Optical Coherence Tomography (OCT) is a non-invasive volumetric imaging technique that offers micron scale resolution over several millimetres of depth penetration in tissue. The aim of the project was to develop Full Field Swept Source OCT (FFSSOCT), charting the specifications of the system throughout and drawing comparisons with available Fourier domain OCT (FDOCT) systems. A super luminescent diode (SLD) light source was tuned to different optical frequencies using an acousto-optical tunable filter. The successive optical frequencies were distributed across the sample in parallel and the sequential interference spectra were recorded with a high speed digital camera. Using a 5mW optical source at 850nm, 70dB sensitivity was ultimately achieved in a single five second acquisition, improving the original performance by 5dB and increasing acquisition and processing time significantly. Ex vivo retinal images of rat and tree shrew were recorded with multiple layers visible. All software was custom written in Labview, improving the user interface and processing time over the existing Matlab code. To enhance the performance of the system, the camera was subsequently upgraded from 15 to 45% quantum efficiency and from 250k to 1.3M pixels. The light source was also upgraded to 20mW. The software was improved with spectral processing and dispersion compensation. 85dB sensitivity was ultimately achieved. Further ex vivo retinal images were taken, showing comparative image quality to those of the same retinal samples recorded with FDOCT. Further attempts to increase the system performance were limited by internal reflections and interfering surfaces within the FFSSOCT design leading to saturation of the digital camera. In vivo imaging was attempted using software based phase jitter compensation. Improvement could be seen with simple reflecting structures.

The experiments which comprise this thesis focused on structure-function relationships in two distinct collagen-rich connective tissues of the eye, the cornea and the trabecular meshwork. The cornea is the transparent tissue that covers the front of the eye and has the ability to transmit and refract light. Corneal transparency is the result of the unique organisation of collagen fibrils in the corneal stroma matrix, of which sulphated proteoglycans are key regulators, owing to the presumed importance of the sulfation pattern of corneal proteoglycans. The trabecular meshwork is the sponge-like tissue located around the cornea through which the bulk of the aqueous humor flows towards the juxtacanalicular tissue and the inner wall of Schlemm’s canal to exit the eye and control intraocular pressure. First part of the current research examined the chemical composition and sulphur speciation during corneal embryogenesis in order to elucidate important changes in the biochemical signature of the corneal matrix associated with the acquisition of transparency. It also investigated the content and distribution of distinct sulphur species through the depth of the mature corneal stroma and assessed biochemical-functional relationships that ultimate render tissue transparency. The research also studied the three-dimensional ultrastructure of the human trabecular meshwork, particularly the ultrastructure of the juxtacanalicular tissue that lies adjacent to the inner wall of Schlemm’s canal and the three-dimensional assembly of collagen type VI in the trabecular meshwork itself. X-ray fluorescence microscopy revealed key differences in the chemical composition of the cornea of the developing chick. In particular, the chemical signature of phosphorus, chlorine, sulphur, potassium and calcium were observably different during the developmental period from day 12 to day 16. S k-edge x-ray near edge structure spectroscopy showed that the main sulphur species present in the embryonic cornea were thiols, organic monosulfides, ester sulphate and inorganic sulphate. The chemical signature of these sulphur species was also noticeably different during embryonic corneal development. The changes in the chemical signature of phosphorus with development are believed to underline changes in the presumptive keratocyte population within the embryonic corneal stroma. Chlorine, potassium and calcium are important elements involved in the regulation and balance of the net negative or positive charge of the embryonic cornea and may influence the interactions of corneal matrix molecules. The changes in the sulphur speciation character amongst different developmental corneas are associated with changes in the sulphation status of corneal proteoglycans which play a fundamental role in governing tissue structure and function, and thus transparency. With regards to the sulphur speciation across the depth of the mature corneal stroma, it was found that there is an inconsistency in the sulphur content and distribution throughout the depth of the tissue, from the stromal region closest to the epithelium against the deeper stromal regions near the endothelium. The heterogeneity of the sulphur species in the most anterior part of the mature corneal stroma, at the interface with the Bowman’s layer supports the view that the differentiation and the transition between these two corneal layers is not very abrupt. The rest of the mature corneal stroma depth does not show any differences regarding its content in the sulphur-containing compounds indicating that the distribution and sulfation status of the corneal glycosaminoglycans have very little impact on the overall sulfur speciation. The three-dimensional ultrastructure of the human trabecular meshwork in large volumes and at high resolution identified giant vacuoles in the endothelial cell layer of the inner wall of Schlemm’s canal and these were grouped into four categories based on whether they formed pores, basal and apical, or not. Interestingly, the distribution of these vacuoles was found to be non-uniform. It was discovered that the juxtacanalicular tissue was not homogenous with respect to the proportion of the electron lucent, matrix free spaces throughout the tissue’s depth away from the inner wall of Schlemm’s canal. Three-dimensional reconstructions of collagen type VI in the trabecular meshwork showed that there is no structural regularity in the organisation of type VI collagen assemblies, or their association with sulphated proteoglycans, suggesting a role in aqueous humor outflow. This data allow us to propose a model of aqueous humor outflow and how this is funneled through the juxtacanalicular tissue towards the lumen of Sclemm’s canal.

Overall, this project aimed to evaluate and advance the use of two techniques in the study of structural changes brought about by in vitro glycation of mouse tail tendon type I collagen. Firstly, using transmission electron microscopy with positive staining, study of collagen glycation by glucose, galactose, fructose and ribose was conducted. Site specificity of glycation along the fibril was seen and it was demonstrated for the first time using this method that there was variation in the progression of the process between the monosaccharides, suggesting different reaction mechanisms and determinants of site specificity for each sugar. From the early changes after 1 week galactose treatment, early-preferred glycation sites for this sugar were indicated. Using sorbitol, broad non-glycation-related sugar binding along the fibril was identified and this was also seen following galactose, fructose and ribose treatment. Secondly, using X-ray diffraction with isomorphous replacement, a 1D electron density map for collagen fibrils in mouse tail was constructed for the first time as a baseline for this and future intended glycation studies in mice. Use of this technique to study tendon incubated for 2 weeks in ribose and galactose showed electron density changes that appeared consistent with the corresponding electron microscopy glycation data. Using HPLC with fluorescence detection, it was shown that the four sugars produced different “fingerprint” profiles of products of glycation. Galactose produced a similar profile to glucose as hypothesised. However despite its chemical similarity to glucose, galactose also produced glycation products that were absent from the glucose profile. The biochemical information produced was invaluable for interpretation of the data from the structural techniques, inasmuch as providing representations of the relative extents of glycation occurring during each monosaccharide and control treatment. In conclusion, this thesis has demonstrated for the first time that transmission electron microscopy with positive staining, and X-ray diffraction with isomorphous replacement techniques together are useful complementary methods for studying glycation-related changes in type I collagen structure. It is anticipated that these techniques together will be of value in further in vitro and in vivo studies of type I collagen glycation, contributing to a better understanding of the structural bases of the deleterious effects of this process during diabetes and ageing.

The research work described in this thesis embodies a number of studies designed to investigate human vision with emphasis on aspects of the pupil response and chromatic mechanisms in relation to the perceived chromatic afterimages. The aim of the first study was to establish the relationship between the perception of chromatic afterimages and the corresponding involuntary pupil responses. We started by designing and developing a new, computer-based, psychophysics program and employed it to measure the strength and duration of perceived chromatic afterimages in normal trichromats and in colour deficient observers. The dynamic luminance noise technique was used to isolate colour signals and to elicit pupil responses to coloured stimuli of known photoreceptor contrast. A model was developed to explain the afterimage results obtained in the normal trichromats and in colour deficient subjects. The model and the pupil colour responses provided an understanding of luminance and colour processing in dichromats that also helped to explain previously reported pupil colour responses. The model also predicts the colour confusion lines and the characteristics of pupil colour responses in dichromats at any given background chromaticity. In the second study, we investigated and compared pupil responses to visual stimuli that isolate photopic luminance and colour in both the sighted and blind region of the visual fields on subjects with either acquired or congenital homonymous hemianopia. The measured pupil responses in the blind hemifield of patients with acquired cortical damage are either absent or of reduced amplitude when compared to those measured in the corresponding regions of the sighted field, whereas the patients with congenital loss of visual field show similar and even enhanced pupil responses when compared to their sighted hemifield. These results suggest that in the absence of normal functioning of the direct geniculostriate projection, other projections to midbrain nuclei or to extrastriate regions can be enhanced and these include the pupillary pathways. These findings suggest that early damage to the brain might be partly compensated for by reorganising the strength of neural projections to the remaining, non-compromised visual areas. The purpose of the last study was to examine whether melanopsin contributes to the dynamic pupil light reflex responses in humans. A light source containing of four primary components was employed to generate pupillary stimuli that isolate luminance, colour or combined rod and melanopsin. Normal trichormats, rod deficient subjects, one subject with retinitis pigmentosa, one rod monochromat, three subjects with Leber’s Hereditary Optic Neuropathy (LHON) and one subject with Optic Neuritis were investigated using this approach. The results from the LHON subjects suggest not all classes of ganglion cells are affected uniformly in LHON, and that the pupil light reflex responses mediated through rod photoreceptors were affected the least. The characteristics of the pupil responses to the rod/melanopsin stimulus from the rod monochromat and the retinis pigmentosa subjects suggest that melanopsin does not contribute to dynamic pupil light reflex response in humans.

This numerical study explored the mechanisms responsible for the re-initiation of a detonation, which quenched while diffracting over a half-cylinder obstacle. Its purpose was to accurately predict when detonation re-initiations occur, determine roles of re-initiation mechanisms, and compare effects of chemical models. The model used reactive Euler equations with the one-step Arrhenius or two-step chain-branching chemical models, calibrated to post-shock conditions to reproduce the ignition delay. Simulations were validated using the stoichiometric methane-oxygen experiments of Bhattacharjee et al.. The model accurately predicted detonation re-initiation conditions found in experiments with good qualitative and quantitative agreement. While the one-step model was sufficient in predicting re-initiation, the two-step model reproduced finer details. Kelvin-Helmholtz and Richtmyer-Meshkov instabilities did not appear to influence detonation re-initiation of the Mach stem. Detonation re-initiation occurred due to adiabatic compression of the Mach stem, or transport of a flame along the wall jet. Transverse detonations were poorly reproduced.

No description available.

There is considerable dissatisfaction with the reliability and sensitivity of the methods used to assess the glaucomatous visual field. Two types of visual field test, which have been proposed as having potential in diagnosing glaucomatous visual field defects, have been modified and tested on a group of patients from a glaucoma clinic, a group of age-matched control subjects and a younger control group. 1. A grating pattern was generated using a laser interferometer which projected a large diameter image onto the retina independent of the subject's refractive error. The experimental set up which produced the most reliable and consistently low contrast threshold values in normal subjects was sought. The display characteristics which were examined included different orientations for the field quadrants as projected to the subject; stationary and flickering patterns using a variety of flicker generation methods; red and green light sources; and concentric or vertical sinusoidal grating patterns. Ultimately the optimal display was found to be a stationary image consisting of a green, vertical sinusoidal grating pattern. Arcuate regions of the visual field (at 10 to 20° from fixation) were stimulated in 4 distinct, obliquely oriented quadrants and a low spatial frequency (one cycle per degree) was chosen. 2. Normal limits were obtained from age-matched control subjects for comparison with the results for the patients from the glaucoma clinic. In the patient group, of the 13 who completed the test, 9 individuals were identified as abnormal with one or more of their contrast threshold scores exceeding that limit. The patients' Friedmann visual field plots were analysed and the amount of loss in each quadrant was quantified. There was a positive correlation between the quantified visual field loss and contrast threshold scores in 6 patients, a statistically borderline correlation in 2 patients and the absence of a correlation was found in 5 patient's results. The results for a subgroup of 6 visually abnormal eyes (not affected by glaucoma) excluded from the age-matched control group are also described. Their visual defects included mild cataract, amblyopia and retinal detachment. There were no clear abnormal results in 5 of the eyes in this group; however, in one subject with retinal scarring due to an infection, there was a distinct elevation of contrast threshold in the affected eye. Humphrey visual field plots were obtained for all but one of the age-matched control subjects. 3. Simultaneous brightness ratios (SBR) have previously been shown to provide an indication of'glaucomatous damage. The same subject groups as described above were tested. SBRs were obtained for central vision in both eyes of subjects (inter-ocular ratio). This technique was now extended for the first time to paired regions within each eye (intra-ocular ratios) producing 'nasal I temporal' and 'upper I lower' ratios. In each test the subject controlled the brightness ratio which was changed in a smoothly graduated and continuou8 way. The most effective procedure for recording repeatable SBRs was first explored, and it was determined that these could be best obtained by alternating the start point of the graduated filter position. For each subject, 5 ratios were obtained: inter-ocular SBR; upper I lower intra-ocular SBR for right eye and left eye; and nasal I temporal intra-ocular SBR for right eye and left eye. 4. Normal limits were obtained from age-matched control subjects for comparison with the results for the patients from the glaucoma clinic. In each of the 5 SBR tests carried out, these limits were wide, reflecting considerable variation in the normal results. Of the 14 patients who completed the tests, 5 were identified as abnormal by one or more of their SBRs being outside normal limits. Three of these were identified as abnormal by their inter-ocular SBRs alone, one was abnormal according to his upper I lower intra-ocular SBR alone and one patient had an abnormal inter-ocular SBR and an abnormal intra-ocular SBR. The corresponding regions of the patients' Friedmann visual fields were quantified, and these values were used to calculate visual field loss ratios. There was a positive correlation between the visual field loss ratios and SBRs in 3 patients, but no correlation in 11 patients. In the sub-group of 6 visually abnormal eyes without glaucoma, mild cataract appeared not to adversely affect SBR. Mean SBRs were normal in the subject with retinal detachment but there was evidence of an enhanced amount of variation in the readings. Two subjects with a damaged retina and one with an amblyopic eye did produce abnormal inter-ocular SBRs, with the normal eye being significantly more sensitive in both cases.

No description available.

Acanthamoeba may cause a painful, potentially blinding, opportunistic infection of the cornea. The incidence of Acanthamoeba keratitis has increased in line with contact lens usage. Only in the last five years, however, has it been recognised that amoebae other than Acanthamoeba may also be associated with keratitis. Several reports implicating Vahlkampfia and Hartmannella now exist. These relatively unknown genera of free-living amoebae had not previously been recognised as causal agents of disease. This thesis investigated the pathogenicity of Acanthamoeba for corneal cells and tissue in vitro, compared, both quantitatively and qualitatively, to that of Vahlkampfla and Hartmannella isolates from a case of amoebal keratitis, termed V-EYE and H-EYE (Aitken et al, 1995). Problems pertinent to the diagnosis of Acanthamoeba, Vahlkampfta and Hartmannella species (sp) in human corneal tissue were also addressed.

Computers have gone from being solely large number crunching machines to small devices capable of performing a myriad of functions in a very small space of time. Computers are now used to control just about every facet of daily life; they can now be found in automobiles, washing machines and home heating systems. This rapid diversification brings a great many problems. Traditional software engineering methodologies are failing to meet and address these new problems. The goal of this thesis is to develop a new approach to organisational requirements engineering. A new modelling approach to representing organisations will be developed which will draw upon the concepts of a systems architecture, modelling the life cycle of responsibilities and the execution of conversations. Using this architecture an organisation will be able to embed social and cultural aspects within the modelling notation. From the modelling of responsibilities a clearer picture of the organisation's aims, objectives and policies will be developed along with a definition of what objects and access rights are required in order for the organisation to function. Using speech act and Petri net based models to model conversations a clearer understanding of the dynamics and constraints governing organisational behaviour can be developed. These modelling approaches are then applied to two real life case studies in order to demonstrate and evaluate their performance and usefulness.