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This study was prompted by a natural inquisitiveness about the concentration of timber buildings in both Braemar on Deeside and Fochabers on Speyside, and the assumed association with the history of timber extraction in the respective river systems. Reinforced by childhood memories of timber buildings in other locations, the idea turned into an ironic quest for a Lost Tradition of Timber buildings in North East Scotland. The fieldwork provides both substantive and extensive material with 198 records of extant buildings, and archival research having produced evidence of 156 others. However, in a field characterised by transience and lack of documentation, this total cannot be considered definitive. Whilst the study presents a significant body of information about a Victorian interest in timber frame building not previously identified in the literature, the lack of any previous research in this area means that the work represents a phenomenon which is isolated both historically and culturally. The study adopts a taxonomic methodology and a selection of case studies offers a comparative analysis in which frame typologies and their characteristics are examined. The geographical area is illustrated in map 1 fieldwork buildings distribution map. This is structured on 10km transects and individual buildings identified numerically in a north to south sequence within these transects. Fieldwork specimens represent a diversity of both buildings and frame types, and the extensive use of timber buildings by the railway companies demonstrates they merely exploited an already established capability and knowledge for timber building and were not responsible for its introduction into the geographical area of study. It is clear that the majority of the fieldwork examples are of building types that would have been `modern' to the late 19th century with only dwellings, church buildings and mills having historic precedence. This aspect introduces the enigma of the antecedents of their construction methods, particularly in view of the parsimony of the contemporaneous literature. A total of four differing frame types have been identified and a previously unrecorded post and rail system is represented across all building types. This frame is described and illustrated in Chapter 3, Construction Types, and features in a comparative drawing of known historical frame designs not previously published. The identification of this frame and its extensive use is considered one of the main contributions of the study. The taxonomy is presented in terms of discrete building types as uncovered by the field study. This has revealed a considerable number of dwellings constructed by tradesmen for their own family's use, a structural elegance represented across the building types and an unexpected lack of agricultural buildings In an attempt to reduce the historical and cultural isolation of the survey data, the data is examined in a broader context, the availability and suitability of materials, the availability of knowledge and skills and prevailing socio-economic and cultural attitudes.

Genomic strategies for diagnosis and management of congenital and childhood hearing loss. Leslie Patricia Molina Ramirez, The University of Manchester, Doctor of Philosophy, 2021. Hearing loss is the most common sensory disorder in children. Over 50% of these cases are genetic, and more than 100 genes have been associated with inheritance and different patterns of hearing loss. Identifying the underlying aetiology of hearing loss is paramount in the diagnosis and management of hearing loss, but the vast clinical and genetic heterogeneity poses a diagnostic challenge. This is problematic because if left untreated, hearing loss can have negative impact on quality of life, language, and social development. Genomic sequencing strategies have demonstrated clinical utility in many genetic conditions with similar diagnostic challenges. In this thesis, approaches were taken to study the diagnostic performance of genomic strategies currently used in the clinic, understand how genomic strategies perform when used with patients with hearing loss, and how integrated genomic and clinical data can reveal insights to inform personalised patient care. Clinical exome sequencing (CES) analysis data and molecular results from 400 patients with rare disorders were analysed. CES results from a subset of 60 patients with ear abnormalities and hearing loss disorders were further studied. To obtain insights into the integrated use of clinical and genomic data, a phenotype-genotype correlation was conducted in patients with USH2A-related disease. Findings from this correlation were further validated using two external datasets. In addition, a review article highlights potential of genomic strategies in current management of patients with hearing loss and the potential benefit of obtaining a molecular diagnosis through genomic sequencing for cochlear implant candidates and recipients. CES in rare disease patients was reported with an overall 24% diagnostic rate. Nervous system, head and neck, skeletal, ear and eye abnormalities were the most commonly reported clinical features in the patient cohort referred for CES. The use of different methods of phenotype-driven gene selection approaches for virtual panels clearly demonstrated a reduction of variant workload without compromising diagnostic rate. Sixty patients with ear disorders and hearing impairment underwent CES. Here, CES was reported with a diagnostic rate of 31%. CES results informed further diagnostic steps in 25% of patients with hearing impairment. The phenotype-genotype correlation in patients with USH2A-related disease identified the presence of specific alleles in patients with retinitis pigmentosa and unaffected hearing or late-onset, mild hearing loss. Furthermore, patients with congenital-onset and moderate-to-severe hearing loss were found to harbour protein truncating variants in their genotypes. Audiological surveillance could then be personalised based on the phenotype anticipated by the molecular diagnosis. In conclusion, this study has demonstrated that clinical genomic sequencing can be a comprehensive and powerful tool in the investigation of genetic congenital and childhood-onset hearing loss. Integrated genomic and clinical data can enable precision medicine approaches in children with genetic hearing loss. This work adds to the increasing body of evidence that supports the use of genetic diagnosis as a potential prognostic factor to inform patient care and hearing habilitation and rehabilitation strategies.

Background: Gastric cancer is a leading cause of cancer-related deaths worldwide. Whilst surgery is the mainstay of curative treatment, it is associated with significant risks. Identifying optimal surgical strategies for gastric cancer should be based on evidence from well-designed trials. However, inconsistencies in the reporting of outcomes from these trials makes evidence synthesis unreliable. This PhD study aims to address these challenges by developing a core outcome set (COS) - a standardised group of important outcomes - which should be reported as a minimum by future trials in this field. Methods: The COS was developed over two stages employing methodological principles based on established guidelines from the field of COS development. Stage 1 involved identifying potentially important outcomes from previous trials and a series of patient interviews. In stage 2, potentially important outcomes were prioritised using a Delphi survey which informed a consensus meeting at which the COS was finalised. Results: 498 outcomes were identified from previously reported trials (n=454) and patient interviews (n=70) and rationalised into 56 items presented in the Delphi survey. International stakeholder participation was facilitated through the establishment of collaborative networks and translation of the surveys using an approach adapted from international guidelines. 952 patients (n=268), surgeons (n=445) and nurses (n=239) from 6 continents enrolled into round 1 of the survey and 662 completed round 2. Demographic and regional differences did not impact on how participants prioritised outcomes in the survey. Following the consensus meeting, 8 outcomes were included in the COS - disease-free survival, disease-specific survival, surgery-related death, recurrence, completeness of tumour removal, overall quality of life, nutritional effects, and complications. Conclusion: A COS for surgical trials in gastric cancer has been developed with international patients and healthcare professionals. This PhD study has also described key methodological considerations for COS development.

The mucopolysaccharidoses are a family of seven rare inherited metabolic disorders caused by specific lysosomal enzyme deficiencies responsible for catabolism of glycosaminoglycan (GAG) substrates. Subsequent accumulation of partially degraded GAGs leads to cellular dysfunction and progressive multisystem disease, presenting with visceral, cardiorespiratory, musculoskeletal and neurocognitive manifestations. The severe form of MPS I, Hurler syndrome, may be successfully treated with haematopoietic stem cell transplant (HSCT), while attenuated forms of MPS I and MPS II, IVA and VI are currently managed with enzyme replacement therapy. Progressive, multilevel airway and respiratory involvement is a well-recognised feature of a number of types of MPS and contributes to the premature morbidity and mortality seen in this disease. The literature regarding this aspect of disease is limited and current knowledge is informed by descriptive studies of small cohorts. The association between outcomes, metabolic and aetiological factors have not been adequately investigated. Following formal systematic review methodology, we have quantitatively assessed the current literature on obstructive sleep apnoea (OSA) in MPS. The prevalence of OSA in MPS prior to treatment is 81%, with MPS I most severely affected. Subsequent assessment of a cohort of 61 MPS I patients, has demonstrated excellent long-term outcomes following HSCT, while identifying causal associations between clinical disease regression, measured by urinary substrate biomarkers, and an improvement in airway obstruction. Multivariate analysis has confirmed that early initiation of treatment and optimal donor selection in HSCT contributes to improved outcomes. Using assays to detect and quantify the function of inhibitory antibodies against ERT, we have identified a cohort of patients with impaired metabolic correction and severe airway obstruction. Finally, analysis of adenotonsillar samples donated by patients and examination of the respiratory tract in a murine model of MPS I allowed us to investigate aetiological factors contributing to airway pathology. Adenotonsillar tissue displayed evidence of alteration in extracellular matrix protein deposition, suggesting remodelling of tissue contributes to the obstructive phenotype observed in patients. We further demonstrated an absence of inflammation in both patient tissue samples and within the lower respiratory tract in mice. Overall, we have ascertained factors which may improve clinical outcomes in the management of airway disease and identified aetiological components contributing to the cascade of events leading to obstructive airway pathology in MPS.

This thesis investigates the suitability of an octapeptide hydrogel scaffold for use in the tissue engineering of cartilage. The work has focused on two main areas; the biocompatibility of the hydrogel scaffold and the ability of the scaffold to sustain chondrocyte morphology and function. Firstly, this thesis presents a protocol for testing the biocompatibility of the FEFEFKFK hydrogel scaffold using an enzyme linked immunosorbent assay. This protocol could subsequently be used as part of the biocompatibility testing of other hydrogel scaffolds prior to in vivo use. The inflammatory potential of the hydrogel was established by encapsulating monocytes which are known to produce inflammatory mediators, within the hydrogel. The production of cytokines TNFα, IL-6 and IL-1β in response to the hydrogel was quantified using an enzyme linked immunosorbent assays. The hydrogel scaffolds tested did not insight a significant pro inflammatory response from the monocytes in any of the studies. The FEFEFKFK hydrogel was encapsulated with bovine and human chondrocytes to investigate the morphology, viability and function of chondrocytes within the hydrogel scaffold. Chondrocyte morphology and viability was assessed using a combination of optical microscopy, cell staining and confocal microscopy. It was found that both bovine and human chondrocytes were viable and maintained a normal morphology within the FEFEFKFK hydrogel up to 35 and 28 days duration respectively. However, aggregation was seen in the bovine samples after 21 days and peripheral cell death in the human samples due the degradation of the hydrogel. Chondrocyte function was evaluated by measuring the production of glycosaminoglycans from the bovine and human chondrocytes encapsulated in the hydrogel over 28 days. The production of glycosaminoglycans increased from day 7 to day 28 in the bovine chondrocyte samples and from day 7 to 21 in the human chondrocyte samples. In addition, the rheology of the hydrogel was quantified with and without chondrocytes to investigate the stiffness and degradation of the scaffold. The rheology revealed that the hydrogels were stiffer when encapsulated with chondrocytes. There was in increase in stiffness in all samples from 0-7 days. However, following this there was a gradual degradation of the hydrogel reflected by a decline in the stiffness. This thesis demonstrates that the FEFEFKFK octapeptide hydrogel supports chondrocyte viability with maintenance of normal cell morphology and function. There is no evidence of the hydrogel inciting an inflammatory response and as such it demonstrates potential for future use in vivo for cartilage engineering. The hydrogel shows degradation over time which affects the chondrocytes encapsulated within it and therefore further work needs to be carried out to improve the longevity of the hydrogel until sufficient extracellular matrix is produced to support the chondrocytes in 3 dimensions.