The focus of this thesis relates to the development and characterisation of novel semiconductor based lasers sources tunable in the broad spectral ranges that are unattainable by conventional lasers due to a lack of suitable laser gain materials. Within the first part, the broad gain spectrum from quantum dot (QD) materials is seen to be an appealing feature for the development of broadly tunable lasers, broadband amplifiers and ultra short pulse generation. As has been previously shown quantum-dot external-cavity passively mode-locked lasers (QD-ECMLLs) are excellent candidates for versatile ultra short pulse generation. This is due to the flexibility that anexternal-cavity mode-locking configuration can offer in terme of a broad tunability for both repetition rate and wavelength which could be achieved. Similarly quantum-dot semiconductor optical amplifiers (QD-SOA) are suitable for the broadband pulse power amplification. Furthermore, master oscillator power amplifier (MOPA) picosecond optical pulse sources using all chirped QD structures were investigated using the MOPA system consisting of two parts, firstly QD-ECMLL and secondly a tilted taper QD-SOA. A further investigation involved a comparison between 1st-order diffraction grating and 2nd-order diffraction grating for this tunable QD-MOPA. The result found was the maximum fundamental mode-locking (FML) wavelength tuning range. Nearly 100 nm (from 1187nm to 1283nm) wavelength tuning range was achieved under a 900 mA current applied to the gain chip with a 2nd-order grating diffraction. Furthermore it was also demonstrated that the peak power spectral density achieved with the 2nd-order diffraction (max; 31.4dBm/nm) is much higher (2-4dB) than that from the 1st-order diffraction under similar conditions. The narrowest optical spectrum width was achieved from the 2nd-order diffraction and the narrowest pulse of 13 ps was found for the setup with the 1st-order diffraction grating. The wavelength tuning range from both orders can be amplified by increasing the injection current of the gain chip without deteriorating the stability of FML. The second part of this thesis focussed on experimental testing of EP-VECSELs, also known as electrically-pumped semiconductor disc lasers (SDLs), which produce high multi watt output power with diffraction limited output beam profile. EP-VECSELs have great potential within the applications where the watt level CW output power and mode-locked light with picosecond pulses sources are required.

The development of biomaterials mainly focuses on the improvement of their biocompatibility. The aim of this research was to develop a range of DLC coatings and micro-nanostructured surfaces with anti-bacterial properties for biomedical applications. In this study a DLC coating and Si- and F- doped DLC coatings with various Si and F contents were prepared by a radio frequency plasma-enhanced chemical vapor deposition (rf-PECVD) technology. Under water contact angle method was used to characterize the surface properties of these DLC type coatings, and bacterial adhesion assess were performed by fluorescence microscopy to evaluate their anti-bacterial ability. The results showed that the DLC coatings can effectively decrease the bacterial adhesion, which reduced the bacterial adhesion by 65%, compared with uncoated stainless steel. The extended DLVO theory was used to explain the bacterial adhesion mechanism. Quartz Crystal Microbalance technology (QCM-D), which is a simple, efficient, reliable, real time and information-rich method for measuring bacterial adhesion and related assesses, was used to measure and record the bacterial adhesion process with time. The frequency change curves and dissipation factor change curves of bacterial adhesion onto the coatings were obtained. The electrochemical corrosion tests showed that the doped DLC coatings has excellent anti-corrosion properties and can protect stainless steel from corrosion. In this study the effects of material topography on bacterial adhesion were investigated both theoretically and experimentally. The interaction energies between bacteria (E.coli) and micro-nanostructure were computed by extended DLVO theory. The results showed that 350nm scale surface structure has the highest interaction energy and should be able to minimize the bacterial adhesion. To verify this finding, a series of surface micro/nano-structures (350-1000nm) were produced on PDMS samples by a soft lithography method. The bacterial adhesion assays were performed with the micro/nano-structured PDMS surfaces. The bacterial adhesion results were consistent with our theoretical prediction. In addition the sterile urine encrustation experiments were also performed with the micro/nano-structured PDMS surfaces. The experimental showed that the micro-nano-structured surfaces significantly reduced or delay the urine encrustation formation on the surfaces.

The cavitation subharmonic signal, emitted at frequency values sub-multiple to that of the acoustic driving, is held to be exclusive to the occurrence of driven bubbles within a host medium. Recently, detection of the subharmonic signal has seen a resurgence of interest, particularly for the prospect of cavitation-mediated therapy during the application of focused ultrasound to tissue. Remarkably, bubble-based mechanisms for the origin of the subharmonic signal - which can account for the range of experimental configurations from which it has been detected - have remained elusive since the signal was first identified, by Esche in 1952. This thesis describes cavitation observations in water, driven by propagating focused ultrasound fields typical of those used for medical therapy, using ultra high-speed shadowgraphic imaging at frame rates well in excess of the fundamental driving frequency. Moreover, single nanosecond laser pulses at energies below the plasma-forming threshold, are used to nucleate acoustic cavitation such that activity may be observed from the outset. Clouds of densely packed and strongly interacting bubbles are seen to rapidly develop from the nucleation event. Within a few acoustic cycles, the cloud adopts a breathing mode response, with component bubbles collectively oscillating, approximately in-phase. The frequency of cloud oscillation matches that of the fundamental driving, however, at intervals dependent on the pressure amplitude of the driving, the cloud undergoes strong collapses, coincident to emitting a shockwave. In parallel to the high-speed imaging, a number of hydrophone detectors are used to collect the acoustic emissions, and confirm that periodic shockwaves mediate the subharmonic signals. Acoustic detection of broadband, impulsive pressure transients is particularly susceptible to convolution with the frequency response of the detector. Accordingly, a PVdF needle hydrophone was calibrated for magnitude and phase from 125 kHz – 20 MHz, at the National Physical Laboratory. Detector deconvolution is demonstrated for shockwaves emitted during the formation of large plasma-mediated bubbles, each generated with a laser pulse of energy above the threshold. Similarly, the needle hydrophone is deconvolved from the emissions collected from acoustic cavitation clouds, indicating peak-positive pressure amplitudes for periodic shockwaves in the order of 10 kPa, at the distance detected. The development of a single element passive cavitation detector, dedicated to the detection of low-amplitude shockwaves with high sensitivity, is subsequently described. Detector construction, specifically the selection of matching and backing layers, is guided via a Finite Element model of the device, adapted to support simulated shockwave propagation. Detector performance is characterised with plasma bubble shockwaves, and evaluated for the detection of the subharmonic signal from a cavitation cloud, against a commercially available device.

Medium chain length-PHAs (MCL-PHAs) have properties that make them exceptional for applications in cardiac tissue engineering. Cardiovascular diseases (CVD) are a major cause of death worldwide. Cardiac patches aim to facilitate the normal functioning of the heart muscle by providing repair and support to the infarcted tissue post myocardial infarction. In this project, two MCL-PHAs, poly(3-hydroxyoctanoate) (P(3HO) homopolymer and poly(3-hydroxynonanoate-co-3-hydroxyheptanoate) P(3HN-co-3HHP) were produced from Pseudomonas mendocina CH50 using sodium octanoate and sodium nonanoate respectively as the carbon source and the growth profiles were monitored for 48 h. The polymers were characterised to confirm the chemical structure of the polymers. Different types of scaffolds were fabricated like plain films, random fibres and aligned fibres, using different ratios of P(3HO) and P(3HN-co-3HHP) which were 100:0 (P(3HO)), 20:80 (P(3HO):P(3HN-co-3HHP), 50:50 (P(3HO):P(3HN-co-3HHP), 80:20 (P(3HO):P(3HN-co-3HHP) and 0:100 P(3HN-co-3HHP). The mechanical and thermal properties of the films were analysed along with the wettability of all the scaffolds. In vitro cytocompatibility studies were also conducted on all the different scaffolds (films, random and aligned fibres) by growing human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CM) on them. The cells were found to be viable and healthy with comparable beating rates and calcium transients to that measured on gelatin which was used as the positive control. The cell alignment quantification on the aligned fibres indicated around 50% of the cells were aligned in one direction. Porous 5 wt% 2D scaffolds and porous 20 wt% 3D structure were fabricated using P(3HO) and different concentrations of the porogen, sucrose and NaCl respectively, to obtain pores in the size range of 250-300 μm which exhibited decreased hydrophobicity compared to the neat scaffolds. In vitro cell culture with C2C12 exhibited higher cell proliferation rate on the porous P(3HO) structures as compared to the neat P(3HO) film. The P(3HO) and PANI (polyaniline) blend scaffolds were fabricated to introduce electrical conductivity and they were analysed for their material characteristics. The effect of the addition of PANI on cardiomyocyte proliferation was studied using neonatal ventricular rat myocardial cells (NVRM). A one step method involving the use of poly(ethylene oxide-stat-propylene oxide) with isocyanate end groups (NCO-sP(EO-stat-PO) was used for the incorporation of RGD, YIGSR peptides and the vascular endothelial growth factor (VEGF) on the surface of P(3HO)/P(3HN-co-3HHP) (80:20) electrospun fibres and enhanced cell viability was studied using NVRMs.

In the healthcare setting, approximately 2 million bioinert devices are implanted into patients on an annual basis. However, interfacial instability of bioinert implants leads to reduced implant survivability and as a result revision surgery. Implant related infections are also a major concern which are associated with considerable repercussions for both the patient and healthcare system. Therefore, to overcome these failures materials that stimulate growth, repair and regeneration of tissues whilst simultaneously preventing infections need to be developed. A growing body of clinical data demonstrates that bioactive glasses offer great hope as they endorse these properties. Melt quench derived 3 mol% gallium doped bioactive glass was tested for antibacterial and cytotoxic activity. The results were compared with archetypal 45S5 Bioglass®, prepared and processed under identical conditions to allow a direct comparison. The antibacterial activity was studied using Escherichia coli (NCTC 10538) and Staphylococcus aureus (ATCC 6538). The cytotoxic activity was evaluated using osteosarcoma Saos-2 cells and bone marrow derived mesenchymal stem cells. The group IIIa metal, gallium is known to possess antibacterial, antiresorptive and osteogenic properties and is therefore of interest for biological and tissue engineering applications. Results of the current work illustrated that 3 mol% gallium doped bioactive glass behaves in a similar manner to 45S5 Bioglass®. The antibacterial studies demonstrated that 3 mol% gallium doped bioactive and 45S5 Bioglass® do not possess a broad-spectrum antibacterial activity, as growth inhibition was only observed for E. coli; they were also rendered ineffective following pH neutralisation. Additionally studies with mammalian cells revealed that 3 mol% gallium doped bioactive glass did not exhibit significant osteogenic activity, in comparison to 45S5 Bioglass®, after pH neutralisation.

This thesis describes the design, implementation and application of bioinformatics systems to aid work in the field of biomarker discovery and diagnostic test development. The aim of the work was to develop a flexible data storage and analysis platform that would be capable of housing and working with data from a variety of modern biomarker analysis techniques. In order to achieve this aim, several tools were developed: a flexible database schema, taking ideas from the field of systems biology, was developed with the goal of being flexible enough to house information about experiments looking at targets such as genes, proteins and metabolites; and API was created to allow easy programmatic interaction with the database; and multivariate data analysis routines were prepared so that data imported into the database could be investigated. Together this toolset was named XPA [for ‘Cross Platform Analysis’]. The XPA system was tested by using it to house and analyse data from two different medical studies, one using quantitative PCR [qPCR] to observe gene expression changes in prostate cancer, and the second using surface enhanced laser desorption/ionisation mass spectrometry [SELDI MS] to generate protein profiles in sufferers of pre-eclampsia. In both studies XPA was used to develop multivariate classification models using partial least squares discriminant analysis [PLS-DA] and support vector machines [SVMs], with the aim of evaluating the data acquired for potential diagnostic use. The results showed the benefit of a tool such as XPA to the field of biomarker discovery.

A portable functional electrical stimulation system has been designed using embedded systems technology. The system, which was applied to patients suffering from foot drop, uses sensors to monitor foot movement and orientation in a unique way, uses sophisticated algorithms for feedback, and drives an array of surface electrodes for stimulation. This system meets British Standards and safety requirements for medical equipment. A new technique was invented based on using the twitch response of muscles to optimise the configuration of the electrode array. This reduces the setup time in the clinic. Using feedback from the sensors, the optimum configuration of electrodes is chosen to produce correct stimulation and movement in real time. The instrument presents the patient with a ranked list of electrode combinations that are likely to be optimum; the patient can then choose a combination that is both effective and comfortable. The system is also able to vary the chosen pattern of electrodes and the stimulation signal parameters during the stimulation process. This may enable some problems associated with fatigue and skin irritation to be reduced. Trials were carried on 30 controls and 12 patients to test the instrument and study and develop the system optimisation and control algorithms. These preliminary clinical trials showed that control of the stimulation during walking, based on the optimisation algorithms developed in this work, gives high quality correction of foot drop. This was shown by gait assessment analysis by the physiotherapists involved in the project and blind assessment using independent researchers. These trials prove that the concept of using the electrode array for stimulation has advantages over using a conventional 2-electrode system.

A biomarker is a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes or pharmacological responses to a therapeutic intervention. The aim of this project was to deal with the identification of potential biomarker candidates from experimental data comparing samples displaying divergent physiological traits. Chapter 1 introduces the topic and the aims of the project. The primary aim was to identify the ideal statistical analysis methods and data pre- and post-treatment options to use for potential biomarker identification from proteomic datasets. The product of this work was a statistical analysis pipeline for identifying potential biomarker candidates from proteomic experimental data. Proteomic data often suffers from missing values, so methods to deal with these were also evaluated in this project. Chapter 2 outlines the data sets that were used as well as presenting an overview of the “Biomarker Hunter” pipeline software solution created in this project. Chapter 3 evaluates the appropriate univariate statistical methods to use for biomarker identification and the results of biomarker identification using these techniques. Chapter 4 evaluates options for data pre- and post-processing. Chapter 5 suggests the use of missing value imputation as well as offering a novel clustering algorithm to deal with missing values. The software pipeline also offers multivariate statistical methods, which are evaluated in Chapter 6. Chapter 7 provides some business context for both biomarker discovery and the statistical analysis software available for the purpose of proteomic biomarker discovery. As well as providing a software pipeline for the identification of biomarkers, the project aimed to identify a suggested strategy for statistical analysis of proteomic experimental data. Strong conclusions regarding the ideal statistical approach could only be made if the list of actual, validated biomarkers were available. Unfortunately this information was not available, but in the absence of this a strategy was suggested based on the available information from both the available literature and the author’s interpretation of the results from this study. In terms of data pre-processing, this strategy involved not averaging technical replicates, and using total abundance normalisation to reduce technical variation. A novel clustering algorithm was suggested to reduce the presence of missing values prior to existing methods of missing value imputation. Following statistical analysis multiple testing correction methods should be implemented to reduce the number of false positives.

Background: Systemic inflammation, whether it is the result of infectious or traumatic insult, typically has a high mortality rate, often with the exact cause of death remaining elusive. Observations in recent years have led to specific definitions for infectious and non-infectious systemic inflammation, as well as a greater understanding of the pathophysiology on the molecular and cellular levels. Despite the multitude of insults that can lead to systemic inflammation, the symptoms and pathophysiology of the condition remain similar, and the development of pharmaceutical or technological treatment typically focuses on the targeting of the intrinsic molecular mechanisms associated with the progression of the condition. Objectives: In this research project, the use of an extracorporeal adsorbent technology is proposed to remove inflammatory mediators from circulating blood. The main objective of this study is to develop a miniaturised portable adsorbent technology. This can be ac hieved by completing a series of smaller objectives, these include; The development of a miniaturised portable blood pump. The immobilisation of adsorbent microbeads in a manner which allows continuous blood flow across the beads without causing an embolism risk or high resistance to flow. The effective integration of these extracorporeal technologies in a manner that leads to effective cytokine removal from circulating blood to a clinically relevant degree with a technology that lends itself to a broad range of applications. Approach: Designs were developed for a series of blood pump concepts, some of which were modelled computationally; others were developed into prototypes and tested in the laboratory. Subsequent to the development of these concepts, laboratory testing of the adsorbent material was performed to further inform the design of the overall device. Following this, a clinical study was undertaken in which the device was deployed in one of the situations in which we envisage its use, post cardiopulmonary bypass cytokine filtration. vi Outcomes: Upon completion of this research project, multiple concepts had been proposed and explored for the development of a portable integrated cytokine adsorption technology. Many remained in a conceptual phase, as a result of various limiting factors. Others were developed into prototypes, and integration was achieved with relatively little complication. In the testing of the adsorbent device, a series of complications was discovered in relation to the use of interleukin proteins in vitro. Limitations were found in using these proteins in the laboratory setting, which were critical to this research as they have a significant impact on the assumption of cytokine stability in control solutions. The subsequent testing of the device in near-clinical studies, reinforced these findings, but also showed the considerable ability of the cytokine adsorption device to perform well under these conditions. Through this res earch, we were able to develop a truly portable cytokine adsorption technology and confirm its efficacy under clinical conditions.

Articular cartilage (AC) is a remarkable tissue in which a complex composition and hierarchical structure provides an optimized function in load support and joint lubrication. Osteoarthritis (OA) is the degeneration and consequent loss of AC. OA is increasingly becoming more of a problem; an increase in OA leads to a greater number of replacement surgeries creating a financial burden on the population. The mechanical etiology and function of OA is not fully understood. Nanoindentation and AFM techniques were investigated to measure the nanomechanical properties of AC. Instrumental nanoindentation was employed to characterize the variation of the mechanical properties of OA across the human femoral head and to understand the OA degenerative process further. Qualitative analysis allowed the visualization and comparison of OA over the femoral head. This demonstrated that the worst affected area of OA was the superior posterior area which corresponds to the area of stiffest cartilage found on healthy cadaveric femoral heads. The qualitative results showed that OA potentially initiates at this location. A potential biomechanical biomarker of OA has been found medially around the fovea capitis ligament. We hypothesize that when the cartilage surface attaches to a nanoindeter tip this indicates signs of a pannus-like tissue, suggestive of early OA. This is crucial for the development of new early osteoarthritis diagnostic tools. Extensive further work is necessary in the development of more effective diagnostic devices.