Doctoral

Incompressible and Compressible Boundary Layers on a Fibre in the Melt Spinning Process

John Harding (Thesis) — Tue, 14 May 2013 06:41:44 PDT

This thesis seeks to investigate shear stress on and heat transfer from the surface of a fibre in the industrial process of melt spinning. Melt spinning is the process whereby molten polymer materials are extruded through the holes of a device known as a spinneret to create continuous filaments of polymer. Fibres manufactured in this way are used in applications as diverse as fashion and clothing, to telecommunications. The magnitude ofthe shear stress on the fibre surface, and also the rate of heat transfer from the fibre to the surrounding environment are of major importance to the overall quality of the finished product, and this thesis examines the shear stress and heat transfer experienced by an idealised fibre in the melt spinning process. Also examined is the effect of compressible fluid flow on the shear stress on the fibre's surface.

A New Versatile Electronic Speckle Pattern Interferometer For Vibration Measurements

Viswanath Bavigadda (Thesis) — Tue, 09 Apr 2013 07:48:19 PDT

Electronic speckle pattern interferometry (ESPI) has been widely used for vibration amplitude and phase measurements. Conventional ESPI systems are bulk and expensive and need careful alignment of all the optical components which is a time consuming task. To overcome these problems alternative compact ESPI systems were developed using fibre-optical components or holographic optical elements (HOEs). The fibre-optic based ESPI systems suffer from random phase fluctuations induced by environmental temperature changes. Hence HOEs can be used as more powerful alternative optical elements to design ESPI systems. The time average ESPI method is widely used for vibration studies. The time average method combined with phase stepping can be used for automatic vibration measurements. Using this technique higher vibration amplitudes cannot be measured because fringe patterns follow Bessel function intensity distribution. To overcome this problem an alternative technique can be used by modulating the phase of the reference beam in an unbalanced interferometer. This thesis reports a novel ESPI system for vibration measurements by combining use of holographic optical elements (HOEs) and optical path length modulation (reference beam phase modulation). The optical path length modulation is implemented using laser diode wavelength (frequency) modulation. Different HOE based ESPI systems are reported in this thesis using either a single HOE or dual HOE. This thesis examines performance of different HOE based ESPI systems that are sensitive to out-of-plane displacement components using laser diodes operating either in the near infrared or visible electromagnetic spectrum. Vibration modes of a circular metal plate clamped at the edges of a loud speaker and a circular metal plate driven by a piezoelectric actuator (PZT) were studied using a single RHOE based ESPI system and a hybrid (transmission HOE with a partially reflecting mirror) HOE based ESPI system respectively using a near infrared laser diode (763nm). Optical path length modulation technique was implemented using a laser diode operating in visible electromagnetic spectrum (658nm). Vibration mode patterns of a circular metal plate driven by a PZT actuator were obtained using both single RHOE and dual HOE based ESPI systems. Using optical path length modulation technique in a dual HOE based ESPI system detailed phase and amplitude maps of a circular metal plate driven by a PZT actuator are obtained. The dual HOE based ESPI system was also used for measuring roations of a circular metal plate mounted on a mirror mount. In conclusion we have developed a compact HOE based ESPI system to conduct vibration measurements. A few potential future developments are also suggested at the end of the thesis.

Raman Micro Spectroscopy for the Characterisation of Cervical Cancer.

Nosheen Rashid — Mon, 11 Mar 2013 09:15:53 PDT

The primary purpose of this study is to evaluate the potential of FTIR and Confocal Raman micro spectroscopy (CRM) in elucidating the biochemical changes occurring in different layers of the cervical epithelium including basal, superficial and the underlying connective tissue known as stroma during the progression of Cervical Intraepithelial Neoplasia (CIN) to cancer. Initially the two techniques were compared and Raman was chosen based on its higher spatial and spectral resolution. The sample preparation and spectral measurement procedures were optimised and all samples were formalin fixed paraffin processed, dewaxed using xylene, and measured on calcium fluoride windows. Raman spectra were recorded using a source wavelength of 785nm and a X100 dry objective lens. Raman micro spectroscopy was able to differentiate the normal region of the cervical tissue sample into three layers including stroma, basal/para-basal and superficial layers on the basis of the spectral features of the collagen, DNA bases and glycogen as well as discrimination of the diseased areas from the normal areas. In particular Raman spectroscopy could describe the biochemical changes in the diseased samples in detail. On moving from normal to abnormal regions of the cervical tissue sample, the characteristic Raman features of the basal layer were observed in the superficial layer and in the stroma. Notably, the normal region of a CIN III sample was found to have biochemical information similar to the abnormal region. This has been indicated by the absence of the collagen Raman spectral bands in the stromal layer as well as absence or minute presence of the glycogen bands in the superficial layer. A comparison of the Principal Components Analysis (PCA) loadings of the HPV negative and positive cell lines (C33A and CaSki), with those of the basal layers of normal and abnormal tissue samples showed no strongly matching Raman signatures which could lead to the identification of signatures of HPV infection in the cervical cancer tissue samples. 3 However, a feature associated with the amide-III beta sheet (1222 cm-1) was found to be consistently present in the PCA loadings contributed by the basal layers of the intermediate and abnormal samples. This was much reduced in intensity in the most extreme abnormal sample and the carcinoma in situ samples. This feature may be considered as an early marker of disease progression, but further investigation is needed to confirm this finding. KMCA indicated the possibility of the migration of basal cells into the superficial and stromal layers and subsequent PCA led to the conclusion that basal cells indicated by high DNA content and lack of glycogen are progressing to the superficial layer due to the progression of the disease. In the case of stroma, the basal like characteristics are actually associated with the biochemical changes in the stromal cells and there is no migration of these cells into the stroma. In addition, during cervical cancer progression, relative to the DNA, collagen has a diminished contribution at some points in the Raman map of the stroma and KMCA recognised the greater similarities with the DNA rich cells of the basal layer. This has been supported by the enhanced expression of p16 protein in the basal and superficial layers rather than in the stroma.

Visual Performance, and it's Response to Intervention, in Subjects with Age-Related Macular Degeneration.

Sarah Sabour-Pickett — Wed, 06 Mar 2013 02:46:04 PST

Abstract Objectives: 1. To explore visual performance status through a range of psychophysical methods beyond corrected distance visual acuity (CDVA), in subjects with age-related macular degeneration (AMD). 2. To investigate the effects on these visual performance parameters in subjects with neovascular age-related macular degeneration (nv-AMD) and in subjects with early AMD undergoing anti-VEGF (vascular endothelial growth factor) therapy and macular carotenoid supplementation, respectively. 3. To understand the role of a supplement containing meso-zeaxanthin (MZ; the third, and currently least explored, macular carotenoid) on the augmentation of macular pigment (MP), on visual performance and on disease progression (graded according to the AREDS [Age-Related Eye Disease Study] criteria), in subjects with early AMD. 4. To explore the impact of macular carotenoid supplementation on vision in subjects presenting with atypical macular pigment optical density (MPOD) spatial profiles at baseline. Outcomes: This study has shown that CDVA is not the most appropriate measure of visual function and does not reflect retinal morphology in cases of early AMD or in cases of nv-AMD. Retinotopic ocular sensitivity (ROS), however, appears to be a more reflective measure of disease severity, where it correlates well with AMD-severity grade (in cases of early AMD) and also with mean foveal thickness (MFT; in cases of nv-AMD). In eyes with nv-AMD undergoing monthly intravitreal ranibizumab injections, there have been demonstrable improvements in a range of parameters of visual function, namely, contrast sensitivity (CS), glare disability (GD), and ROS but no significant change in CDVA, despite a reduction in MFT. MP can be augmented, and CS enhanced, in subjects with early AMD who receive supplemental macular carotenoids. Subjects with low baseline central MPOD had the greatest increases in MPOD and the greatest improvements in CS, when compared with subjects with medium or high baseline MPOD, suggesting that the 4 optimisation of CS (and putatively visual performance in general) is somewhat dependent on central MP levels. The literature review has concluded that supplementation with the macular carotenoids offers the best means of fortifying the antioxidant defenses of the macula, thus putatively reducing the risk of AMD and/or its progression, and of optimising visual performance. Conclusions: The findings of this work suggest the incorporation of tests, complimentary to CDVA, such as CS, GD, and particularly ROS, when attempting to understand disease severity in cases of AMD. In terms of monitoring change over time, the results of this study do seem to indicate that measures of ROS may be particularly useful in monitoring subjects with nv-AMD, while measures of CS and GD may be more apt in monitoring change in subjects with early AMD. Macular carotenoid supplementation can enhance visual performance in subjects with early AMD.

Mathematical and Computational Modelling for Biosensors: A Modular Approach

Yupeng Liu — Thu, 18 Oct 2012 01:29:24 PDT

Biosensors are analytic devices which detect biochemical and physiological changes and represent an emerging technology for low-cost, rapid and simple-to-operate biomedical diagnostic tools. Biosensor design and functionality are based on well understood physical and chemical processes which can be easily translated into mathematical models involving ordinary and partial di erential equations. Using mathematical and computational modelling techniques to characterize the biosensor response as a function of its input parameters in a wide range of physical contexts can guide the experimental work, thus reducing development time and costs.
This thesis is based on a close collaboration with Biochemistry researchers at the National Centre for Sensor Research (NCSR) and Biomedical Diagnostics Institute (BDI) at Dublin City University and the mathematical models we develop are relevant to ongoing experimental work in these centres relating to design optimization of biocatalytic and bioanity devices. Our approach is to use numerical solutions as a rst step towards determining the accuracy of these models, since the simulations successfully reproduce the experimental outcomes; future work can then concentrate on a more detailed theoretical analysis.

An Analysis of Drug Dissolution in Vivo

David McDonnell (Thesis) — Mon, 10 Sep 2012 05:46:28 PDT

The testing of drug dissolution rates from solid dosage forms is a very important area of research within the pharmaceutical industry. The ability to produce drugs with a given dissolution rate will lead to improved performance in the treatment of patients and will be of economic benefit to the pharmaceutical industry. However, dissolution testing in laboratories, aimed at reflecting in-vivo conditions, can be both time consuming and costly. Currently, most simulations of drug dissolution take place in standardized USP (United States Pharmaceutical) apparatuses. A number of these apparatuses exist, and it is the aim of this thesis to analyse drug dissolution in both the USP Paddle Apparatus and the USP Flow Through Apparatus. The first part of this thesis examines drug dissolution from a solid dosage form (compact) in the USP Paddle Apparatus. The process is set up as a boundary layer problem for which there exists both a momentum boundary layer and a concentration boundary layer. The dominant mass transfer mechanism is that of forced convection. A semi-analytical technique is used to solve the boundary layer equations for which velocity data has been provided from computational fluid dynamic simulations. Wherever possible the results from this semi-analytical approach have been compared with that of an exact solution. The second part of the thesis concentrates on the USP Flow Through Apparatus. As the process of drug dissolution in the Flow Through Apparatus is dependent on a vertical flow, the analysis is complicated by the introduction of buoyancy effects. Chapters five to nine analyse a number of general cases for buoyancy driven flows on both flat and curved surfaces. Later, in chapter ten, these general cases are then applied to the process of drug dissolution from the surface of a compact in the USP Flow Through Apparatus. Throughout the thesis, the predicted dissolution rates from the theoretical approach are compared with those of experiment.

Molecular Genetic and DNA Methylation Profiling of Chronic Lymphocytic Leukaemia: a Focus on Divergent Prognostic Subgroups and Subsets

Nicola Cahill (Thesis) — Mon, 10 Sep 2012 05:46:27 PDT

Advancements in prognostication have improved the subdivision of chronic lymphocytic leukaemia (CLL) into diverse prognostic subgroups. In CLL, IGHV unmutated and IGHV3-21 genes are associated with a poor-prognosis, conversely, IGHV mutated genes with a favourable outcome. The finding of multiple CLL subsets expressing ‘stereotyped’ B-cell receptors (BCRs) has suggested a role for antigen(s) in leukemogenesis. Patients belonging to certain stereotyped subsets share clinical and biological characteristics, yet limited knowledge exists regarding the genetic and epigenetic events that may influence their clinical behaviour. This thesis aimed to, further investigate Swedish IGHV3-21-utilising patients, screen for genetic and DNA methylation events in CLL subgroups/subsets and study DNA methylation over time and within different CLL compartments. In paper I, IGHV gene sequencing of 337 CLL patients from a Swedish population-based cohort revealed a lower (6.5%) IGHV3-21 frequency relative to previous Swedish hospital-based studies (10.1-12.7%). Interestingly, this frequency remained higher compared to other Western CLL (2.6-4.1%) hospital-based cohorts. Furthermore, we confirmed the poor-outcome for IGHV3-21 patients to be independent of mutational and stereotypy status. In paper II, genomic events in stereotyped IGHV3-21-subset #2, IGHV4-34- subset #4 and subset #16 and their non-stereotyped counterparts were investigated via SNP arrays (n=101). Subset #2 and non-subset #2 carried a higher frequency of V events compared to subset #4. A high frequency of del(11q) was evident in IGHV3- 21 patients particularly subset #2 cases, which may partially explain their poorprognosis. In contrast, the lower prevalence of aberrations and absence of poorprognostic alterations may reflect the inherent low-proliferative disease seen in subset #4 cases. In papers III and IV, differential methylation profiles in IGHV mutated and IGHV unmutated patients were identified using DNA-methylation microarrays. CLL prognostic genes (CLLU1, LPL), tumor-suppressor genes (TSGs) (ABI3, WISP3) and genes belonging to TGF-ß and NFkB/ TNFR1 pathways were differentially methylated between the subgroups. Additionally, the re-expression of methylated TSGs by use of methyl and deacetyl inhibitors was demonstrated. Interestingly, analysis of patient-paired diagnostic/follow-up samples and patient-matched lymph node (LN) and peripheral blood (PB) cases revealed global DNA methylation to be relatively stable over time and remarkably similar within the different compartments. Altogether, this thesis provides insight into the aberrant genomic and DNA methylation events in divergent CLL subgroups. Moreover this thesis helps distinguish the extent to which DNA methylation changes with respect to time and microenvironment in CLL.

Analysis of HPV-16 Late Gene Expression

Beatrice Orru (Thesis) — Fri, 27 Jul 2012 07:35:09 PDT

Human papillomaviruses (HPVs) are present in 99.7% of all cervical cancers and HPV type 16 (HPV-16) is the major cause of cervical cancer. Expression of the viral capsid gene L1 and L2 can be detected only in the terminally epithelial cells and we speculate that inhibition of HPV-16 late gene expression in the early stage of the life cycle is probably a prerequisite for persistence of infection. The products of the late genes, L1 and L2, are highly immunogenic and expression of these proteins in the lower layers of the cervical epithelium could lead to clearance of the virus. Therefore, it is of interest to understand how HPV late gene expression is regulated. The goal of this thesis was to examine the regulation of late genes in HPV-16. To this end we wished to generate reporter plasmids based on the HPV-16 genome with the L1 gene replaced by an easily measurable reporter gene, such as chloramphenicol acetyltransferase (CAT), green fluorescent protein (GFP), secreted alkaline phosphatase (SEAP) or luciferase, and to establish reporter stable cell lines useful for large scale screening of small molecules or cellular factors that influence RNA processing events during late gene expression. CAT and GFP proved to be functional surrogate markers of late gene expression and their expression was dependent on the levels of known inducers of HPV-16 late gene expression such as adenovirus E4orf4 protein (E4orf4), polypyrimidine tract binding protein (PTB), arginine/serine-rich SRp30c protein (SRp30c) or alternative splicing factor/splicing factor 2 (ASF/SF2). Functional stable cell lines with CAT reporter plasmids, separately integrated into the HeLa cellular genome, were also generated allowing the identification of a number of small molecules capable of modulating CAT expression. Phorbol 12-myristate 13-acetate (TPA), valproic acid and tannic acid were identified as inducers of HPV-16 late gene expression. Further experiments identified the TPA inducible, hnRNP A2/B1 protein as a novel regulator of HPV-16 late gene expression. Immunohistochemical analysis of this protein in cervical epithelium at the different stages of the development of cervical cancer demonstrated that hnRNP A2/B1 is highly expressed in normal cervical epithelium and low-grade squamous intraepithelial lesion (LSIL) and decreased in highgrade squamous intraepithelial lesion (HSIL) and squamous cell carcinoma (SCC). In conclusion, the HPV-16 reporter plasmids and reporter cell lines described herein are functional and can be used for the investigations of HPV-16 late gene expression.

The Preparation and Characterisation of Silver Nanomaterials and Their Application in Sensing Techniques

Aoife Power (Thesis) — Tue, 06 Mar 2012 09:56:14 PST

In this work the impact of nanomaterial, specifically silver nanostructures, on sensing techniques is investigated. The work can be divided in to three sections, preparation and characterisation of silver nanoparticles, their application as a nanocomposite based chemiresistor humidity sensing device and finally their application within the surface enhanced (resonance) Raman spectroscopy, SE(R)RS, technique. In the first study silver nanoparticles were prepared as aqueous colloidal dispersions. The colloids were of either a defined diameter (average diameter ~ 20 nm) with high silver loading or lower loaded colloids of tuneable morphology and hence optical properties. In a subsequent study the high load colloid when cast on platinum interdigital electrodes as a nanocomposite coating proved to be useful as a humidity sensor. The sensor gave a reversible, selective and rapid response which was proportional to humidity levels within the range of 10% RH to 60% RH. An investigation into the mechanism of the sensor’s response was conducted and the response was found to correlate well with a second order Langmuir adsorption model. The final study was multi faceted as it first determined the suitability of the tuneable colloids as SE(R)RS substrates using a number of probe molecules. A clear sensing trend was observed, where the Raman signal emitted was significantly enhanced by the addition of silver nanoparticles. This prompted an additional investigation where both colloids were again cast as films (fabricating alternative SERS substrates) to determine the degree outside factors could influence the enhancement seen by the SERS technique. The suitability of the SERS substrates in a real world application was investigated, with SERS being used to monitor the action mechanism of components of a commercially available volatile corrosion inhibitor.

A Community Dietetics Intervention to Improve the Use of Oral Nutritional Supplements in the Community Setting

Sharon Kennelly (Thesis) — Tue, 21 Feb 2012 08:16:14 PST

Evaluation of a community dietetics intervention to improve oral nutritional supplement prescribing practices in the community. Background: Healthcare professionals working in the community do not always prescribe oral nutritional supplements (ONS) according to best practice guidelines and expenditure on ONS has increased. The aim of this study was to investigate ONS prescribing practices and to determine the impact of a community dietetics intervention on these practices and expenditure one year later. Methods: At baseline ONS prescribing practices were investigated by patient interview with a community dietitian. The intervention involved an education programme for general medical practitioners (GPs), practice nurses, nurses in nursing homes and community nurses together with the provision of a new community dietetics service. Changes in healthcare professionals‟ practices and knowledge were determined by selfadministered questionnaires immediately after and six months after the intervention, and by examining community dietetics records one year after the intervention. ONS prescribing volume and expenditure were assessed using data from the Primary Care Reimbursement Service of the Irish Health Service Executive. Results: Seventy-eight and 42 patients were included in the study pre and postintervention respectively. Ninety-six healthcare professionals participated in the nutrition education programme (including seven of ten principal GPs). Six months post-intervention improvement in healthcare professional nutritional knowledge was observed (P<0.001). One year post-intervention, screening for malnutrition risk was better (62% vs 0%, P < 0.001), dietary advice provided more often (90% vs 26%, P < 0.001), and ONS prescribed for a greater proportion of patients who were at „high risk‟ of malnutrition than before (88% vs 37%, P < 0.001). There was a trend (not significant) towards fewer patients being prescribed ONS (18% reduction, P = 0.074) and there was no significant change in expenditure on ONS by participating GPs (3% reduction, P = 0.499), despite a 28% increase nationally by GPs on ONS. Conclusion: The community dietetics intervention improved ONS prescribing practices by healthcare professionals, in accordance with best practice guidelines, without increasing expenditure on ONS during the year after intervention.

An Analysis of the Mortality Risks Associated with Heat and Heat Waves in Ireland, to Assist in Planning for Climate Change

Mathilde Pascal (Thesis) — Mon, 06 Feb 2012 02:14:57 PST

Although extreme temperatures have not been identified as a major cause of mortality in Ireland, climate change calls for an evaluation of the past, present and future health risks associated with heat and heat waves. The health impacts of heat were investigated using mortality and temperature data for the period 1981-2003. Data were aggregated in urban areas (Dublin, Cork, Drogheda, Arklow, Dundalk, Galway, Limerick, Waterford and Wexford) and rural areas. Seven heat waves were identified between 1981 and 2003, corresponding to 254 excess deaths (197 in rural areas, and 57 in urban areas). A major episode was observed in rural areas in 1983: +115 [confidence interval CI 95% 96:137] extra deaths between the 5th and the 23rd July 1983. During summer, a 1°C increase above 15°C in the mean temperature was associated with a 1.5% [CI 95% 0.9:2.1] increase in total mortality in rural areas, and a 1.6% [0.6:2.5] increase in total mortality in urban areas. Risks were modified by the mortality observed in the preceding winter. There are indications that the heat-related risks have been decreasing between the 80s and the 90s. A better geographical resolution of the mortality data is an asset to refine this analysis and to study any relationship between a health topic and an environmental exposure. Despite limits on the data, an increase in temperature was associated with an increase in mortality during summer in Ireland, and past heat waves were associated with a small but observable excess mortality. With the perspective of climate change, and with the ageing of the population, it may be that more severe heat episodes results in a larger mortality burden, as was observed during the July 1983 heat wave. Steps to reduce vulnerability to heat during extreme episodes should be considered.

Completeness of Interacting Particles

Pavel Abramski (Thesis) — Tue, 31 Jan 2012 01:50:24 PST

This thesis concerns the completeness of scattering states of n _-interacting particles in one dimension. Only the repulsive case is treated, where thereare no bound states and the spectrum is entirely absolutely continuous, so the scattering Hilbert space is the whole of L2(Rn). The thesis consists of 4 chapters: The first chapter describes the model, the scattering states as given by the Bethe Ansatz, and the main completeness problem. The second chapter contains the proof of the completeness relation in the case of two particles: n = 2. This case had in fact already been treated by B. Smit (1997), [17], but it is useful to include this case as it clarifies the more general case. In particular, the more algebraic approach used for the n-particle case is illustrated in this simple example. In Chapter 3 the case n = 3 is examined. This is useful for illustrative purposes as the scattering states can still be written explicitly term by term and it is not yet necessary to introduce the complicated notation used in the general case. On the other hand, this case shows up certain technical difficulties to do with the non-commutativity of the permutation group (S3) which do not occur in the 2-particle case. Finally, Chapter 4 contains the proof of the completeness relation in the general n-particle case. The method used is the same as in the 3-particle case, but the algebra is much more complicated. In particular a number of interesting lemmas and one theorem is proved. The first lemma for 3-particle case and its generalisation - theorem for n-particle case essentially concerns the Yang-Baxter relation for this model, as first written by Yang. Indeed, Yang proposed his version of these relations as a consistency condition for the Bethe Ansatz solution of the model but never actually gave a complete proof of the consistency given these relations. Here a complete inductive proof is given. Some algebraic manipulation reduces the left-hand side of the completeness relation to a simpler form. Another lemma, which seems to be new, then shows that this expression does not contain divergent terms and consists of a sum of integrals similar to those encountered in the 2- and 3-particle cases. Evaluation of these integrals then leads to the required _-relation.

Mathematical Methods for Biosensor Models

Qi Wang (Thesis) — Mon, 30 Jan 2012 04:54:18 PST

A biosensor is defined as a compact analytical device incorporating a biological sensing element integrated within a physico-chemical transducer whose aim is to produce optical or electronic signals proportional to the concentration of an analyte in a sample. Biosensors offer enormous potential to detect a wide range of analytes in health care, the food industry, environmental monitoring, security and defence. The beneficial impact on society as a result of the availability of such systems is immense, therefore investigating any strategy that could reduce development times and costs and reveal alternative designs is of utmost importance. In particular, mathematical modelling and simulation, the so-called \virtual experimentation", is a relatively inexpensive and yet powerful tool for scientific analysis and prediction. Biosensor modelling is a rich source of mathematical challenges. The main components of biosensors are based on well-understood physical processes (such as diffusion, convective flow, energy and mass transfer) as well as chemical and biological reactions, all of which are amenable to mathematical modelling using ordinary and partial differential equations. The objective of this project is to provide a foundation for mathematical and computational modelling of biosensors, through identifying analytical and numerical methods applicable to the study of electrochemical and optical biosensors, with a view to optimising their design process. The models will be relevant to ongoing experimental work in the National Centre for Sensor Research (NCSR) and the Biomedical Diagnostics Institute (BDI) at Dublin City University.

Development and Validation of Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Methods for the Analysis of Veterinary Drugs in Various Biological and Feed Matrices Utilizing Efficient Extraction Protocols

Mark Cronly (Thesis) — Tue, 03 Jan 2012 01:49:12 PST

The transfer of farming practices from low intensity farming systems for livestock production to commercial enterprises which employ intensive practices has resulted in the use of veterinary drugs becoming a critical component of food production. Resulting residues of veterinary drugs occurring in food of animal origin may give rise to potential health risks to consumers. The aim of this research is the development of analytical methods capable of screening and confirming increased number of these residues in more target matrices by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Its focus is the analysis of nitroimidazole residues in food of animal origin and authorised and prohibited medicinal additives in animal feed. This research resulted in the development and validation of methods for analysis of nitroimidazoles (NMZs) in plasma, eggs, milk and honey and prohibited and authorised medicinal additives in animal feed. The analytical technique used in all methods was the highly selective and sensitive LC-MS/MS. This technique allowed for multi-analyte methods to be developed for different matrices. NMZ residues examined were metronidazole, dimetridazole, ronidazole, ipronidazole, ternidazole, ornidazole, carnidazole and tinidazole along with three metabolite, hydroxymetronidazole, 2-Hydroxymethyl-1-methyl-5-nitroimidazole (HMMNI) and hydroxy-ipronidazole. Chloramphenicol was included with the analysis of NMZs in the matrices of milk and honey. Fourteen medicinal additives; metronidazole, dimetridazole, ronidazole, ipronidazole, clopidol, carbadox, sulfadiazine, sulfamethazine, dinitolimide, chloramphenicol, ethopabate, avilamycin, tylosin and virginiamycin were analysed for in animal feed. The final method developed allowed for coccidiostats; halofuginone, robenidine, nicarbazin, diclazuril, decoquinate, iii semduramicin, lasalocid, salinomycin, monensin, narasin and maduramicin to be analysed for at levels related to unavoidable carryover in feed. All veterinary residue methods used were validated in accordance with EU legislation; Commission Decision 2002/657/EC. This legislation is concerned with the performance of analytical methods and the interpretation of results. Validation criteria were examined using protocols set out in this legislation and these included specificity, accuracy, precision, repeatability, reproducibility, decision limits (CCα), detection capabilities (CCβ) along with measurement uncertainty (MU). In the four methods developed for the analysis of NMZ residues in plasma, egg, milk and honey the accuracy and precision for all analytes ranged from 87.2% to 108.9% and 3.7% to 11.3% respectively in all matrices. CCα and CCβ for all nitroimidazole residues ranged from 0.33 to 1.60 g L-1 / g kg-1 and 0.56 to 2.64 g L-1 / g kg-1 respectively with MUs ranging from 18 to 90% for all compounds in the various matrices. Chloramphenicol CCα and CCβ values were below its minimum required performance level (MRPL) of 0.3 g L-1 / g kg-1. At present there is no legislation in place describing validation approaches for methods used for the analysis of medicinal additives in animal feed. Therefore for the validation of the two feed methods developed as part of this research the veterinary residue legislation was used as a basis. In the case of the analysis of coccidiostats at unavoidable carry over levels; the method was validated entirely in accordance with veterinary residue legislation, Commission Decision 2002/657/EC. However the method for the analysis of 14 prohibited medicinal additives in feed was validated with some adaptations to this legislation. To ensure that the method was fit for purpose a wide variety of feed was used in validation and a wider concentration range was examined. Parameters of specificity, accuracy, precision, iv repeatability, reproducibility were all examined and deemed to be acceptable along with measurement uncertainty.

Solar Radiation Damage to Human Skin Mitochondria

Luciene Zanchetta (Thesis) — Fri, 25 Nov 2011 01:23:04 PST

The central objective of this study was to assess solar radiation-induced changes in cellular function, mitochondrial function and mitochondrial DNA to further investigate the role of these energy-dedicated and metabolically essential organelles in the response to the main environmental stressor associated with skin cancer initiation. An in vitro approach was chosen employing the human malignant melanoma (A375) and human amelanotic melanoma (C32) cells and the human spontaneously immortalized keratinocytes (HaCaT). A Q-Sun Solar Simulator was used to expose cells to low-level simulated solar radiation (SSR) as it provides a mimic of solar radiation that is environmentally relevant in the UV spectrum. Cell viability, apoptosis, DNA and protein content were analysed as cellular response end-points and they have been observed to change in a cell type-specific and time- dependent manner post SSR. Increases in mitochondrial genome number and mtDNA3895 were observed as an early response to low-dose SSR in human skin cells. The common deletion mtDNA4977t,h ough detected, did not directly increase in frequency with solar radiation exposure though the mtDNA3895 deletion, previously found to be associated with solar radiation exposure, was observed to be substantially increased in a cell-type and dose-dependent manner in skin cells post SSR. Impaired mitochondrial bioenergetics, dynamics and recycling may play a significant role in the melanoma tumour initiation and progression in humans post systematic solar radiation over-exposure. Furthermore the sensitive nature of the mitochondrial population of skin cells should not be underestimated as dynamic changes in their biology are evident even in cell populations that received low level irradiation of simulated solar radiation.

Investigation of UV-LED Initiated Photopolymerisation of Bio-compatible HEMA

Sharon McDermott (Thesis) — Thu, 24 Nov 2011 07:53:27 PST

Ultraviolet (UV) fluorescent lamps are widely used in photopolymerisation processes. However, there a number of disadvantages to these lamps, namely, their intensity varies over time and has to be constantly monitored. This thesis is concerned with the possibility of replacing these lamps with UV Light Emitting Diodes (UV-LEDs). A number of emission characteristics of both the fluorescent lamp and the UV-LEDs were measured and compared to ensure that the optical properties of the UV-LEDs were equivalent to those of the lamps. From this study it was shown that the UV-LEDs have a quicker warm up time and exhibit a more stable output than the fluorescent lamps, while also emitting in the required region for photopolymerisation. The ability of each source to initiate photopolymerisation in a HEMA sample was then monitored using FTIR (Fourier Transform Infrared) and Raman spectroscopy and the percentage cure calculated. These studies proved that UVLEDs could produce a degree of cure that was comparable to that produced by the fluorescent lamp. The last section of the study was concerned with investigating how pulsed UV radiation affected the curing process and thus the mechanical properties of the final polymer. This work was performed using FTIR spectroscopy and Dynamic mechanical analysis (DMA). The study showed that the curing profiles and the mechanical properties of the polymer were not only affected by the irradiation wavelength but also by the duration of the pulsing. The findings of this thesis show that due to the inherent advantages that LEDs have over fluorescent lamps and the fact that they produce a comparable photopolymerisation as that achieved with the fluorescent lamps, LED photopolymerisation is a viable possibility in replacing fluorescent lamps in the manufacturing of biomaterials.

Development of Acrylamide Based Photopolymer for Full Colour Display Holography

Chakrapani Meka (Thesis) — Thu, 24 Nov 2011 06:42:48 PST

Holography is a firmly established discipline that can be used as a tool for scientific and engineering studies and as a display medium as well. Until now both silver halide photographic emulsions (SHPE) and dichromated gelatine (DCG) have been the most common materials used for high efficiency full colour reflection hologram recording. However, these materials require wet chemical processing for developing the holograms which is laborious and costly from the point of view of commercial applications. Self-developing photopolymers such as acrylamide based photopolymer (ABP) which do not require development are the ideal choice for real-time recording and reconstruction of holograms. This thesis reports on the development of an acrylamide based photopolymer system for full colour reflection holographic display. Firstly ABP was dye sensitised separately at 633 nm and 473 nm using methyleneblue and acriflavine respectively to record holographic reflection gratings and the corresponding diffraction efficiencies were measured. Following this, the ABP material which had already been sensitised at 532 nm at the IEO centre by using erythrosine B as a dye, a panchromatic ABP was developed at IEO sensitised at all three selected primary wavelengths which were available, namely 633 nm, 473 nm and 532 nm. The Bidirectional Scattering Distribution Function (BSDF) was measured for the ABP and scattering obtained was relatively low compared with that of air and glass in the visible region. Reflection holographic gratings were recorded at 633 nm, 532 nm, and 473 nm wavelengths to evaluate the diffraction efficiencies at spatial frequencies of 4200 lineslmm, 5000 lineslmm and 5700 lineslmm respectively. An optical setup was established to record multicolour holograms by combining three selected laser beams (at 633 nm, 532 nm, and 473 nm). Further multicolour reflection holographic gratings were recorded using a combined single RGB beam so that all wavelengths illuminated the same spot. Spectral characterisation was carried out on the multicolour reflection holographic gratings and the Bragg peaks of the diffracted beam were monitored and compared with the recording wavelengths to reveal the shifts which were considered due to the dimensional changes inside the photopolymer. These spectral shifts in the photopolymer response were minimised by using zeolite nanoparticles (Si-MFI 30nm). Reflection holograms of objects were successfully recorded at all three primary wavelengths, and also using a combined RGB beam. The results provided a strong confirmation that this acrylamide based photopolymer can be used as a panchromatic recording material and can be employed in future commercial holographic applications.

Solar Radiation Investigations; a Foundation Study

Alanna Maguire (Thesis) — Thu, 24 Nov 2011 06:09:08 PST

Skin cancer is a global epidemic that is increasing annually. However, our knowledge of the mechanisms involved in skin carcinogenesis is relatively poor. Investigative studies to date have predominantly employed fluorescent UV A and I or UVB lamps. The information gained from such studies has pioneered this area of research effectively, however, the typical unimodal Gaussian distribution of such irradiators do not reflect that of solar radiation nor do they account for potential waveband interactions. Advancing technologies in solar simulation have opened up this field to more environmentally and biologically relevant exposures, not only in terms of distribution but also irradiance. To begin, this study addressed issues regarding the biological relevance of four different irradiators with respect to solar radiation. During this investigation the different exposure media employed (cell culture medium and PBS) were found to elicit significantly different results in terms of cell survival which were in direct conflict with the transmittance properties of the exposure media. The differential effects of the media were further investigated using endpoints that assessed the role of reactive oxygen species, mechanistic processes ( caspase-3 activity, mitochondrial membrane potential) and genomic perturbations (mitotic index, comet assay) in response to solar simulated irradiation. These results prompted further investigations into the effects of solar simulated radiation on cell culture medium. Medium transfer experiments showed that cell culture medium irradiated in the absence of cells was cytotoxic to unirradiated cells. Solar simulated radiation induced bystander effects were also investigated to determine if the presence of cells during irradiation had an effect on the cytotoxicity of the irradiated medium. Thus, this study assessed the two most fundamental parameters in non-ionising radiation in vitro investigations in order to form solid foundations upon which more detailed investigations into the mechanisms of skin carcinogenesis can confidently be performed.

The Role of Colour Duplex Ultrasound in the Surveillance of Patients Undergoing Endovascular Aneurysm Repair

Cleona Gray (Thesis) — Mon, 21 Nov 2011 04:19:28 PST

Photoactive Supramolecular Cyclodextrin Assemblies

Muath Atmeh (Thesis) — Wed, 16 Nov 2011 07:51:27 PST

Ligands with a macrocyclic host unit attached to a photoactive metal core are of interest across a range of applications from luminescent or electrochemical sensors, light harvesting and energy-collection purposes. Their versatile properties and possibility of associating cyclodextrins with other molecules both covalently and non-covalently mean that these macrocyclic ligands can be employed in the design and the formation of supramolecular complexes. A particularly attractive proposition is to combine the selective inclusion capabilities of CD with luminophores which may act as reporters of binding or other interactions at the cyclodextrin cavity. Ruthenium, osmium, and iridium polypyridyl complexes are particularly attractive reporters in this regard because of their visible emission and their useful redox properties. Their long lived excited states are particularly attractive providing significant scope for interaction with an included species compared with organic fluorphores, which can be very insensitive to their environments due to their fast radiative decays. In this thesis, we exploited the properties of CD and ruthenium polypyridyl complexes in designing photoactive metallocyclodextrin where 5-amino-1, 10-phenanthroline has been attached to the primary side of β-cyclodextrin. This ligand. β -CD-aphen has been used to design [Ru(bpy)2(aphen-CD). [Ru(bpy)2(aphen-CD) ][PF6]2 exhibits an intense luminescence ascribed to a 3MLCT state at room temperature in DMF and water with , λmax at 618 nm, a lifetime of approximately 1 μs and quantum yield of φ= 0.013 in deaerated solution. The secondary side of cyclodextrin is still available. We exploited the idea that metals like Copper and Zinc can be coordinated to the secondary side in constructing of molecular assembly where the donor and acceptor are held together via covalent link through a bridge. We have designed a trinuclear metallocyclodextrin-based donor-acceptor complex where the dicopper (II) sites are hydroxo bridged to the secondary side of β-CD in [Ru(bpy)2(aphen-CD)]. The donor and acceptor in our system are linked via a β-Cyclodextrin On the account of their relatively hydrophobic interiors; CDs have the ability to form inclusion complexes with wide range of Substrates. This idea has been exploited to bring the donor and the acceptor in a close proximity and study the energy and/or electron transfer in these novel supramoluclar assemblies. The effect of anthraquinone and anthraquinonecarboxcyclic on the luminescence of ruthenium was investigated in chapter three. In addition we demonstrate, for the first time, that the luminescence quantum yield and lifetime of Ru (II) polypyridyl center shows remarkable sensitivity to pH and we present detailed pH titrations for luminescence intensity and lifetime. The range of pH response is extremely broad, from pH 1 to pH 13 and alterations to luminescence quantum yield of greater than 60% are observed. In chapter 6 we have examined photoinduced transfer process between Ru and Ir metal centers in water mediated by non-covalent interactions through a cyclodextrin cavity. On the basis of the inclusion ability of β-CD and the redox properties of pyrene we have studied Ru-Ir interaction in trimer [Ir-(RuCD)2] in aqueous solution. Formation of the Ru-Py-Ir trimer through cyclodextrins induces significant changes in the photophysical behavior of both pyrene and appended Ruthenium. We couldn’t detect a significant change in the photophysical of Iridium metal centre. This means that communication between the two metal centers is very weak. This behavior may be attributed to the presence of pyrene moiety which blocks the interaction between the two metal centers. In [Ir-(RuCD)2] pyrene acts as a store for the energy instead of mediating the transfer process. Future work on these complexes will include further studies on the nature of the electron transfer process. This will include, for example, more detailed transient absorption spectroscopy to discern the direction of transfer either Ir→ Ru or Py→Ru or both. We then extended our work to make homonuclear photoactive cyclodextrins dimers. These dimers comprised of two photoactive metal centers covalently attached to the primary side of γ-cyclodextrin. In chapter 5, we exploit the inclusion ability to design a tetrameric metallocyclodextrins containing photoactive Ru(II) polypyridyl units covalently bonded to γ-CD. Then the cyclodextrin complexes were self-assembled with a fullerene moiety in 2:1 ratio to produce the tetramer. The synthesis and characterization of the complexes and in particular their spectroscopic electrochemical and photophysical properties described. We provide evidence for photoinduced processes and discuss the possibility of electron and energy transfers in these novel supramolecular assemblies.