Living long-term with acquired brain injury in Ireland: towards a counter discourse

Irish literature on Acquired Brain Injury (ABI) is very scant and is mainly deficits and/or needs based. The focus is generally on how to manage the short term needs of the younger population with ABI. The starting position of my thesis is that people living long-term with ABI are important participants in developing knowledge about this social phenomenon, living with ABI while accepting that their brain injury does not determine them. Six mature adults with ABI and their six significant others participated in this longitudinal study. Using a narrative approach in interviews, over twenty months, five repeat individual interviews with each of the twelve participants was held. From this I gained an understanding of their lived experiences, their life-world and their experiences of our local public ABI/disability services, systems and discourse. Along with this new empirical data, theoretical developments from occupational therapy, occupational science, sociology, and disability studies were also used within a meta-narrative informed by critical theory and critical realism to develop a synthesis of this study. Social analysis of their narratives co-constructed with me, allowed me generate nuanced insights into tendencies and social processes that impacted and continues to impact on their everyday-everynight living. I discuss in some depth here, the relational attitudinal, structural, occupational and environmental supports, barriers or discrimination that they face(d) in their search for social participation and community inclusion. Personal recognition of the disabled participants by their family, friends and/or local community, was generally enhanced after much suffering, social supports, slow recovery, and with some form of meaningful occupational engagement. This engagement was generally linked with pre-injury interests or habits, while Time itself became both a major aid and a need. The present local ABI discourse seldom includes advocacy and inclusion in everyday/every night local events, yet most participants sought both peer-support or collective recognition, and social/community inclusion to help develop their own counter-discourse to the dominant ABI discourse. This thesis aims to give a broad social explanation on aspects of their social becoming, 'self-sameness' and social participation, and the status of the disabled participants wanting to live 'the slow life'. Tensions and dialectical issues involved in moving from the category of a person in coma, to person with a disability, to being a citizen should not demote the need for special services. While individualized short-term neuro-rehabilitation is necessary, it is not sufficient. Along with the participants, this researcher asks that community health and/or social care planners and service-providers rethink how ABI is understood and represented, and how people with ABI are included in their local communities

The impact of conifer plantation forestry on the ecology of peatland lakes

Blanket bog lakes are a characteristic feature of blanket bog habitats and harbour many rare and threatened invertebrate species. Despite their potential conservation value, however, very little is known about their physico-chemical or biological characteristics in western Europe, and their reference conditions are still unknown in Ireland. Furthermore, they are under considerable threat in Ireland from a number of sources, particularly afforestation of their catchments by exotic conifers. Plantation forestry can potentially lead to the increased input of substances including hydrogen ions (H+), plants nutrients, dissolved organic carbon (DOC), heavy metals and sediment. The aims of this study were to investigate the effect of conifer plantation forestry on the hydrochemistry and ecology of blanket bog lakes in western Ireland. Lake hydrochemistry, littoral Chydoridae (Cladocera) and littoral macroinvertebrate communities were compared among replicate lakes selected from three distinct catchment land use categories: i) unplanted blanket bog only present in the catchment, ii) mature (closed-canopy) conifer plantation forests only present in the catchment and iii) catchments containing mature conifer plantation forests with recently clearfelled areas. All three catchment land uses were replicated across two geologies: sandstone and granite. Lakes with afforested catchments across both geologies had elevated concentrations of phosphorus (P), nitrogen (N), total dissolved organic carbon (TDOC), aluminium (Al) and iron (Fe), with the highest concentrations of each parameter recorded from lakes with catchment clearfelling. Dissolved oxygen concentrations were also significantly reduced in the afforested lakes, particularly the clearfell lakes. This change in lake hydrochemistry was associated with profound changes in lake invertebrate communities. Within the chydorid communities, the dominance of Alonopsis elongata in the unplanted blanket bog lakes shifted to dominance by the smaller bodied Chydorus sphaericus, along with Alonella nana, Alonella excisa and Alonella exigua, in the plantation forestry-affected lakes, consistent with a shift in lake trophy. Similarly, there was marked changes in the macroinvertebrate communities, especially for the Coleoptera and Heteroptera assemblages which revealed increased taxon richness and abundance in the nutrient-enriched lakes. In terms of conservation status, despite having the greatest species-quality scores (SQS) and species richness, three of the four International Union for the Conservation of Nature (IUCN) red-listed species of Coleoptera and Odonata recorded during the study were absent from lakes subject to catchment clearfelling. The relative strengths of bottom-up (forestry-mediated nutrient enrichment) and top-down (fish) forces in structuring littoral macroinvertebrate communities was investigated in a separate study. Nutrient enrichment was shown to be the dominant force acting on communities, with fish having a lesser influence. These results confirmed that plantation forestry poses the single greatest threat to the conservation status of blanket bog lakes in western Ireland. The findings of this study have major implications for the management of afforested peatlands. Further research is required on blanket bog lakes to prevent any further plantation forestry-mediated habitat deterioration of this rare and protected habitat.

Vaccinia virus assembly and motility

Vaccinia virus, the prototype member of the orthopoxviruses, is the largest and the most complex virus known. After replication of its genome and expression of the viral proteins, vaccinia undergoes a complicated assembly process which produces two distinct infectious forms. The first of these, the intracellular mature virus (IMV), develops from the immature virion (IV) after packaging of the genome and cleavage of the core proteins. During the transition of the IV to the IMV, a new core structure develops in the centre of the virion, concomitantly with the appearance of spike-like structures which extend between this core and the surrounding membranes of the IMV. I describe the characterization of p39 (gene A4L) which is hypothesized to be one component of these spikes. p39 is a core protein, but has strong associations with the membranes surrounding the IMV, possibly due to an interaction with p21 (A17L). Due to its location between the core and the membranes of the IMV, p39 is ideally situated to act as a matrix-like linker protein and may play a role in the formation of the core during the transition of the IV to the IMV. The IMV is subsequently wrapped by a membrane cisterna derived from the trans Golgi network, to form the intracellular enveloped virus (IEV). I show that the IEV can co-opt the actin cytoskeleton of the host cell in order to induce the formation of actin tails which extend from one side of the virion. These actin tails propel the virus particle, both intra- and intercellularly, at speeds of up to 2.8µm/min. On reaching the plasma membrane, the virus particles project out from the cell surface at the tip of virally induced microvilli. The outer membrane of the IEV is thought to fuse with the plasma membrane at the tip of these projections, thus exposing the second infectious form of vaccinia. This is thought to be the means by which the cell-associated enveloped virus is presented to neighbouring cells, thereby facilitating the direct cell-to-cell spread of virus particles.

Micropropagation of Begonia and a study of genome stability in Begonia rex

The development of procedures and media for the micropropagation of B. rex are described. Media for the production of plantlets from a number of other Begonia hybrids are also provided. Growth analysis data is given for plants produced in vivo from leaf cuttings and in vitro from mature leaf petioles and immature leaves derived from singly and multiply recycled axenic plantlets. No significant difference was found in phenotype or quantitative vegetative characters for any of the populations assessed. The results presented from studies on the development of broad spectrum media for the propagation of a number of B. rex cultivars using axenic leaf explants on factorial combinations of hormones illustrate the major influence played by the genotype on explant response in vitro and suggest media on which a range of B. rex cultivars may be propagated. Procedures for in vitro irradiation and colchicine treatments to destabilize the B. rex genome have also been described. Variants produced from these treatments indicate the utility of in vitro procedures for the expression of induced somatic variation. Colour variants produced from irradiation treatment have been cultured and prove stable. Polyploids produced as variants from irradiation treatment have been subcultured but prove unstable. Media for the induction and proliferation of callus are outlined. The influence of callus subculture and aging on the stability of the B. rex genome is assessed by chromosomal analysis of cells, in vitro and in regenerants. The B. rex genome is destabilized in callus culture but attenuation of variation occurs on regeneration. Diploid cell lines are maintained in callus subcultures and supplementation of regenerative media with high cytokinin concentrations, casein hydrolysate or adenine failed to produce variants. Callus aging however resulted in the production of polyploids. The presence and expression of pre-existing somatic variation in B. rex pith and root tissue is assessed and polyploids have been produced from pith tissues cultured in vitro. The stability of the B. rex genome and the application of tissue culture to micropropagation and breeding of B. rex are discussed.

The life history and ecology of black scabbardfish (Aphanopus carbo Lowe 1839) in the north-east Atlantic

The black scabbardfish is a deep water species that supports commercial fisheries across a large area of the NE Atlantic shelf. The life history of black scabbardfish is poorly understood and a major unresolved issue is population structure. In this study it was used a combination of methodologies to get further knowledge in the life history and population structure of A. carbo over its wide distribution range in the Northeast Atlantic. The new knowledge acquired during this study, will increase our ability to better manage this species in the NE Atlantic. It has been postulated that fish caught to the west of the British Isles are pre-adults that migrate further south (to Madeira) for spawning, implying a single panmictic population. In this study, specimens of Aphanopus carbo were sampled between September 2008 and May 2010 from two different areas: NW Scotland (French trawlers and deep water surveys) and Madeira Islands (longliners commercial landings). Geographical differences in reproductive state of scabbardfish were evident, supportive of a north-south migration theory. In the northern area, all specimens found were immature, while in Madeira all maturity stages were observed. In Madeira, spawning occurred during the fourth quarter, with peak maturity in October (males) and in November (females). The age of this species has proven difficult and has led to different and contradictory age and growth estimates. For this study, we used two reading interpretations to determine age and estimate the growth parameters. To the west of the British Isles, specimens reached a lower maximum age and had a higher growth rate than those caught off Madeira. These differences are consistent with the theory of a single population of black scabbardfish in the NE Atlantic, highly segregate, with smaller, immature and younger fish caught to the west of the British Isles and bigger and mature caught in Madeira Islands. The feeding ecology showed strong evidence that the diet of black scabbardfish is associated with the spawning migration of blue whiting, which may support a northerly feeding migration theory for black scabbardfish. The stable isotope analyses in the muscle of black scabbardfish identified that black scabbardfish feeds on species with epipelagic and benthopelagic affinities. Comparison with stable isotope analysis in Madeira samples indicated that black scabbardfish feed at a similar trophic level and has the same trophic niche width in both areas, assuming similar baseline isotope compositions. Otolith stable isotopes (oxygen - δ18O and nitrogen - δ15N) analyses were used as a tool to clarify migratory behaviour. Otolith isotope ratios can provide insight into whether adults caught around Madeira fed in an isotopically depleted northerly ecosystem (NW Scotland) during their pre-adult period and then migrate towards south to spawn. Overall, the results support a south-north migration of pre adult fish from spawning areas around Madeira and a north-south migration from the west of Scotland to the spawning areas. Given its life cycle there is an urgent need that the management process recognizes the existence of a continuous widely distributed stock of black scabbardfish between the west of the British Isles and Madeira. The results highlight large scale dispersal in this species which needs to be treated as a highly migratory species and be managed as a single population.

Expression and function of the neurotrophic factors GDF5 and GDNF in the nigrostriatal system during development and in rat models of Parkinson's disease

Growth/differentiation factor 5 (GDF5) and glial cell line-derived neurotrophic factor (GDNF) are neurotrophic factors that promote the survival of midbrain dopaminergic neurons in vitro and in vivo. Both factors have potent neurotrophic and neuroprotective effects in rat models of Parkinson's disease (PD), and may represent promising new therapies for PD. The aim of the present study was to investigate the endogenous expression and function of GDF5 and GDNF in the nigrostriatal dopaminergic system during development and in rat models of PD. Examination of the temporal expression patterns of endogenous GDF5, GDNF, and their respective receptors, in the developing and adult nigrostriatal dopaminergic system suggest that these factors play important roles in promoting the survival and maturation of midbrain dopaminergic neurons during the period of postnatal programmed cell death. The relative levels of GDF5 and GDNF mRNAs in the midbrain and striatum, and their individual temporal expression patterns during development, suggest that their modes of actions are quite distinct in vivo. Furthermore, the sustained expression of GDF5, GDNF, and their receptors into adulthood suggest roles for these factors in the continued support and maintenance of mature nigrostriatal dopaminergic neurons. The present study found that endogenous GDF5, GDNF, and their receptors are differentially expressed in two 6-hydroxydopamine-induced lesion adult rat models of PD. In both terminal and axonal lesion models of PD, GDF5 mRNA levels in the striatum increased at 10 days post-lesion, while GDNF mRNA levels in the nigrostriatal system decreased at 10 and 28 days post-lesion. Thus, despite the fact that exogenous GDF5 and GDNF have similar effects on midbrain dopaminergic neurons in vitro and in vivo, their endogenous responses to a neurotoxic injury are quite distinct. These results highlight the importance of studying the temporal dynamic changes in neurotrophic factor expression during development and in animal models of PD.

Electrical machine characterisation and analysis for renewable energy applications

There has been an increased use of the Doubly-Fed Induction Machine (DFIM) in ac drive applications in recent times, particularly in the field of renewable energy systems and other high power variable-speed drives. The DFIM is widely regarded as the optimal generation system for both onshore and offshore wind turbines and has also been considered in wave power applications. Wind power generation is the most mature renewable technology. However, wave energy has attracted a large interest recently as the potential for power extraction is very significant. Various wave energy converter (WEC) technologies currently exist with the oscillating water column (OWC) type converter being one of the most advanced. There are fundemental differences in the power profile of the pneumatic power supplied by the OWC WEC and that of a wind turbine and this causes significant challenges in the selection and rating of electrical generators for the OWC devises. The thesis initially aims to provide an accurate per-phase equivalent circuit model of the DFIM by investigating various characterisation testing procedures. Novel testing methodologies based on the series-coupling tests is employed and is found to provide a more accurate representation of the DFIM than the standard IEEE testing methods because the series-coupling tests provide a direct method of determining the equivalent-circuit resistances and inductances of the machine. A second novel method known as the extended short-circuit test is also presented and investigated as an alternative characterisation method. Experimental results on a 1.1 kW DFIM and a 30 kW DFIM utilising the various characterisation procedures are presented in the thesis. The various test methods are analysed and validated through comparison of model predictions and torque-versus-speed curves for each induction machine. Sensitivity analysis is also used as a means of quantifying the effect of experimental error on the results taken from each of the testing procedures and is used to determine the suitability of the test procedures for characterising each of the devices. The series-coupling differential test is demonstrated to be the optimum test. The research then focuses on the OWC WEC and the modelling of this device. A software model is implemented based on data obtained from a scaled prototype device situated at the Irish test site. Test data from the electrical system of the device is analysed and this data is used to develop a performance curve for the air turbine utilised in the WEC. This performance curve was applied in a software model to represent the turbine in the electro-mechanical system and the software results are validated by the measured electrical output data from the prototype test device. Finally, once both the DFIM and OWC WEC power take-off system have been modeled succesfully, an investigation of the application of the DFIM to the OWC WEC model is carried out to determine the electrical machine rating required for the pulsating power derived from OWC WEC device. Thermal analysis of a 30 kW induction machine is carried out using a first-order thermal model. The simulations quantify the limits of operation of the machine and enable thedevelopment of rating requirements for the electrical generation system of the OWC WEC. The thesis can be considered to have three sections. The first section of the thesis contains Chapters 2 and 3 and focuses on the accurate characterisation of the doubly-fed induction machine using various testing procedures. The second section, containing Chapter 4, concentrates on the modelling of the OWC WEC power-takeoff with particular focus on the Wells turbine. Validation of this model is carried out through comparision of simulations and experimental measurements. The third section of the thesis utilises the OWC WEC model from Chapter 4 with a 30 kW induction machine model to determine the optimum device rating for the specified machine. Simulations are carried out to perform thermal analysis of the machine to give a general insight into electrical machine rating for an OWC WEC device.

Interaction of additive and quantization noises in digital PLLs

Phase-locked loops (PLLs) are a crucial component in modern communications systems. Comprising of a phase-detector, linear filter, and controllable oscillator, they are widely used in radio receivers to retrieve the information content from remote signals. As such, they are capable of signal demodulation, phase and carrier recovery, frequency synthesis, and clock synchronization. Continuous-time PLLs are a mature area of study, and have been covered in the literature since the early classical work by Viterbi [1] in the 1950s. With the rise of computing in recent decades, discrete-time digital PLLs (DPLLs) are a more recent discipline; most of the literature published dates from the 1990s onwards. Gardner [2] is a pioneer in this area. It is our aim in this work to address the difficulties encountered by Gardner [3] in his investigation of the DPLL output phase-jitter where additive noise to the input signal is combined with frequency quantization in the local oscillator. The model we use in our novel analysis of the system is also applicable to another of the cases looked at by Gardner, that is the DPLL with a delay element integrated in the loop. This gives us the opportunity to look at this system in more detail, our analysis providing some unique insights into the variance `dip' seen by Gardner in [3]. We initially provide background on the probability theory and stochastic processes. These branches of mathematics are the basis for the study of noisy analogue and digital PLLs. We give an overview of the classical analogue PLL theory as well as the background on both the digital PLL and circle map, referencing the model proposed by Teplinsky et al. [4, 5]. For our novel work, the case of the combined frequency quantization and noisy input from [3] is investigated first numerically, and then analytically as a Markov chain via its Chapman-Kolmogorov equation. The resulting delay equation for the steady-state jitter distribution is treated using two separate asymptotic analyses to obtain approximate solutions. It is shown how the variance obtained in each case matches well to the numerical results. Other properties of the output jitter, such as the mean, are also investigated. In this way, we arrive at a more complete understanding of the interaction between quantization and input noise in the first order DPLL than is possible using simulation alone. We also do an asymptotic analysis of a particular case of the noisy first-order DPLL with delay, previously investigated by Gardner [3]. We show a unique feature of the simulation results, namely the variance `dip' seen for certain levels of input noise, is explained by this analysis. Finally, we look at the second-order DPLL with additive noise, using numerical simulations to see the effects of low levels of noise on the limit cycles. We show how these effects are similar to those seen in the noise-free loop with non-zero initial conditions.

The political philosophy of Miki Kiyoshi: A close reading of the philosophical foundations of cooperative communitarianism

The thesis is a historical and philological study of the mature political theory of Miki Kiyoshi (1897-1945) focused on Philosophical Foundations of Cooperative Communitarianism (1939), a full translation of which is included. As the name suggests, it was a methodological and normative communitarianism, which critically built on liberalism, Marxism and Confucianism to realise a regional political community. Some of Miki’s Western readers have wrongly considered him a fascist ideologue, while he has been considered a humanist Marxist in Japan. A closer reading cannot support either view. The thesis argues that the Anglophone study of Japanese philosophy is a degenerating research programme ripe for revolution in the sense of returning full circle to an original point. That means returning to the texts, reading them contextually and philologically, in principle as early modern European political theory is read by intellectual historians, such as the representatives of Cambridge School history of political thought. The resulting reading builds critically on the Japanese scholarship and relates it to contemporary Western and postcolonial political theory and the East Asian tradition, particularly neo-Confucianism. The thesis argues for a Cambridge School perspective radicalised by the critical addendum of geo-cultural context, supplemented by Geertzian intercultural hermeneutics and a Saidian ‘return to philology’. As against those who have seen radical reorientations in Miki’s political thought, the thesis finds gradual progression and continuity between his neo-Kantian, existentialist, Marxian anthropology, Hegelian and finally communitarian phases. The theoretical underpinnings are his philosophical anthropology, a structurationist social theory of praxis, and a critique of liberalism, Marxism, nationalism and idealism emphasising concrete as opposed to abstract theory and the need to build on existing cultural traditions to modernise rather than westernise East Asia. This post-Western fusion was imagined to be the beginning of a true and pluralistic universalism.

Merleau-Ponty and Nishida: Artistic expression as 'motor-perceptual faith'

This dissertation carries out a dialogue between Maurice Merleau-Ponty and Nishida Kitarō concerning their theories of artistic expression and faith. Both philosophers go through remarkably similar trajectories in their philosophic projects: In their early works they focus on the motor-perceptual body of the artist, and as they move towards the mature articulation of their ontologies, the concept of faith becomes central. I propose the term “motor-perceptual faith” to bring these seemingly diverse sets of concerns into a conceptual continuity. My study explores this connection, and argues that the artist’s motor-perceptual expressive body, as colourfully and sometimes poetically articulated in their early works, enacts the form of faith developed more abstractly in their later writings. Exploring these relations fosters a mutual expansion of the early by the later works, thus thickening the concept of faith by seeing it as enacted by the artist, while enlarging the concept of artistic expression by understanding it as a practice of motor‐perceptual faith. Framing these philosophers as putting forth a traditionally religious concept as illustrated by way of artistic expression, offers a new articulation of both of their writings, an important conceptual bridge between the two, while challenging un-ambiguous distinctions between art, philosophy and religion, and ultimately philosophy East and West.

The impact of whey protein isolate on energy balance regulation

Using C57BL/6J mice fed whey protein isolate (WPI) enriched high fat (HFD) or low-fat diets (LFD), this study tested the hypothesis that WPI directly impacts on adiposity by influencing lipid metabolism. WPI suppressed HFD-induced body fat and increased lean mass at 8 weeks of dietary challenge despite elevated plasma triacylglycerol (TAG) levels, suggesting reduced TAG storage. WPI reduced HFD-associated hypothalamic leptin and insulin receptor (IR) mRNA expression, and prevented HFD-associated reductions in adipose tissue IR and glucose transporter 4 expression. These effects were largely absent at 21 weeks of HFD feeding, however WPI increased lean mass and cause a trend towards decreased fat mass, with notable increased Lactobacillus and decreased Clostridium gut bacterial species. Increasing the protein to carbohydrate ratio enhanced the above effects, and shifted the gut microbiota composition away from the HFD group. Seven weeks of WPI intake with a LFD decreased insulin signalling gene expression in the adipose tissue in association with an increased fat accumulation. WPI reduced intestinal weight and length, suggesting a potential functional relationship between WPI, gastro-intestinal morphology and insulin related signalling in the adipose. Extending the study to 15 weeks, did not affect adipose fat weight, but decreased energy intake, weight gain and intestinal length. The functionality of protein sensing lysophosphatidic acid receptor 5 (LPA5) in 3T3-L1 pre-adipocytes was assessed. Over-expression of the receptor in 3T3-L1 pre-adipocytes provided a growth advantage to the cells and suppressed cellular differentiation into mature fat cells. In conclusion, the data demonstrates WPI impacts on adiposity by influencing lipid metabolism in a temporal manner, resulting possibly due to changes in lean mass, hypothalamic and adipose gene expression, gut microbiota and gastrointestinal morphology. The data also showed LPA5 is a novel candidate in regulating of preadipocyte growth and differentiation, and may mediate dietary protein effects on adipose tissue.