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Electrochemical sensors have the capability to sensitively and reliably detect target molecules in complex media. Aptamers are single stranded nucleotide sequences capable of specifically and selectively bind a large variety of target molecules. The purpose of this project, comprising three main parts, was to establish an aptamer based electrochemical platform as a new analytical method for the real-time continuous monitoring of small molecules released in the brain. In the first part, the protocol for the production of an aptamer-based electrochemical sensing platform capable of continuous monitoring was established and optimised using the ATP/adenosine aptamer as a model. The redox-decorated aptamer was immobilised on a gold surface and the signal generated by the displacement of the electron donor upon binding of the target molecule with the DNA strand. The fabrication and its properties were assessed via cyclic voltammetry (CV) and the sensor response recorded via square wave voltammetry (SWV). Three aptamers for ATP/ Adenosine were employed and their performance on the platform was evaluated both against the target and the downstream molecules. In the second part, the characterised platform was employed to record a biological event: the in vitro release of adenosine from a hypoxic brain slice. Prior to performing the measurement that required tissue, all the control measurements were performed to evaluate influence of different environmental factors e.g. pH, temperature, buffer composition. Another preliminary measurement aimed to verify whether the sensor could be inserted in the tissue, by recording the sensor response whilst inserted in an agar block. Lastly the recording of adenosine release from hypoxic brain tissue was performed simultaneously with electrophysiology recordings. In the third and last part capture-SELEX was employed to select two novel structure-switching aptamers against UTP and UDP-glucose, two neurochemicals connected to pathological conditions such as epilepsy, dry eye disease and metastatic cancer. The sequenced libraries were then analysed and the emerged candidates were at first screened with SYBRGreen assay, a high throughput fluorescence assay, and the results confirmed via microscale thermophoresis (MST). The final selected aptamer, for each target molecule, underwent the first truncation round. Finally, the binding affinity of the two obtained sequences were characterised via MST.

This thesis explored the interaction between oral language and reading skills in children with Down syndrome. Study 1 looked at the longitudinal relationship between reading accuracy, reading comprehension and oral language across three time-points. Study 2 taught new spoken words with or without the orthographic form present and Study 3 examined the effect of phonological pre-training on orthographic learning. In all three studies, typically developing children matched for reading accuracy also participated. The effect of phonological and non-phonological oral language skills on reading accuracy was examined in Studies 1 and 3. In Study 1, phoneme awareness and vocabulary were evaluated as predictors of reading accuracy. Neither were longitudinal predictors in either group due to the strength of the autoregressor. However, vocabulary was a concurrent predictor for the children with Down syndrome. In Study 3, children with Down syndrome showed poorer orthographic learning than typically developing children. However when equated for decoding skill, the level of orthographic learning and the benefit from phonological pre-training were equivalent in the two groups. The proposed benefit of learning to read on oral language development was tested in Studies 1 and 2. In Study 1, reading accuracy had a moderate effect on vocabulary development for children with Down syndrome and typically developing children. In Study 2, children with Down syndrome and typically developing children showed similar levels of phonological learning, which was facilitated by orthographic support to the same extent. The relative contribution of reading accuracy and oral language to reading comprehension was evaluated in Study 1. Reading accuracy predicted concurrent reading comprehension for the children with Down syndrome and typically developing children, whereas oral language did not. However, only oral language was a longitudinal predictor in the children with Down syndrome. Theoretical and practical implications of the findings from all three studies are considered.

My PhD thesis Changing Social and Cultural Identities in a Border Area. The Case of Pre-Imperial and Early Imperial Sichuan discusses the funerary remains of the Sichuan region dated from the Warring States period to the Western Han dynasty (V-I cent. BC.) My research specifically addresses issues of identity, boundaries and social interaction, immediately prior to and during the early incorporation of the region into the empire, as well as the relevance of these concepts for the interpretation of global trends and local variations identified in the archaeological record. My aims were on the one hand to question the attribution of specific cultural traits to distinct "archaeological cultures", as the local "Ba" and "Shu" cultures", and on the other hand to detect from the discontinuities of the archaeological record the existence of cross-cutting and overlapping social and cultural identities. The research entails a qualitative and quantitative analysis of a dataset composed of around 300 burials and their grave goods assemblages recorded in Chinese publications and field records. Special attention was given to the use and association of different burial types, specific classes of items (pottery, bronze weapons, bronze vessels, bronze objects, ornaments, seals, iron and lacquer), and distinct decorative motifs on weapons. The patterns identified in the temporal and spatial variability of the selected funerary elements have suggested the existence of a complex social landscape, characterised by various horizontal and vertical differentiations within and between sites, and by the presence and interaction of different social and cultural groups involved in a process of adjustment, negotiation and redefinition of their own identities. This overall picture is opposed to a more classical and culture-historical perspective which tends to explain variability in the region with the existence of different "archaeological cultures".

Osteoarthritis is a degenerative disease of the joint leading to pain and disability. The knee is the most common site for osteoarthritis. Bone marrow lesions (BMLs) have been associated with knee osteoarthritis symptoms and progression, however there has been limited investigation of the mechanical effects of BMLs on joint function. Subchondroplasty has been proposed as a minimally invasive surgical treatment for BMLs where the lesion site is augmented with bone substitute material in attempt to restore biomechanical function. However, it is not known how the presence of BMLs affect knee joint contact mechanics and whether augmentation of this area could address this. The aim of the work presented in this thesis was to investigate the effect of BMLs on knee joint mechanics and to investigate the efficacy of augmentation of BML areas to restore knee joint mechanics. Computational methods were developed to model BMLs in the knee joint and augmentation cases using finite element (FE) models. Experimental methods were also developed to characterize the mechanical properties of bone in BML areas. The experimental and computational methods developed were combined to create specimen-specific models of human knee joints incorporating BMLs with derived mechanical properties.

Lower back pain, which has been associated with intervertebral disc degeneration, is a leading cause of disability worldwide and is associated with a large socioeconomic cost. A proposed treatment for disc degeneration is nucleus augmentation, where a biomaterial is injected into the nucleus pulpous of the disc aiming to restore disc height and biomechanics. Current laboratory test methods have not been adapted for evaluating soft tissue mechanics. The aim of this project was to develop and utilise a suite of methods to evaluate the mechanical properties and effects of injectable treatments on the intervertebral disc. A further goal was to develop a prototype delivery device to meet the unique requirements of the University of Leeds peptide hydrogel. High magnitude loading was applied to bovine tail intervertebral discs in native, degenerated, and treated states. Discs were cyclically tested under high magnitude to 20,000 cycles aiming to exacerbate potential mechanical consequences across the different states. A rapid enzymatic degeneration procedure was performed to replicate an early stage degeneration state. Predictive modelling was applied to the 20,000 cycle data and showed the mechanical behaviour in the native and degenerate states can be estimated with approximately 1,000 to 5,000 cycles. A further study was performed using 1,000 cycles which evaluated different parameters with respect to mechanical restoration. The test method found a strong relationship with the clinically measurable parameters volume injected (r2=0.7) and change in disc height from the injection (r2=0.8). The developed bovine tissue in vitro model was transferred to human tissue. Several issues with the transfer were addressed and a preliminary set of data was analysed. Finally, a novel prototype device was developed that is able to deliver the University of Leeds patented hydrogel. In vitro and clinical studies were completed to evaluate the efficacy of the novel device. These studies examined the performance of the design and highlighted the need to assess the delivery requirements for injectable treatments. Overall, a suite of tests has been developed that were able to mechanically evaluate the performance of injectable nucleus augmentation treatments. Mechanical testing was shown to be an important factor that can help optimise the surgical process, mitigate risks, and contribute towards clinical translation.

Haemophilia is a rare disease that causes musculoskeletal bleeds in up to 80% of patients. These bleeds cause arthritic changes to the targeted joint; the aim of the research carried out in this thesis was to investigate the influence of these arthritic changes on the ankle joint. In order to achieve this, longitudinal morphological analysis and finite element studies were carried out on a patient cohort with haemarthropathy of the ankle. Robust, patient specific models were generated in order to carry out novel studies into the influence of features of subchondral bone cysts, such as size, location and depth; and to develop a quasi-dynamic method of modelling patient specific haemophilic gait. The results gathered from these models highlighted the importance of patient specificity in a disease with such variable joint outcomes. Despite a small sample size, and informational constraints, the results of the studies undertaken highlighted structural and functional changes of the haemophilic ankle, and demonstrated potential relationships between the two. Morphological analysis showed a significant flattening of the talus in the medial and lateral regions of the haemophilic ankle. Upon investigation of the link between this morphological variation and consequent joint function, a significant negative correlation between talar collapse and cartilage contact pressure, and bone stresses was found in static modelling; and through the gait cycle the regions of high contact forces related to regions of significant talar collapse.

The state-of-the-art for generating accurate and high-quality hexahedral meshes of irregular geometries for finite element (FE) simulations is a laborious and time-consuming endeavour. Mesh-morphing is a technique which modifies the vertices of an existing mesh to match the boundary prescribed by another. This technique has been chosen as it has the capacity to automatically create accurate and high-quality hexahedral meshes of irregular geometries from a single template. The meniscus was chosen as it is an important component of the knee and challenging structure to simulate. Hexahedral discretisation is often required due to: multi-body contact, large deformations and complex material properties (nearly-incompressible and anisotropic). In this research, a novel, automatic and general-purpose mesh-morphing strategy was developed. Additionally, several robust and thorough methodologies were developed to assess the sensitivity and validate the performance of the mesh-morphing strategy. This was achieved through performance comparisons against a state-of-the-art procedure - the multi-block method (IA-FEMesh). The performance metrics not only assessed the capacity of the mesh-morphing strategy (i.e. speed, accuracy and mesh-quality), but also the functionality for meaningful FE simulations. The mesh-morphing strategy generated 20 challenging meniscus meshes in under a minute compared to an average of 26 minutes, with comparable surface error and mesh-quality metrics to the state-of-the-art. Also, there was no significant difference in the FE simulation outcomes. The mesh-morphing strategy offers a faster, competitive and automated alternative to the semi-automatic state-of-the-art, and only required one template mesh. The strategy can already be applied to a diverse range of geometries, and with some trivial modifications can approach a larger proportion. The developed tool can be used to improve productivity and automate the development of FE models. This could enable the design of large-scale studies and assist the development of digital twins. A wide-range of industries that require automatic and accurate meshing from 3D scanning technologies could utilise this work.

Background: Endodontically treated teeth have an increased risk of biomechanical failure because of significant loss of tooth structure. The ideal restorative technique and material for such teeth is always a challenge for the clinician. Aims: The aim of this project was to evaluate the effect of using different dental CAD/CAM materials on the biomechanical behaviour of endodontically treated teeth restored with a new technique named endocrown. Methodology: In this study, a thorough comparison of endocrown restorations fabricated from new types of all-ceramic, resin based composite and zirconia dental restorative materials through a series of systematic tests on human permanent premolars was performed. An extensive thermal and mechanical cyclic testing, static mechanical loading, micro-computed tomography analysis, scanning electron microscopy, optical profilometry, and finite element analysis evaluated the efficiency of endocrowns in terms of their mechanical properties and behaviour, fitting accuracy and stress distribution pattern. Results: The current study reported significant effects for material selection along with restoration design and remaining sound tooth structure on the restoration efficiency of endodontically treated teeth. A significant interaction between restoration design and material type was observed, in which resin-based composite resulted in highest fracture strength among endocrowns, however all materials tested were able to survive dynamic thermo-mechanical fatigue testing simulating 2.5 years of clinical service. Monolithic translucent zirconia resulted in the highest number of catastrophic failures in restored teeth. The stress distribution pattern in the studied models revealed that the use of glass ceramics with endocrowns could enhance their long term bonding efficiency and retention, while resin composite endocrowns present a lower risk of catastrophic failure. Glass ceramics showed superior fitting accuracy and exhibited the smoothest and most homogenous fitting surface's roughness profile. Conclusions: The mechanical behaviour, stress distribution and adaptation of resin based composite and glass ceramic endocrowns were clinically acceptable providing sufficient amount of sound tooth structure is preserved. Zirconia endocrowns should be avoided with premolar teeth owing to the low fracture resistance and high risk of catastrophic failures. Endocrowns are not recommended in cases with no remaining buccal and lingual coronal walls.

An increasingly younger population are seeking treatment for osteoarthritis of the ankle. Current late-stage surgical interventions sacrifice the upper levels of the distal tibia and talus to allow for joint replacement implantation. This can lead to multiple failure modes with regards to the success of the device, as well as low bone stock at revision. Changes to subchondral bone with osteoarthritis is well studied in the hip and knee, but the ankle remains highly under-reported. Medical imaging and validated computational modelling can provide predictive capabilities of bone properties in the ankle and help to inform surgical interventions. Hence, the aim of the studies compiled in this thesis was to characterise the structural and mechanical changes to subchondral bone in the late-stage osteoarthritic ankle. Using mechanical characterisation and medical imaging, a specimen-specific finite element methodology was developed using porcine tissue and translated for use on non-diseased human trabecular bone to estimate tissue-level properties through the optimisation of grayscale-based material properties. Nanoindentation was used to directly measure tissue mechanical properties, which aided in assessing changes to the apparent-level stiffness of osteoarthritic bone. High-resolution medical imaging provided a means of detailed, three-dimensional morphological evaluation of the trabecular architecture, thus providing an insight to the remodelling of the bone with osteoarthritis and its influence on bone stiffness. The porcine and non-diseased human FE models showed good agreement between computational and experimental stiffness values. Evaluation of osteoarthritic bone showed significant remodelling of trabecular microarchitecture, higher apparent stiffness, and altered tissue properties. Further investigation is needed to fully understand the impact of multiscale bone changes with osteoarthritis in the ankle, but this work has provided the foundations for understanding these changes. Such information will be crucial to aid future implant design and the development of joint strength prediction models using medical images, to inform surgical decisions.

Abnormal hip contact mechanisms can be associated with acetabular soft tissue damage and the progression of osteoarthritis. One morphological cause of this abnormal mechanical environment is a cam-shaped femoral head that results in impingement with the acetabular rim and labrum during hip motions. In this thesis, cam-type femoroacetabular impingement (FAI) related loading was mimicked on the acetabular cartilage-labral junction in vitro and in silico. During loading, computed tomography scans were obtained whereby radiopaque solution was used in order to separate acetabular soft tissues in the hip during contact. Measurements of overall cartilage strain were taken at the centre of the contact region and the labral apex displacement was established in three-dimensional space. The circumferential properties of the labrum were also assessed by re-loading the tissue sample following introducing a cut to the labrum. Two-dimensional finite element models of the femoral head and acetabulum were developed based on an image slice through the centre of the contact region. Geometrical features of the acetabulum and femur at the contact site were captured in the models. Computational results were compared with experimental results. A parametric study was conducted on the models for verification and for investigation of hip parameters regarding the soft tissue behaviour under load. Contact occurred at the anterior-superior region of the acetabulum in all samples, as would be expected if the conditions of cam-type FAI were replicated. The cartilage strain ranged from 20% to 60% and the labrum maximum displacement ranged from 1.5 to 5.0 mm, measured from CT scans in all samples. The circumferential effect in the labrum was demonstrated with an averaged factor of 1.4 of increase in the labrum apex displacement per applied force in labrum-cut cases. The cartilage strain and load distribution in soft tissues were found to be sensitive to the femoral head position in the computational models, with strain differences up to 41% and cartilage contact force differences up to 237%. The ratio between the cartilage and labrum Young's modulus affected the tensile strain at the cartilage-labral junction by up to 14%. The position of cartilage-labral junction affected the total contact force on the soft tissue by up to 49%. This work measured the soft tissue behaviour under cam-type FAI loading via an experimental approach and characterised the soft tissue behaviour under various set-ups via computational approach. The importance of adapting reliable tissue alignment and three-dimensional modelling were highlighted. It can be concluded that, stiffer labrum compared to the cartilage, along with focused loading at the cartilage-labral junction, would cause high strain in the cartilage and concentrated tensile strain at the junction, suggesting the damage mechanism in hips with FAI.

Low back pain is a common complaint in people of all ages. The long-term success rates of many surgical devices to treat the spine have been relatively low and improved methods of pre-clinical testing of these devices are therefore needed. Sheep spine models are commonly employed in pre-clinical research studies for the evaluation of spinal devices. The anterior and posterior longitudinal ligaments (ALL and PLL) provide passive stability to the spine, however, limited studies have been conducted to characterise the mechanical properties of the ovine longitudinal ligaments or compare them to the human. Moreover, previous studies have derived material properties for the human ALL and PLL directly from force-displacement data, assuming uniform cross sectional area and length, and these values have been used extensively in finite element models of the spine for the analysis of clinical interventions. The aim of this study was to develop a methodology to test and compare the stiffness of human and ovine spinal longitudinal ligaments and to uniquely combine experimental and specimen-specific finite element (FE) modelling approaches to determine the ligament mechanical properties. The methodology was developed on ovine thoracic spines and then applied to human thoracic spines. The spines were dissected into functional spinal units (FSUs) with the posterior elements removed and imaged under micro computed tomography (µCT). The specimens were sectioned through the disc to leave only either the ALL or PLL intact and tested in tension to determine the stiffness. The µCT images from each FSU were used to build specimen-specific FE models of the ligaments and bony attachments. Hyper-elastic material models were used to represent the ligament behaviour. Initial values for the material model were derived using mean cross sectional area (CSA) and length (L), with the assumption that ligament was uniaxially loaded. The parameters were then iteratively changed until a best fit to the corresponding experimental load-displacement data was found for each specimen. The stiffness of the ligaments for the ovine specimens were found to be higher than for the human specimens. This may have implications for the use of ovine FSUs for preclinical testing of devices. There was poor agreement between the material parameters derived from FE models and the initial values derived by assuming a mean CSA and L. This work demonstrates that a specimen-specific image-based approach needs to be applied to derive the elastic properties of the ligaments due to their non-uniform shape and cross-sectional area.

Abnormal bony morphology is a factor implicated in hip joint soft tissue damage and an increased lifetime risk of osteoarthritis. One geometric feature causing impingement and thus resulting in such damage is a bony lump on the femoral neck, known as a cam deformity. A three-dimensional geometric parameterisation system was developed to capture key variations in the femur and acetabulum of subjects with clinically diagnosed cam deformity. Novel quantitative measures of the size and position of cams were taken and used to assess differences in morphological deformities between males and females. The precision of the measures was sufficient to identify differences between subjects that could not be seen using two-dimensional imaging; cams were found to be more superiorly located in males than in females. As well as providing a means to distinguish between subjects more clearly, the geometric hip parameterisation facilitated flexible and rapid automated generation of a range of hip geometries including cams. These were used to develop finite element models. Patient-specific parametric finite element models of hips under impingement conditions were verified with comparison to their patient-specific segmentation-based equivalents. The parameterisation system was then used to generate further models to investigate the effects of bone morphology on tissue strains. This demonstrated that a combination of cam location and extent affect impingement severity, highlighting the importance of reporting the full three-dimensional geometry used for parametric models.