Simplified preparation of human arterial sections for PCR analysis of Chlamydia pneumoniae and human DNA

AIMS: To investigate multiple techniques for the preparation of solid tissue for polymerase chain reaction (PCR) analysis, and to identify the most simple techniques for routine use in the laboratory. METHODS: Techniques for the preparation of arterial tissue samples including homogenisation, ultrafiltration, and treatments involving proteinase K, Gene Clean, lectin, and Fe3+ specific chelators were evaluated using the PCR to amplify both Chlamydia pneumoniae and human DNA. RESULTS: Treatment with either Gene-Clean or lectin and the Fe3+ specific chelator deferoxamine mesylate removed PCR inhibitors from tissue homogenates. Homogenisation followed by GeneClean treatment resulted in the amplification of C pneumoniae DNA from within a section of atherosclerotic carotid artery, implying that C pneumoniae elementary bodies had been disrupted. In eight further clinical samples from patients not known to have C pneumoniae infection, human DNA was amplified and no cross contamination was observed between samples. These samples contained no evidence of C pneumoniae by PCR. CONCLUSIONS: A simple preparation of solid tissue for PCR analysis, involving homogenisation followed by GeneClean treatment has been developed, and is effective for the amplification of both C pneumoniae and human DNA.

Flow field analysis of some mixing and conveying screw element regions, within a closely intermeshing, co-rotating twin-screw extruder.

Grafting of antioxidants and other modifiers onto polymers by reactive extrusion, has been performed successfully by the Polymer Processing and Performance Group at Aston University. Traditionally the optimum conditions for the grafting process have been established within a Brabender internal mixer. Transfer of this batch process to a continuous processor, such as an extruder, has, typically, been empirical. To have more confidence in the success of direct transfer of the process requires knowledge of, and comparison between, residence times, mixing intensities, shear rates and flow regimes in the internal mixer and in the continuous processor.The continuous processor chosen for the current work in the closely intermeshing, co-rotating twin-screw extruder (CICo-TSE). CICo-TSEs contain screw elements that convey material with a self-wiping action and are widely used for polymer compounding and blending. Of the different mixing modules contained within the CICo-TSE, the trilobal elements, which impose intensive mixing, and the mixing discs, which impose extensive mixing, are of importance when establishing the intensity of mixing. In this thesis, the flow patterns within the various regions of the single-flighted conveying screw elements and within both the trilobal element and mixing disc zones of a Betol BTS40 CICo-TSE, have been modelled using the computational fluid dynamics package Polyflow. A major obstacle encountered when solving the flow problem within all of these sets of elements, arises from both the complex geometry and the time-dependent flow boundaries as the elements rotate about their fixed axes. Simulation of the time dependent boundaries was overcome by selecting a number of sequential 2D and 3D geometries, used to represent partial mixing cycles. The flow fields were simulated using the ideal rheological properties of polypropylene and characterised in terms of velocity vectors, shear stresses generated and a parameter known as the mixing efficiency. The majority of the large 3D simulations were performed on the Cray J90 supercomputer situated at the Rutherford-Appleton laboratories, with pre- and postprocessing operations achieved via a Silicon Graphics Indy workstation. A mechanical model was constructed consisting of various CICo-TSE elements rotating within a transparent outer barrel. A technique has been developed using coloured viscous clays whereby the flow patterns and mixing characteristics within the CICo-TSE may be visualised. In order to test and verify the simulated predictions, the patterns observed within the mechanical model were compared with the flow patterns predicted by the computational model. The flow patterns within the single-flighted conveying screw elements in particular, showed good agreement between the experimental and simulated results.

Precise orbit determination and analysis from satellite altimetry and laser ranging

For optimum utilization of satellite-borne instrumentation, it is necessary to know precisely the orbital position of the spacecraft. The aim of this thesis is therefore two-fold - firstly to derive precise orbits with particular emphasis placed on the altimetric satellite SEASAT and secondly, to utilize the precise orbits, to improve upon atmospheric density determinations for satellite drag modelling purposes. Part one of the thesis, on precise orbit determinations, is particularly concerned with the tracking data - satellite laser ranging, altimetry and crossover height differences - and how this data can be used to analyse errors in the orbit, the geoid and sea-surface topography. The outcome of this analysis is the determination of a low degree and order model for sea surface topography. Part two, on the other hand, mainly concentrates on using the laser data to analyse and improve upon current atmospheric density models. In particular, the modelling of density changes associated with geomagnetic disturbances comes under scrutiny in this section. By introducing persistence modelling of a geomagnetic event and solving for certain geomagnetic parameters, a new density model is derived which performs significantly better than the state-of-the-art models over periods of severe geomagnetic storms at SEASAT heights. This is independently verified by application of the derived model to STARLETTE orbit determinations.

The dynamics of organizational change : an analysis of power, professions and new managerialism in the case of CoastElectric

It is widely accepted that the Thatcher years and their immediate aftermath were associated with substantive social and organizational change. The privatisation programme, 'the rolling back of the State', prosecuted by the successive Conservative Governments from 1979-1997 was a central pillar of Governmental policy. This thesis seeks to engage with privatization through the of CoastElectric, a newly privatised Regional Electricity Company. This thesis contributes to the extant understanding of the dynamics of organizational change in four major ways. Firstly, the study into CoastElectric addresses the senior management decision making within the organization: in particular, it will attempt to make sense of 'why' particular decisions were made. The theoretical backdrop to this concern will draw on the concepts of normalization, cultural capital and corporate fashion. The argument presented in this thesis is that the decision-making broadly corresponded with that which could be considered to be at the vanguard of mangerialist thought. However, a detailed analysis suggested that at different junctures in CoastElectric's history there were differences in the approach to decision making that warranted further analysis. The most notable finding was that the relative levels of new managerialist cultural capital possessed by the decision-making elite had an important bearing upon whether the decision was formulated either endogenously or exogenously, with the assistance of cultural intermediaries such as management consultants. The thesis demonstrates the importance of the broader discourse of new managerialism in terms of shaping what is considered to be a 'commonsensical, rational' strategy. The second concern of this thesis is that of the process of organizational change. The study of CoastElectric attempts to provide a rich account of the dynamics of organizational change. This is realized through, first, examining the pre-existing context of the organization; second, through analyzing the power politics of change interventions. The master concepts utilised in this endeavour are that of: dividing practices, the establishment of violent hierarchies between competing discourses; symbolic violence; critical turning points; recursiveness; creative destruction; legitimation strategies and the reconstitution of subjects in the workplace.

Meta-analysis of the population and phenotypic expression of CYP2C9/2C19 polymorphism on drug metabolism in different ethnicities

The term "pharmacogenetics" has been defined as the scientific study of inherited factors that affect the human drug response. Many pharmacogenetie studies have been published since 1995 and have focussed on the principal enzyme family involved in drug metabolism, the cytochrome P450 family, particularly cytochrome P4502C9 and 2C19. In order to investigate the pharmacogenetic aspect of pharmacotherapy, the relevant studies describing the association of pharmacogenetic factor(s) in drug responses must be retrieved from existing literature using a systematic review approach. In addition, the estimation of variant allele prevalence for the gene under study between different ethnic populations is important for pharmacogenetic studies. In this thesis, the prevalence of CYP2C9/2C19 alleles between different ethnicities has been estimated through meta-analysis and the population genetic principle. The clinical outcome of CYP2C9/2C19 allelic variation on the pharmacotherapy of epilepsy has been investigated; although many new antiepileptic drugs have been launched into the market, carbamazepine, phenobarbital and phenytoin are still the major agents in the pharmacotherapy of epilepsy. Therefore, phenytoin was chosen as a model AED and the effect of CYP2C9/2C19 genetic polymorphism on phenytoin metabolism was further examined.An estimation of the allele prevalence was undertaken for three CYP2C9/2C19 alleles respectively using a meta-analysis of studies that fit the Hardy-Weinberg equilibrium. The prevalence of CYP2C9*1 is approximately 81%, 96%, 97% and 94% in Caucasian, Chinese, Japanese, African populations respectively; the pooled prevalence of CYP2C19*1 is about 86%, 57%, 58% and 85% in these ethnic populations respectively. However, the studies of association between CYP2C9/2C19 polymorphism and phenytoin metabolism failed to achieve any qualitative or quantitative conclusion. Therefore, mephenytoin metabolism was examined as a probe drug for association between CYP2C19 polymorphism and mephenytoin metabolic ratio. Similarly, analysis of association between CYP2C9 polymorphism and warfarin dose requirement was undertaken.It was confirmed that subjects carrying two mutated CYP2C19 alleles have higher S/R mephenytoin ratio due to deficient CYP2C19 enzyme activity. The studies of warfarin and CYP2C9 polymorphism did not provide a conclusive result due to poor comparability between studies.The genetic polymorphism of drug metabolism enzymes has been studied extensively, however other genetic factors, such as multiple drug resistance genes (MDR) and genes encoding ion channels, which may contribute to variability in function of drug transporters and targets, require more attention in future pharmacogenetic studies of antiepileptic drugs.

Experiments and analysis of combined diffraction and self diffraction effects in a nematic liquid crystal cell

The potential for nonlinear optical processes in nematic-liquid-crystal cells is great due to the large phase changes resulting from reorientation of the nematic-liquid-crystal director. Here the combination of diffraction and self-diffraction effects are studied simultaneously by the use of a pair of focused laser beams which are coincident on a homeotropically aligned liquid-crystal cell. The result is a complicated diffraction pattern in the far field. This is analyzed in terms of the continuum theory for liquid crystals, using a one-elastic-constant approximation to solve the reorientation profile. Very good comparison between theory and experiment is obtained. An interesting transient grating, existing due to the viscosity of the liquid-crystal material, is observed in theory and practice for large cell-tilt angles.

Exploratory data analysis with non-linear and missing data in geochemistry

Exploratory analysis of data seeks to find common patterns to gain insights into the structure and distribution of the data. In geochemistry it is a valuable means to gain insights into the complicated processes making up a petroleum system. Typically linear visualisation methods like principal components analysis, linked plots, or brushing are used. These methods can not directly be employed when dealing with missing data and they struggle to capture global non-linear structures in the data, however they can do so locally. This thesis discusses a complementary approach based on a non-linear probabilistic model. The generative topographic mapping (GTM) enables the visualisation of the effects of very many variables on a single plot, which is able to incorporate more structure than a two dimensional principal components plot. The model can deal with uncertainty, missing data and allows for the exploration of the non-linear structure in the data. In this thesis a novel approach to initialise the GTM with arbitrary projections is developed. This makes it possible to combine GTM with algorithms like Isomap and fit complex non-linear structure like the Swiss-roll. Another novel extension is the incorporation of prior knowledge about the structure of the covariance matrix. This extension greatly enhances the modelling capabilities of the algorithm resulting in better fit to the data and better imputation capabilities for missing data. Additionally an extensive benchmark study of the missing data imputation capabilities of GTM is performed. Further a novel approach, based on missing data, will be introduced to benchmark the fit of probabilistic visualisation algorithms on unlabelled data. Finally the work is complemented by evaluating the algorithms on real-life datasets from geochemical projects.

Technology flows, outsourcing and productivity:an analysis of UK trade and FDI

The literature on technology spillovers from trade and FDI is ambiguous in its findings. This may in part be because of the assumption in much of the work that trade and FDI flows are homogeneous in their determinants and thus in their effects. We develop a taxonomy of trade and FDI determinants based on R&D intensity and unit labour cost differentials, and test for the presence of spillovers from inward investment and imports on an extensive sample of UK manufacturing plants. We find that both trade and FDI have measurable spillover effects, but the sign and extent of these effects varies depending on the technological and factor cost differentials between the recipient and host economies. There is therefore an identifiable link between the determinants and effects of trade and FDI which the previous literature has not explored.

Technology flows, outsourcing and productivity:an analysis of UK trade and FDI

The literature on technology spillovers from trade and FDI is ambiguous in its findings. This may in part be because of the assumption in much of the work that trade and FDI flows are homogeneous in their determinants and thus in their effects. We develop a taxonomy of trade and FDI determinants based on R&D intensity and unit labour cost differentials, and test for the presence of spillovers from inward investment and imports on an extensive sample of UK manufacturing plants. We find that both trade and FDI have measurable spillover effects, but the sign and extent of these effects varies depending on the technological and factor cost differentials between the recipient and host economies. There is therefore an identifiable link between the determinants and effects of trade and FDI which the previous literature has not explored.

Experiments and analysis of combined diffraction and self diffraction effects in a nematic liquid crystal cell

The potential for nonlinear optical processes in nematic-liquid-crystal cells is great due to the large phase changes resulting from reorientation of the nematic-liquid-crystal director. Here the combination of diffraction and self-diffraction effects are studied simultaneously by the use of a pair of focused laser beams which are coincident on a homeotropically aligned liquid-crystal cell. The result is a complicated diffraction pattern in the far field. This is analyzed in terms of the continuum theory for liquid crystals, using a one-elastic-constant approximation to solve the reorientation profile. Very good comparison between theory and experiment is obtained. An interesting transient grating, existing due to the viscosity of the liquid-crystal material, is observed in theory and practice for large cell-tilt angles.

Analysis of secretory, immunostaining and clinical characteristics of human "functionless" pituitary adenomas:transdifferentiation or gonadotropinomas?

In this study, the central technique of in vitro culture has been used to further investigate whether LH/FSH-expressing, but clinically "functionless" pituitary adenomas are gonadotropinomas or whether their hormone secretion is due to transdifferentiation events. 664 "functionless" pituitary adenomas were examined for hormone secretion by in vitro culture and for hormone content by immunostaining. The results were correlated with the clinical findings. 40% of the tumours (n = 263) secreted at least one of the gonadotropins alone, 8% (n = 53) exhibited various patterns of anterior pituitary hormones, whilst the remaining 52% of tumours were not associated with any hormone. In the secretory tumours, immunostaining revealed only a few scattered hormone-containing cells (5 to 15%). Mild hyperprolactinaemia was observed in some cases, presumably because of pressure effects of the tumours. The majority of the patients suffered clear cut hypopituitarism (p < 0.05). Pre-operatively, gonadotropin hypersecretion was observed in 3 cases, but only one of these secreted hormones in culture. Interestingly, a higher proportion of tumours removed from patients with hypopituitarism showed secretory activity in vitro than those tumours removed from patients showing no hormonal dysfunction or hyperprolactinaemia. We conclude that the term "gonadotropinoma" to describe functionless pituitary tumours associated with LH and/or FSH secretion is a misnomer, because the presence of LH and/or FSH confirmed by in vitro methods in the present series is a result of only a few scattered cells. We suggest that primary pituitary tumour cells differentiate into a secretory type (transdifferentiation), possibly in response to altered serum hormone levels such as decreased steroids. Further work is required to identify the factors which trigger the altered cells' characteristics. © J. A. Barth Verlag in Georg Thieme Verlag KG.

A data structure for improved gp analysis via efficient computation and visualisation of population measures

Population measures for genetic programs are defined and analysed in an attempt to better understand the behaviour of genetic programming. Some measures are simple, but do not provide sufficient insight. The more meaningful ones are complex and take extra computation time. Here we present a unified view on the computation of population measures through an information hypertree (iTree). The iTree allows for a unified and efficient calculation of population measures via a basic tree traversal. © Springer-Verlag 2004.