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Parkinson’s disease (PD) is the most common neurodegenerative movement disorder, currently affecting 6.3 million people worldwide. Although it is associated, in the longterm, with severe complications (dyskinesias), L-DOPA remains the gold standardtreatment. An alternative approach to the treatment of PD is the replacement of the lost striatal dopaminergic innervation by transplantation of foetal ventral mesencephalon (VM) dopaminergic precursor cells. Opened trials have provided the proof of concept that intrastriatal VM transplant can survive, integrate and in some cases, restore motor functions. Nevertheless, later double blind studies reported inconsistent benefit of the therapy and the development of dyskinesias remaining after withdrawal of L-DOPA medication. The failure of the animal models in predicting these problems raises concern about their reliability. Therefore, the global aim of this PhD work was to identify some of the critical factors that can influence the functional outcome of cell therapy for PD, and on the basis of this, to develop an improved 6-OHDA unilaterally lesioned rat model for transplantation. The first step was to determine the most reliable method to assess dyskinesias in rats. The second part of this thesis was set out to determine the effect that chronic L-DOPA treatment, administered at different time could had on the survival and function of immunologically incompatible foetal VM transplant. The results demonstrated that L-DOPA administered chronically post-grafting increases the host immune response around the xenogeneic transplant. Therefore, the last set of experiments were designed to create a model of mixed donors graft to better reproduce the patient situation, where each transplant required up to 8 donors from unknown immunological background. All of these experiments come together to help to develop a rat model that more accurately represents all aspects of patients undergoing transplantation for PD.

Duplication of the proteolipid protein (PLP1) gene, which encodes the most abundant protein of central nervous system (CNS) myelin, is the most common cause of Pelizaeus Merzbacher disease (PMD). Various animal models have been generated to study the effect of Plp1 gene overexpression on oligodendrocyte and myelin sheath integrity. The #72 line harbours 3 additional copies of the murine Plp1 gene per haploidic chromosomal set. Homozygous #72 mice appear phenotypically normal until three months of age, after which they develop seizures leading to premature death at around 4 months of age. An earlier study examining the optic nerve showed a progressive demyelination accompanied by marked microglial and astrocytic responses. Using electron microscopy and immunohistochemistry, I demonstrated that initial myelination of the #72 corpus callosum was followed by a progressive demyelination, probably mediated by a distal “dying back” phenomenon of the myelin sheath. No evidence of effective remyelination was observed despite the presence and proliferation of oligodendrocyte progenitor cells (OPCs). A marked increase in density and reactivity of microglia/macrophages and astrocytes, and the occurrence of axonal swellings, accompanied the demyelination. In situ and in vitro evaluation of adult #72 OPCs provided evidence of impaired OPC differentiation. Transplantation of neurospheres (NS) into adult #72 mouse corpus callosum confirmed that axons were capable of undergoing remyelination. Furthermore, NS transplanted into neonatal CNS integrated into the parenchyma and survived up to 120 days, demonstrating the potential of early cell replacement therapy. Taking advantage of the spatially distinct pathologies between the retinal and chiasmal region of the #72 optic nerve, I evaluated the capability of diffusion weighted MRI to identify lesion type. I found significant differences between #72 and wild type optic nerves, as well as between the two distinct pathological regions within the #72 optic nerve. These results confirm the potential of the #72 mouse to serve as a model to study chronic demyelination. The study also demonstrates the utility of the #72 mouse to evaluate cell transplant strategies for the treatment of chronic CNS white matter lesions and PMD. Additionally, DW MRI has potential as a modality capable of diagnosing myelin-related white matter changes, and may be applicable to the clinical setting.

In Chapter 1, I introduce ischaemic stroke, thrombolytic therapy, thrombolysis trials and then discuss the rationale for exclusion criteria in stroke thrombolysis guidelines.In Chapter 2, I describe methods for examining outcomes in patients that are currently recommended for exclusions from receiving alteplase for acute ischaemic stroke. In Chapter 3, I examine Virtual International Stroke Trials Archive (VISTA) data to test whether current European recommendation suggesting exclusion of elderly patients (older than 80 years) from thrombolysis for acute ischaemic stroke is justified. Employing non-randomised controlled comparison of outcomes, I show better outcomes amongst all patients (P < 0.0001; OR, 1.39; 95% CI, 1.26 to 1.54), young patients (P < 0.0001; OR, 1.42; 95% CI, 1.26 to 1.59) and the elderly patients (P = 0.002; OR, 1.34; 95% CI, 1.05 to 1.70). Odds Ratios are consistent across all age deciles > 30 years. Outcomes assessed by National Institutes of Health Scale (NIHSS) score and dichotomised modified Rankin Scale score are consistently similar. In Chapter 4, I compare thrombolysed patients in Safe Implementation of Thrombolysis in Stroke International Stroke Thrombolysis Register (SITS-ISTR) with VISTA non-thrombolysed patients ("comparators" or "controls") and test exactly similar question as in Chapter 3. Distribution of scores on modified Rankin scale are better amongst all thrombolysis patients than controls (odds ratio 1.6, 95% confidence interval 1.5 to 1.7; Cochran-Mantel-Haenszel P<0.001). Association occurs independently amongst patients aged ≤80 (0R 1.6, 95%CI1.5 to 1.7; P<0.001; n=25,789) and in those aged >80 (OR 1.4, 95% CI 1.3 to 1.6; P<0.001; n=3439). Odds ratios are consistent across all 10 year age ranges above 30, and benefit is significant from age 41 to 90; dichotomised outcomes (score on modified Rankin scale 0-1 v 2-6; 0-2 v 3-6; and 6 (death) versus rest) are consistent with the results of ordinal analysis. These findings are consistent with results from VISTA reported in Chapter 3. Age alone should not be a criterion for excluding patients from receiving thrombolytic therapy.In Chapter 5, I employ VISTA data to examine whether patients having diabetes and previous stroke have improved outcomes from use of alteplase in acute ischaemic stroke. Employing a non-randomised controlled comparison, I show that the functional outcomes are better for thrombolysed patients versus nonthrombolysed comparators amongst non-diabetic (P < 0.0001; OR 1.4 [95% CI 1.3-1.6]) and diabetic (P = 0.1; OR 1.3 [95% CI1.05-1.6]) patients. Similarly, outcomes are better for thrombolysed versus nonthrombolysed patients who have not had a prior stroke (P < 0.0001; OR 1.4 [95% CI1.2-1.6]) and those who have (P = 0.02; OR 1.3 [95% CI1.04-1.6]). There is no interaction of diabetes and prior stroke with treatment (P = 0.8). Neurological outcomes (NIHSS) are consistent with functional outcomes (mRS). In Chapter 6, I undertake a non-randomised controlled comparison of SITS-ISTR data with VISTA controls and examine whether patients having diabetes and previous stroke have improved outcomes from use of alteplase in acute ischaemic stroke. I show that adjusted mRS outcomes are better for thrombolysed versus non-thrombolysed comparators amongst patients with diabetes mellitus (OR 1.45[95% CI1.30-1.62], N=5354), previous stroke (OR 1.55[95% CI1.40-1.72], N=4986), or concomitant diabetes mellitus and previous stroke (OR 1.23 [95% CI 0.996-1.52], P=0.05, N=1136), all CMH p<0.0001. These are comparable to outcomes between thrombolysed and non-thrombolysed comparators amongst patients suffering neither diabetes mellitus nor previous stroke: OR=1.53(95%CI 1.42-1.63), p<0.0001, N=19339. There are no interaction between diabetes mellitus and previous stroke with alteplase treatment (t-PA*DM*PS, p=0.5). Present data supports results obtained from the analyses of VISTA data in chapter 5. There is no statistical evidence to recommend exclusion of patients with diabetes and previous stroke from receiving alteplase.In Chapter 7, I examine VISTA data to test whether exclusion of patients having a mild or severe stroke at baseline would be justified. Stratifying baseline stroke severity for quintiles of NIHSS scores, I observe that there are significant associations of use of alteplase with improved outcomes for baseline NIHSS levels from 5 to 24 (p<0.05). This association lose significance for baseline NIHSS categories 1 to 4 (P = 0.8; OR, 1.1; 95% CI, 0.3-4.4; N = 8/161) or ≥ 25 (P = 0.08; OR, 1.1; 95% CI, 0.7-1.9; N = 64/179) when sample sizes are small and confidence interval wide. These findings fail to provide robust evidence to support the use of alteplase in the mild or severe stroke patients, though potential for benefit appears likely.In Chapter 8, I present a meta-analysis of trials that investigated mismatch criteria for patients’ selection to examine whether present evidence supports delayed thrombolysis amongst patients selected according to mismatch criteria. I collate outcome data for patients who were enrolled after 3 hours of stroke onset in thrombolysis trials and had mismatch on pre-treatment imaging. I compare favourable outcome, reperfusion and/or recanalisation, mortality, and symptomatic intracerebral haemorrhage between the thrombolysed and non-thrombolysed groups of patients and the probability of a favourable outcome among patients with successful reperfusion and clinical findings for 3 to 6 versus 6 to 9 hours from post stroke onset. I identify articles describing the DIAS, DIAS II, DEDAS, DEFUSE, and EPITHET trials, giving a total of 502 mismatch patients thrombolysed beyond 3 hours. The combined adjusted odds ratios (a-ORs) for favourable outcomes are greater for patients who had successful reperfusion (a-OR=5.2; 95% CI, 3 to 9; I2=0%). Favourable clinical outcomes are not significantly improved by thrombolysis (a-OR=1.3; 95% CI, 0.8 to 2.0; I2=20.9%). Odds for reperfusion/recanalisation are increased amongst patients who received thrombolytic therapy (a-OR=3.0; 95% CI, 1.6 to 5.8; I2=25.7%). The combined data show a significant increase in mortality after thrombolysis (a-OR=2.4; 95% CI, 1.2 to 4.9; I2=0%), but this is not confirmed when I exclude data from desmoteplase doses that are abandoned in clinical development (a-OR=1.6; 95% CI, 0.7 to 3.7; I2=0%). Symptomatic intracerebral haemorrhage is significantly increased after thrombolysis (a-OR=6.5; 95% CI, 1.2 to 35.4; I2=0%) but not significant after exclusion of abandoned doses of desmoteplase (a-OR=5.4; 95% CI, 0.9 to 31.8; I2=0%). Delayed thrombolysis amongst patients selected according to mismatch imaging is associated with increased reperfusion/recanalisation. Recanalisation/reperfusion is associated with improved outcomes. However, delayed thrombolysis in mismatch patients was not confirmed to improve clinical outcome, although a useful clinical benefit remains possible. Thrombolysis carries a significant risk of symptomatic intracerebral haemorrhage and possibly increased mortality. Criteria to diagnose mismatch are still evolving. Validation of the mismatch selection paradigm is required with a phase III trial. Pending these results, delayed treatment, even according to mismatch selection, cannot be recommended as part of routine care.In Chapter 9, I summarise the findings of my research, discuss its impact on the research community, and discuss weaknesses inherent in registry data and limitation of statistical methods. Then, I elaborate the future directions I may take to further research on the theme of this thesis.

The prime topic of research presented in this report is the development and validation of methodologies for the solution of the forward problem in Magnetic field Tomography based on Magnetoencephalography. Throughout the report full aspects of the accurate solution are discussed, including the development of algorithms and methods for realistic brain model, development of realistic neuronal source, computational approaches, and validation techniques. Every delivered methodology is tested and analyzed in terms of mathematical and computational errors. Optimizations required for error minimization are performed and discussed. Presented techniques are successfully integrated together for different test problems. Results were compared to experimental data where possible for the most of calculated cases. Designed human brain model reconstruction algorithms and techniques, which are based on MRI (Magnetic Resonance Imaging) modality, are proved to be the most accurate among existing in terms of geometrical and material properties. Error estimations and algorithm structure delivers the resolution of the model to be the same as practical imaging resolution of the MRI equipment (for presented case was less than 1mm). Novel neuronal source modelling approach was also presented with partial experimental validation showing improved results in comparison to all existing methods. At the same time developed mathematical basis for practical realization of discussed approach allows computer simulations of any known neuronal formation. Also it is the most suitable method for Finite Element Method (FEM) which was proved to be the best computer solver for complex bio-electrical problems. The mathematical structure for Inverse problem solution which is based on integrated human brain modelling technique and neuronal source modelling approach is delivered and briefly discussed. In the concluding part of the report the practical application case of developed techniques is performed and discussed.

Cerebrovascular disease, has an enormous, and increasing, impact on global health. As well as causing clinical stroke, cerebrovascular disease is thought to be a major contributor to cognitive decline and dementia. Socioeconomic status (SES) is associated with risk of stroke. Those in the lowest SES group are estimated to be at twice the risk of stroke compared to those in the highest SES group. Those with low SES may also have a more severe stroke and a poorer outcome. It is imperative that the extent and mechanism of this association is clarified. This thesis aims to determine if the association between SES and stroke is explained by a greater prevalence of traditional vascular risk factors amongst those of low SES. It also explains the link with a novel risk factor, poor oral health. Lastly it addresses the long-term cognitive outcome in older people at risk of vascular disease. A systematic review and meta-analysis was undertaken to establish if vascular risk factors explain the association between SES and stroke incidence / post-stroke mortality. This demonstrated that lower SES was associated with an increased risk of stroke and that a greater burden of vascular risk factors in those with low SES explained about 50% of the additional risk of stroke. However this meta-analysis could not clarify what vascular risk factors are most critical. Low SES was also associated with increased mortality risk in those who have a stroke although study results were heterogeneous and this link was not readily explained by known vascular risk factors. A prospective study of 467 consecutive stroke and transient ischameic attack (TIA) patients from three Scottish hospitals was undertaken with the aim of establishing whether those with low SES carry higher levels of vascular risk factors, have a more severe stroke and have equal access to stroke care services and investigations. Stroke / TIA patients with low SES were younger and more likely to be current smokers but there was no association with other vascular risk factors /co-morbidity. Those who had lower SES had a more severe stroke. The lowest SES group were less likely to have neuroimaging or an electrocardiogram although differences were not significant on multivariate analysis. There was however equal access to stroke unit care. A secondary analysis of a prospective cohort study of 412 stroke patients was conducted. The aim was to explore oral health after acute stroke and assess if poor oral health explains the association between SES and stroke. Dry mouth amongst acute stroke patients was very common, however there was no association between oral health and low SES. There was an association of dry mouth with pre-stroke disability and Urinary Tract Infection. There was also a link with oral Candida glabrata colonisation, although the clinical relevance of this is uncertain. In the acute phase after stroke there was no convincing association of dry mouth with dysphagia or pneumonia. Therefore there was no association between SES and poor oral health as measured in this study but oral health may still be part of the explanation of the association between SES and acute stroke and this needs further investigation. Vascular disease is an important contributor to cognitive decline and dementia. Low SES may be associated with an increased risk of cognitive decline in later life and vascular disease may be a mediating factor. More effective prevention of vascular disease may slow cognitive decline and prevent dementia in later life, particularly in low SES groups. Lipid lowering with statins might be effective in preventing dementia but so far evidence from randomised control trials does not show benefit from statins in preventing cognitive decline and dementia. However the duration of follow-up in these trials was short and there may be benefit in the long-term. My aim was therefore to establish if long-term follow-up of the Prospective Study of Pravastatin in the Elderly at Risk (PROSPER) study was feasible. I found that it was feasible to follow-up 300 elderly survivors from the Scottish arm of the PROSPER study and the methods could be extended to the whole group. As expected nearly half of the PROSPER participants were dead. Additionally a large proportion of traceable participants had significant cognitive impairment. Smoking cessation, control of blood pressure and management of other vascular risk factors should be made a priority in areas of low SES. Additionally further research is needed to fully clarify the association between SES and stroke incidence. Avenues for exploration might include the possibilities of poorer access to effective stroke care, reduced uptake of care and poorer oral health in lower SES groups. In addition public health campaigns regarding smoking cessation should be directed at lower SES groups. I have shown that a large scale follow-up of the PROSPER participants is feasible and may determine new and novel risk factors for dementia and assess the long-term effect of a period of treatment with pravastatin.

Counterfactual reasoning, an understanding of events that are counter to reality, or false, is an essential ingredient of our everyday cognition. Counterfactual situations are frequently depicted through language, yet surprisingly little is known of how they are processed during reading or listening. This is remarkable given the social importance of understanding counterfactuals and the wealth of psychological research that has focused on the production of counterfactual statements. In this thesis, I present eight experiments that investigate how a counterfactual discourse can disrupt or facilitate processing of some subsequent linguistic input and address related comprehension issues involving negation and theory of mind. The main findings suggest that a counterfactual scenario (e.g. ‘If cats were vegetarians’) leads the comprehender to rapidly update their processing model to incorporate a counterfactual continuation. However, a secondary process briefly interferes at the point of ambiguity resolution in cases where world knowledge has been violated (e.g. ‘Families could feed their cat a bowl of fish/ carrots’). The effects are compared across the different experimental paradigms used, including eye- tracking, event- related brain potentials and the visual world paradigm, which reveal distinct integration, neural and anticipatory processes. Finally, these findings are discussed in relation to existing research on counterfactuals and the processing relationships between counterfactuals, negation and theory of mind reasoning.

Alzheimer's disease is the most common form (~60-80%) of dementia, currently affecting approximately half a million people in the UK and ~30 million people worldwide. The autosomal dominant form of AD represents a small proportion (~1-2%) of AD cases and is genetically well characterised. The vast majority of AD cases that show symptoms later in life (>65 years of age) are genetically complex. This type of AD, also known as late onset Alzheimer's disease (LOAD) disease, is still highly heritable with an estimated heritability of up to 76% (Gatz et al., 2006). Unfortunately, there is no cure for this devastating disease. Investigating genetic factors influencing the risk of LOAD is imperative for development of effective therapeutic treatments and more accurate diagnosis. A cross-platform comparison of four Genome-wide association studies (GWAS) was performed in an effort to identify novel genetic associations with LOAD (Chapter 3). A TRIM15 SNP rs929156 demonstrated significant evidence of association with LOAD with a p-value approaching genome-wide significance (p = 8.77 x 10-8) and an odds ratio that showed consistent effect on risk (OR = 1.1, p = 0.03). Within this chapter, a bio-informatic program to automate the process of GWAS meta-analysis taking into account linkage disequilibrium (LD) is also presented. Subsequently two fragments of the TRIM15 gene (including both 5’ and 3’ end flanking regions) were sequenced using the ABI SOLiDTM next generation sequencing technology. This was a pilot study using a DNA pooling strategy to determine whether this region harbours multiple rare variants which are associated with the disease (Chapter 4). Lastly, a candidate gene study combined with whole genome analysis was performed in an effort to search for genetic variants influencing human ageing using LOAD GWAS data (Chapter 5).

This thesis explores the role of a large-scale brain network comprising of the insula and anterior cingulate cortex in the pathophysiology of psychosis using structural and functional neuroimaging. Primarily, anatomical changes affecting the grey matter structure and patterns of dysconnectivity involving the insula are investigated. Various meta-analytic studies have reported consistent reduction in insular grey matter across various psychotic disorders. Despite these robust observations, the role played by this brain region in the generation of psychotic symptoms remains unexplored. In this thesis, using a meta-analytic approach, the relevance of insula for the clinical expression of psychosis is highlighted. Further, significant reduction in the cortical folding of the insula was noted in patients with schizophrenia. Reduced gyrification is accompanied by reduced functional connectivity between the insula and the rest of the brain. Using an effective connectivity approach (Granger Causal Analysis), the primacy of insula in driving the dorsolateral prefrontal cortex is demonstrated in healthy controls; this relationship is significantly affected in schizophrenia amounting to aberrant connectivity within a putative salience-execution loop. Reduced primacy of the salience-execution loop relates to illness severity. It is argued that the insula, as a key region of the salience network, plays a crucial role in the generation of symptoms of psychosis. The evidence in support of this theory is discussed, together with its implications for clinical practice aimed at reducing the burden of psychosis.

The aim of this research was to investigate the incorporation of a 'structured approach' to teaching children with autism, with precision teaching assessment methods. The rationale for the research focused on the limited evidence base regarding educational approaches for children with autism (Jones, 2002), and the growing need to provide appropriate educational provision for this group (Ali & Frederickson, 2006). One of the more widely used approaches in the UK is 'Treatment and Education of Autistic and related Communication handicapped Children' (TEACCH) (Tutt, Powell, & Thornton, 2006), with a derivative of this, called a 'structured approach', in place in the local context of the research. The use of fluency building approaches in education, such as precision teaching, has been proposed as potentially beneficial for children with autism due to their dysfluencies and difficulties generalising skills (Weiss, 2001), however there is limited research for this population. The 'structured approach' within the local context did not incorporate fluency building procedures, and therefore the research sought to investigate whether a precision teaching framework could augment a 'structured approach' for children with autism. A pragmatic, mixed methods approach was utilised in this research. It employed a series of three case studies, each incorporating multiple A-B single case experimental designs (SCED), in order to explore the impact of the precision teaching intervention on the pupils' learning, affect, and behaviour. A focus group provided additional information regarding the implementation of the precision teaching intervention. The SCED measures were analysed through graphical visual inspection and the focus group data was thematically analysed. The research found that precision teaching positively augmented a structured approach for the focus children, which was particularly apparent when it was implemented consistently. Improvements were identified in the pupils' learning, affect, and behaviour. The implications of this research are discussed and opportunities for further research highlighted.