscopy is always developing, aided by new techniques and, perhaps even more so, new technological developments. This thesis also demonstrates two new methods of light sheet microscopy, that use both new equipment made available because of technological developments to allow time resolved imaging and traditional microscopic aspects to form a light sheet system based on polarisation. It outlines the design and how to build these systems and presents their function to show their great promise. Both techniques presented in this thesis utilise aspects of light not conventionally used in light sheet microscopy. Further development of these systems and application of emerging technologies will yield a system capable of outperforming current light sheet fluorescence microscopy-based fluorescence lifetime imaging techniques. The implementation of polarisation control into such a system would enable three-dimensional anisotropy based SPIM-FLIM measurements, an indispensable tool in researching molecular orientation and mobility at a macroscopic level in developing organisms.