The application of phonetic distribution normalisation to likelihood-maximising speech enhancement for robust ASR

Traditional speech enhancement methods optimise signal-level criteria such as signal-to-noise ratio, but such approaches are sub-optimal for noise-robust speech recognition. Likelihood-maximising (LIMA) frameworks on the other hand, optimise the parameters of speech enhancement algorithms based on state sequences generated by a speech recogniser for utterances of known transcriptions. Previous applications of LIMA frameworks have generated a set of global enhancement parameters for all model states without taking in account the distribution of model occurrence, making optimisation susceptible to favouring frequently occurring models, in particular silence. In this paper, we demonstrate the existence of highly disproportionate phonetic distributions on two corpora with distinct speech tasks, and propose to normalise the influence of each phone based on a priori occurrence probabilities. Likelihood analysis and speech recognition experiments verify this approach for improving ASR performance in noisy environments.

Wellness in older adults

Understanding perception of wellness in older adults is a question to be understood against the backdrop of concerns about whether global ageing and the ‘bulge’ of ageing baby boomers will increase health care cost beyond what modern economies can deal with. Older adults who age in a healthy way and who take responsibility for their own health offer a positive alternative and change the perception that older adults are a burden on their society’s health system. The concept of successful ageing introduced by Rowe and Kahn (1987; 1997) suggested that older adults age successfully if they avoid disease and disability, maintain high cognitive and physical functioning and remain actively engaged with life. This concept, however, did not reflect older adults’ own perceptions of what constitutes successful ageing or how perceptions of wellness or health-related quality of life influenced the older adult’s understanding of his or her own health and ageing. A research project was designed to examine older adults’ perceptions of wellness in order to gain an understanding of the factors that influence perception of their own wellness. Specifically, the research wanted to explore two aspects: whether belonging to a unique organisation, in this instance a Returned Services Club, influenced perceptions of wellness; and whether there are significant gender differences for the perception of wellness. A mixed method project with two consecutive studies was designed to answer these questions: a quantitative survey of members of a Returned Services Club and of the surrounding community in Queensland, Australia, and a qualitative study conducting focus groups to explore findings of the survey. The results of the survey were used to determine the composition of the focus groups. The participants for the first study, (N=257), community living adults 65 years and older, were chosen from the membership role of a Returned Services Club or recruited by personal approach from the community surrounding the Services Club. Participants completed a survey that consisted of a perception of wellness instrument, a health-related quality of life instrument, and questions on morbidities, modifiable life style factors and demographics. Data analysis found that a number of individual factors influenced perception of wellness and health-related quality of life. Positive influences were independent mobility, exercise and gambling at non-hazardous levels, and negative influences were hearing loss, memory problems, chronic disease and being single. Membership of the Services Club did not contribute to perception of wellness beyond being a member of a social group. While there may have been an expectation that members of an organisation that is traditionally associated with high alcohol use and problematic gambling may have lower perceptions of wellness, this study suggested that the negative influences may have been counteracted by the positive effects of social interaction, thus having neither negative nor positive influences on perception of wellness. There were significant differences in perception of wellness and in health-related quality of life for women and men. The most significant difference was for women aged 85-90 who had significantly lower scores for perception of wellness than men or than any other age group. This result was the impetus for conducting focus groups with adults aged 85-90 years of age. Focus groups were conducted with 24 women and four men aged 85-90 to explore the survey findings for this age group. Results from the focus groups indicated that for older adults perception of wellness was a multidimensional construct of more complexity than indicated by the survey instrument. Elite older women (women over 85 years of age) related their perception of wellness to their ability to do what they wanted to do, and what they wanted to do significantly more than anything else, was to stay connected to family, friends and the community to which they belonged. From the focus group results it appeared that elite older women identified with the three elements of successful ageing – low incidence of disability and disease, high physical and cognitive functioning, and active engagement with life – but not in a flat structure. It appears that for elite older women good physical and mental health function to enable social connectedness. It is the elements of health that impact on the ability to do what they wanted to do that were identified as key factors: independent mobility, hearing and memory - factors that impact on the ability to interact socially. These elements were only identified when they impacted on the person’s ability to do what they wanted to do, for example mobility problems that were managed were not considered a problem. The study also revealed that older women use selection, optimisation and compensation to meet their goal of staying socially connected. The shopping centre was a key factor in this goal and older women used shopping centres to stay connected to the community and for exercise as well as shopping. Personal and public safety and other environmental concerns were viewed in the same context of enabling or disabling social connectedness. This suggested that for elite older women the model of successful ageing was hierarchical rather than flat, with social connectedness at the top, supported by cognitive functioning and good physical and mental health. In conclusion, this research revealed that perception of wellness in older adults is a complex, multidimensional construct. For older adults good health is related to social connectedness and is not a goal in itself. Health professionals and the community at large have a responsibility to take into account the ability of the older adult to stay socially connected to their community and to enable this, if the goal is to keep older adults healthy for as long as possible. Maintaining or improving perception of wellness in older adults will require a broad biopsychosocial approach that utilises findings such as older adults’ use of shopping centres for non-shopping purposes, concerns about personal and environmental safety and supporting older adults to maintain or improve their social connectedness to their communities.

Multilevel converter structure and control

In recent years, multilevel converters are becoming more popular and attractive than traditional converters in high voltage and high power applications. Multilevel converters are particularly suitable for harmonic reduction in high power applications where semiconductor devices are not able to operate at high switching frequencies or in high voltage applications where multilevel converters reduce the need to connect devices in series to achieve high switch voltage ratings. This thesis investigated two aspects of multilevel converters: structure and control. The first part of this thesis focuses on inductance between a DC supply and inverter components in order to minimise loop inductance, which causes overvoltages and stored energy losses during switching. Three dimensional finite element simulations and experimental tests have been carried out for all sections to verify theoretical developments. The major contributions of this section of the thesis are as follows: The use of a large area thin conductor sheet with a rectangular cross section separated by dielectric sheets (planar busbar) instead of circular cross section wires, contributes to a reduction of the stray inductance. A number of approximate equations exist for calculating the inductance of a rectangular conductor but an assumption was made that the current density was uniform throughout the conductors. This assumption is not valid for an inverter with a point injection of current. A mathematical analysis of a planar bus bar has been performed at low and high frequencies and the inductance and the resistance values between the two points of the planar busbar have been determined. A new physical structure for a voltage source inverter with symmetrical planar bus bar structure called Reduced Layer Planar Bus bar, is proposed in this thesis based on the current point injection theory. This new type of planar busbar minimises the variation in stray inductance for different switching states. The reduced layer planar busbar is a new innovation in planar busbars for high power inverters with minimum separation between busbars, optimum stray inductance and improved thermal performances. This type of the planar busbar is suitable for high power inverters, where the voltage source is supported by several capacitors in parallel in order to provide a low ripple DC voltage during operation. A two layer planar busbar with different materials has been analysed theoretically in order to determine the resistance of bus bars during switching. Increasing the resistance of the planar busbar can gain a damping ratio between stray inductance and capacitance and affects the performance of current loop during switching. The aim of this section is to increase the resistance of the planar bus bar at high frequencies (during switching) and without significantly increasing the planar busbar resistance at low frequency (50 Hz) using the skin effect. This contribution shows a novel structure of busbar suitable for high power applications where high resistance is required at switching times. In multilevel converters there are different loop inductances between busbars and power switches associated with different switching states. The aim of this research is to consider all combinations of the switching states for each multilevel converter topology and identify the loop inductance for each switching state. Results show that the physical layout of the busbars is very important for minimisation of the loop inductance at each switch state. Novel symmetrical busbar structures are proposed for multilevel converters with diode-clamp and flying-capacitor topologies which minimise the worst case in stray inductance for different switching states. Overshoot voltages and thermal problems are considered for each topology to optimise the planar busbar structure. In the second part of the thesis, closed loop current techniques have been investigated for single and three phase multilevel converters. The aims of this section are to investigate and propose suitable current controllers such as hysteresis and predictive techniques for multilevel converters with low harmonic distortion and switching losses. This section of the thesis can be classified into three parts as follows: An optimum space vector modulation technique for a three-phase voltage source inverter based on a minimum-loss strategy is proposed. One of the degrees of freedom for optimisation of the space vector modulation is the selection of the zero vectors in the switching sequence. This new method improves switching transitions per cycle for a given level of distortion as the zero vector does not alternate between each sector. The harmonic spectrum and weighted total harmonic distortion for these strategies are compared and results show up to 7% weighted total harmonic distortion improvement over the previous minimum-loss strategy. The concept of SVM technique is a very convenient representation of a set of three-phase voltages or currents used for current control techniques. A new hysteresis current control technique for a single-phase multilevel converter with flying-capacitor topology is developed. This technique is based on magnitude and time errors to optimise the level change of converter output voltage. This method also considers how to improve unbalanced voltages of capacitors using voltage vectors in order to minimise switching losses. Logic controls require handling a large number of switches and a Programmable Logic Device (PLD) is a natural implementation for state transition description. The simulation and experimental results describe and verify the current control technique for the converter. A novel predictive current control technique is proposed for a three-phase multilevel converter, which controls the capacitors' voltage and load current with minimum current ripple and switching losses. The advantage of this contribution is that the technique can be applied to more voltage levels without significantly changing the control circuit. The three-phase five-level inverter with a pure inductive load has been implemented to track three-phase reference currents using analogue circuits and a programmable logic device.

Axisymmetric shell structures for multi-use

Shell structures find use in many fields of engineering, notably structural, mechanical, aerospace and nuclear-reactor disciplines. Axisymmetric shell structures are used as dome type of roofs, hyperbolic cooling towers, silos for storage of grain, oil and industrial chemicals and water tanks. Despite their thin walls, strength is derived due to the curvature. The generally high strength-to-weight ratio of the shell form, combined with its inherent stiffness, has formed the basis of this vast application. With the advent in computation technology, the finite element method and optimisation techniques, structural engineers have extremely versatile tools for the optimum design of such structures. Optimisation of shell structures can result not only in improved designs, but also in a large saving of material. The finite element method being a general numerical procedure that could be used to treat any shell problem to any desired degree of accuracy, requires several runs in order to obtain a complete picture of the effect of one parameter on the shell structure. This redesign I re-analysis cycle has been achieved via structural optimisation in the present research, and MSC/NASTRAN (a commercially available finite element code) has been used in this context for volume optimisation of axisymmetric shell structures under axisymmetric and non-axisymmetric loading conditions. The parametric study of different axisymmetric shell structures has revealed that the hyperbolic shape is the most economical solution of shells of revolution. To establish this, axisymmetric loading; self-weight and hydrostatic pressure, and non-axisymmetric loading; wind pressure and earthquake dynamic forces have been modelled on graphical pre and post processor (PATRAN) and analysis has been performed on two finite element codes (ABAQUS and NASTRAN), numerical model verification studies are performed, and optimum material volume required in the walls of cylindrical, conical, parabolic and hyperbolic forms of axisymmetric shell structures are evaluated and reviewed. Free vibration and transient earthquake analysis of hyperbolic shells have been performed once it was established that hyperbolic shape is the most economical under all possible loading conditions. Effect of important parameters of hyperbolic shell structures; shell wall thickness, height and curvature, have been evaluated and empirical relationships have been developed to estimate an approximate value of the lowest (first) natural frequency of vibration. The outcome of this thesis has been the generation of new research information on performance characteristics of axisymmetric shell structures that will facilitate improved designs of shells with better choice of shapes and enhanced levels of economy and performance. Key words; Axisymmetric shell structures, Finite element analysis, Volume Optimisation_ Free vibration_ Transient response.

The design and testing of a daylighting device : optimising the energy and optical performance of Australian commercial buildings

The effective daylighting of multistorey commercial building interiors poses an interesting problem for designers in Australia’s tropical and subtropical context. Given that a building exterior receives adequate sun and skylight as dictated by location-specific factors such as weather, siting and external obstructions; then the availability of daylight throughout its interior is dependant on certain building characteristics: the distance from a window façade (room depth), ceiling or window head height, window size and the visible transmittance of daylighting apertures. The daylighting of general stock, multistorey commercial buildings is made difficult by their design limitations with respect to some of these characteristics. The admission of daylight to these interiors is usually exclusively by vertical windows. Using conventional glazing, such windows can only admit sun and skylight to a depth of approximately 2 times the window height. This penetration depth is typically much less than the depth of the office interiors, so that core areas of these buildings receive little or no daylight. This issue is particularly relevant where deep, open plan office layouts prevail. The resulting interior daylight pattern is a relatively narrow perimeter zone bathed in (sometimes too intense) light, contrasted with a poorly daylit core zone. The broad luminance range this may present to a building occupant’s visual field can be a source of discomfort glare. Furthermore, the need in most tropical and subtropical regions to restrict solar heat gains to building interiors for much of the year has resulted in the widespread use of heavily tinted or reflective glazing on commercial building façades. This strategy reduces the amount of solar radiation admitted to the interior, thereby decreasing daylight levels proportionately throughout. However this technique does little to improve the way light is distributed throughout the office space. Where clear skies dominate weather conditions, at different times of day or year direct sunlight may pass unobstructed through vertical windows causing disability or discomfort glare for building occupants and as such, its admission to an interior must be appropriately controlled. Any daylighting system to be applied to multistorey commercial buildings must consider these design obstacles, and attempt to improve the distribution of daylight throughout these deep, sidelit office spaces without causing glare conditions. The research described in this thesis delineates first the design optimisation and then the actual prototyping and manufacture process of a daylighting device to be applied to such multistorey buildings in tropical and subtropical environments.

The transformation of banana with potential virus resistance genes

One approach to reducing the yield losses caused by banana viral diseases is the use of genetic engineering and pathogen-derived resistance strategies to generate resistant cultivars. The development of transgenic virus resistance requires an efficient banana transformation method, particularly for commercially important 'Cavendish' type cultivars such as 'Grand Nain'. Prior to this study, only two examples of the stable transformation of banana had been reported, both of which demonstrated the principle of transformation but did not characterise transgenic plants in terms of the efficiency at which individual transgenic lines were generated, relative activities of promoters in stably transformed plants, and the stability of transgene expression. The aim of this study was to develop more efficient transformation methods for banana, assess the activity of some commonly used and also novel promoters in stably transformed plants, and transform banana with genes that could potentially confer resistance to banana bunchy top nanovirus (BBTV) and banana bract mosaic potyvirus (BBrMV). A regeneration system using immature male flowers as the explant was established. The frequency of somatic embryogenesis in male flower explants was influenced by the season in which the inflorescences were harvested. Further, the media requirements of various banana cultivars in respect to the 2,4-D concentration in the initiation media also differed. Following the optimisation of these and other parameters, embryogenic cell suspensions of several banana (Musa spp.) cultivars including 'Grand Nain' (AAA), 'Williams' (AAA), 'SH-3362' (AA), 'Goldfinger' (AAAB) and 'Bluggoe' (ABB) were successfully generated. Highly efficient transformation methods were developed for both 'Bluggoe' and 'Grand Nain'; this is the first report of microprojectile bombardment transformation of the commercially important 'Grand Nain' cultivar. Following bombardment of embryogenic suspension cells, regeneration was monitored from single transfom1ed cells to whole plants using a reporter gene encoding the green fluorescent protein (gfp). Selection with kanamycin enabled the regeneration of a greater number of plants than with geneticin, while still preventing the regeneration of non-transformed plants. Southern hybridisation confirmed the neomycin phosphotransferase gene (npt II) was stably integrated into the banana genome and that multiple transgenic lines were derived from single bombardments. The activity, stability and tissue specificity of the cauliflower mosaic virus 358 (CaMV 35S) and maize polyubiquitin-1 (Ubi-1) promoters were examined. In stably transformed banana, the Ubi-1 promoter provided approximately six-fold higher p-glucuronidase (GUS) activity than the CaMV 35S promoter, and both promoters remained active in glasshouse grown plants for the six months they were observed. The intergenic regions ofBBTV DNA-I to -6 were isolated and fused to either the uidA (GUS) or gfjJ reporter genes to assess their promoter activities. BBTV promoter activity was detected in banana embryogenic cells using the gfp reporter gene. Promoters derived from BBTV DNA-4 and -5 generated the highest levels of transient activity, which were greater than that generated by the maize Ubi-1 promoter. In transgenic banana plants, the activity of the BBTV DNA-6 promoter (BT6.1) was restricted to the phloem of leaves and roots, stomata and root meristems. The activity of the BT6.1 promoter was enhanced by the inclusion of intron-containing fragments derived from the maize Ubi-1, rice Act-1, and sugarcane rbcS 5' untranslated regions in GUS reporter gene constructs. In transient assays in banana, the rice Act-1 and maize Ubi-1 introns provided the most significant enhancement, increasing expression levels 300-fold and 100-fold, respectively. The sugarcane rbcS intron increased expression about 10-fold. In stably transformed banana plants, the maize Ubi-1 intron enhanced BT6.1 promoter activity to levels similar to that of the CaMV 35S promoter, but did not appear to alter the tissue specificity of the promoter. Both 'Grand Nain' and 'Bluggoe' were transformed with constructs that could potentially confer resistance to BBTV and BBrMV, including constructs containing BBTV DNA-1 major and internal genes, BBTV DNA-5 gene, and the BBrMV coat protein-coding region all under the control of the Ubi-1 promoter, while the BT6 promoter was used to drive the npt II selectable marker gene. At least 30 transgenic lines containing each construct were identified and replicates of each line are currently being generated by micropropagation in preparation for virus challenge.

Modelling and solving train scheduling problems under capacity constraints

Many large coal mining operations in Australia rely heavily on the rail network to transport coal from mines to coal terminals at ports for shipment. Over the last few years, due to the fast growing demand, the coal rail network is becoming one of the worst industrial bottlenecks in Australia. As a result, this provides great incentives for pursuing better optimisation and control strategies for the operation of the whole rail transportation system under network and terminal capacity constraints. This PhD research aims to achieve a significant efficiency improvement in a coal rail network on the basis of the development of standard modelling approaches and generic solution techniques. Generally, the train scheduling problem can be modelled as a Blocking Parallel- Machine Job-Shop Scheduling (BPMJSS) problem. In a BPMJSS model for train scheduling, trains and sections respectively are synonymous with jobs and machines and an operation is regarded as the movement/traversal of a train across a section. To begin, an improved shifting bottleneck procedure algorithm combined with metaheuristics has been developed to efficiently solve the Parallel-Machine Job- Shop Scheduling (PMJSS) problems without the blocking conditions. Due to the lack of buffer space, the real-life train scheduling should consider blocking or hold-while-wait constraints, which means that a track section cannot release and must hold a train until the next section on the routing becomes available. As a consequence, the problem has been considered as BPMJSS with the blocking conditions. To develop efficient solution techniques for BPMJSS, extensive studies on the nonclassical scheduling problems regarding the various buffer conditions (i.e. blocking, no-wait, limited-buffer, unlimited-buffer and combined-buffer) have been done. In this procedure, an alternative graph as an extension of the classical disjunctive graph is developed and specially designed for the non-classical scheduling problems such as the blocking flow-shop scheduling (BFSS), no-wait flow-shop scheduling (NWFSS), and blocking job-shop scheduling (BJSS) problems. By exploring the blocking characteristics based on the alternative graph, a new algorithm called the topological-sequence algorithm is developed for solving the non-classical scheduling problems. To indicate the preeminence of the proposed algorithm, we compare it with two known algorithms (i.e. Recursive Procedure and Directed Graph) in the literature. Moreover, we define a new type of non-classical scheduling problem, called combined-buffer flow-shop scheduling (CBFSS), which covers four extreme cases: the classical FSS (FSS) with infinite buffer, the blocking FSS (BFSS) with no buffer, the no-wait FSS (NWFSS) and the limited-buffer FSS (LBFSS). After exploring the structural properties of CBFSS, we propose an innovative constructive algorithm named the LK algorithm to construct the feasible CBFSS schedule. Detailed numerical illustrations for the various cases are presented and analysed. By adjusting only the attributes in the data input, the proposed LK algorithm is generic and enables the construction of the feasible schedules for many types of non-classical scheduling problems with different buffer constraints. Inspired by the shifting bottleneck procedure algorithm for PMJSS and characteristic analysis based on the alternative graph for non-classical scheduling problems, a new constructive algorithm called the Feasibility Satisfaction Procedure (FSP) is proposed to obtain the feasible BPMJSS solution. A real-world train scheduling case is used for illustrating and comparing the PMJSS and BPMJSS models. Some real-life applications including considering the train length, upgrading the track sections, accelerating a tardy train and changing the bottleneck sections are discussed. Furthermore, the BPMJSS model is generalised to be a No-Wait Blocking Parallel- Machine Job-Shop Scheduling (NWBPMJSS) problem for scheduling the trains with priorities, in which prioritised trains such as express passenger trains are considered simultaneously with non-prioritised trains such as freight trains. In this case, no-wait conditions, which are more restrictive constraints than blocking constraints, arise when considering the prioritised trains that should traverse continuously without any interruption or any unplanned pauses because of the high cost of waiting during travel. In comparison, non-prioritised trains are allowed to enter the next section immediately if possible or to remain in a section until the next section on the routing becomes available. Based on the FSP algorithm, a more generic algorithm called the SE algorithm is developed to solve a class of train scheduling problems in terms of different conditions in train scheduling environments. To construct the feasible train schedule, the proposed SE algorithm consists of many individual modules including the feasibility-satisfaction procedure, time-determination procedure, tune-up procedure and conflict-resolve procedure algorithms. To find a good train schedule, a two-stage hybrid heuristic algorithm called the SE-BIH algorithm is developed by combining the constructive heuristic (i.e. the SE algorithm) and the local-search heuristic (i.e. the Best-Insertion- Heuristic algorithm). To optimise the train schedule, a three-stage algorithm called the SE-BIH-TS algorithm is developed by combining the tabu search (TS) metaheuristic with the SE-BIH algorithm. Finally, a case study is performed for a complex real-world coal rail network under network and terminal capacity constraints. The computational results validate that the proposed methodology would be very promising because it can be applied as a fundamental tool for modelling and solving many real-world scheduling problems.

Optimal traffic control at railway junctions

Conflict occurs when two or more trains approach the same junction within a specified time. Such conflicts result in delays. Current practices to assign the right of way at junctions achieve orderly and safe passage of the trains, but do not attempt to reduce the delays. A traffic controller developed in the paper assigns right of way to impose minimum total weighted delay on the trains. The traffic flow model and the optimisation technique used in this controller are described. Simulation studies of the performance of the controller are given.

Signalling layout for fixed-block railway lines with real-coded genetic algorithms.

Signalling layout design is one of the keys to railway operations with fixed-block signalling system and it also carries direct effect on overall train efficiency and safety. Based on an analysis to system objectives, this paper presents an optimization model with two objectives in order to devise an efficient signalling layout scheme. Taking into account the present railway line design practices in China, the paper describes steps of the computer-based signalling layout optimisation with real-coded genetic algorithms. A computer-aided system, based on train movement simulator, has also been employed to assist the optimisation process. A case study on a practical railway line has been conducted to make comparisons between the proposed GA-based approach and the current practices. The results illustrate the improved performance of the proposed approach in reducing signal block joints and shortening minimum train service headway.

The conflict resolution in connected railway junctions

Purpose of study: Traffic conflicts occur when trains on different routes approach a converging junction in a railway network at the same time. To prevent collisions, a right-of-way assignment is needed to control the order in which the trains should pass the junction. Such control action inevitably requires the braking and/or stopping of trains, which lengthens their travelling times and leads to delays. Train delays cause a loss of punctuality and hence directly affect the quality of service. It is therefore important to minimise the delays by devising a suitable right-of-way assignment. One of the major difficulties in attaining the optimal right-of-way assignment is that the number of feasible assignments increases dramatically with the number of trains. Connected-junctions further complicate the problem. Exhaustive search for the optimal solution is time-consuming and infeasible for area control (multi-junction). Even with the more intelligent deterministic optimisation method revealed in [1], the computation demand is still considerable, which hinders real-time control. In practice, as suggested in [2], the optimality may be traded off by shorter computation time, and heuristic searches provide alternatives for this optimisation problem.

Coasting control of train operation by genetic algorithm

Balancing between the provision of high quality of service and running within a tight budget is one of the biggest challenges for most metro railway operators around the world. Conventionally, one possible approach for the operator to adjust the time schedule is to alter the stop time at stations, if other system constraints, such as traction equipment characteristic, are not taken into account. Yet it is not an effective, flexible and economical method because the run-time of a train simply cannot be extended without limitation, and a balance between run-time and energy consumption has to be maintained. Modification or installation of a new signalling system not only increases the capital cost, but also affects the normal train service. Therefore, in order to procure a more effective, flexible and economical means to improve the quality of service, optimisation of train performance by coasting point identification has become more attractive and popular. However, identifying the necessary starting points for coasting under the constraints of current service conditions is no simple task because train movement is attributed by a large number of factors, most of which are non-linear and inter-dependent. This paper presents an application of genetic algorithms (GA) to search for the appropriate coasting points and investigates the possible improvement on computation time and fitness of genes.

The development of Lactococcus lactis as an antimicrobial agent

Non-pathogenic lactic acid bacteria are economically important Gram-positive bacteria used extensively in the food industry. Due to their “generally regarded as safe” status, certain species from the genera Lactobacillus and Lactococcus are also considered desirable as candidates for the production and secretion of recombinant proteins, particular those with therapeutic applications. The hypothesis examined by this thesis is that Lactococcus lactis can be modified to be an effective antimicrobial agent. Therefore, the aims of this thesis were to investigate the optimisation of the expression, secretion and/or activities of potential heterologous antimicrobial proteins by the model lactic acid bacterium, Lactococcus lactis subsp. cremoris MG1363. L. lactis strains were engineered to express and secrete the recombinant CyuC surface protein from Lactobacillus reuteri BR11, and a fusion protein consisting of CyuC and lysostaphin using the Sep promoter and secretion signal. CyuC has been characterised as a cystine-binding protein, but has also been demonstrated to have fibronectin binding activity. Lysostaphin is a bacteriolytic enzyme with specific activity against the Gram-positive pathogen, Staphylococcus aureus. These modified L. lactis strains were then investigated to see if they had the ability to inhibit the adhesion of S. aureus to host extracellular matrix (ECM) proteins. It was observed that the cell extracts of the L. lactis strain with the vector only (pGhost9:ISS1) was able to inhibit the adhesion of S. aureus to fibronectin, whilst the cell extracts of the L. lactis strain expressing lysostaphin was able to inhibit adhesion to keratin. Finally, this thesis has identified specific lactococcal genes that affect the secretion of lysostaphin through the use of random transposon mutagenesis. Ten mutants with higher lysostaphin activity contained insertions in four different genes encoding: (i) an uncharacterised putative transmembrane protein (llmg_0609), (ii) an enzyme catalysing the first step in peptidoglycan biosynthesis (murA2), (iii) a homolog of the oxidative defence regulator (trmA), and (iv) an uncharacterised putative enzyme involved in ubiquinone biosynthesis (llmg_2148). The higher lysostaphin activity observed in these mutants was found to be due to higher amounts of lysostaphin being secreted. The findings of this thesis contribute to the development of this organism as an antimicrobial agent and also to our understanding of L. lactis genetics.

The effects of muscle fatigue on knee function during landing

The human knee acts as a sophisticated shock absorber during landing movements. The ability of the knee to perform this function in the real world is remarkable given that the context of the landing movement may vary widely between performances. For this reason, humans must be capable of rapidly adjusting the mechanical properties of the knee under impact load in order to satisfy many competing demands. However, the processes involved in regulating these properties in response to changing constraints remain poorly understood. In particular, the effects of muscle fatigue on knee function during step landing are yet to be fully explored. Fatigue of the knee muscles is significant for 2 reasons. First, it is thought to have detrimental effects on the ability of the knee to act as a shock absorber and is considered a risk factor for knee injury. Second, fatigue of knee muscles provides a unique opportunity to examine the mechanisms by which healthy individuals alter knee function. A review of the literature revealed that the effect of fatigue on knee function during landing has been assessed by comparing pre and postfatigue measurements, with fatigue induced by a voluntary exercise protocol. The information is limited by inconsistent results with key measures, such as knee stiffness, showing varying results following fatigue, including increased stiffness, decreased stiffness or failure to detect any change in some experiments. Further consideration of the literature questions the validity of the models used to induce and measure fatigue, as well as the pre-post study design, which may explain the lack of consensus in the results. These limitations cast doubt on the usefulness of the available information and identify a need to investigate alternative approaches. Based on the results of this review, the aims of this thesis were to: • evaluate the methodological procedures used in validation of a fatigue model • investigate the adaptation and regulation of post-impact knee mechanics during repeated step landings • use this new information to test the effects of fatigue on knee function during a step-landing task. To address the aims of the thesis, 3 related experiments were conducted that collected kinetic, kinematic and electromyographic data from 3 separate samples of healthy male participants. The methodologies involved optoelectronic motion capture (VICON), isokinetic dynamometry (System3 Pro, BIODEX) and wireless surface electromyography (Zerowire, Aurion, Italy). Fatigue indicators and knee function measures used in each experiment were derived from the data. Study 1 compared the validity and reliability of repetitive stepping and isokinetic contractions with respect to fatigue of the quadriceps and hamstrings. Fifteen participants performed 50 repetitions of each exercise twice in randomised order, over 4 sessions. Sessions were separated by a minimum of 1 week’s rest, to ensure full recovery. Validity and reliability depended on a complex interaction between the exercise protocol, the fatigue indicator, the individual and the muscle of interest. Nevertheless, differences between exercise protocols indicated that stepping was less effective in eliciting valid and reliable changes in peak power and spectral compression, compared with isokinetic exercise. A key finding was that fatigue progressed in a biphasic pattern during both exercises. The point separating the 2 phases, known as the transition point, demonstrated superior between-test reliability during the isokinetic protocol, compared with stepping. However, a correction factor should be used to accurately apply this technique to the study of fatigue during landing. Study 2 examined alterations in knee function during repeated landings, with a different sample (N =12) performing 60 consecutive step landing trials. Each landing trial was separated by 1-minute rest periods. The results provided new information in relation to the pre-post study design in the context of detecting adjustments in knee function during landing. First, participants significantly increased or decreased pre-impact muscle activity or post-impact mechanics despite environmental and task constraints remaining unchanged. This is the 1st study to demonstrate this effect in healthy individuals without external feedback on performance. Second, single-subject analysis was more effective in detecting alterations in knee function compared to group-level analysis. Finally, repeated landing trials did not reduce inter-trial variability of knee function in some participants, contrary to assumptions underpinning previous studies. The results of studies 1 and 2 were used to modify the design of Study 3 relative to previous research. These alterations included a modified isokinetic fatigue protocol, multiple pre-fatigue measurements and singlesubject analysis to detect fatigue-related changes in knee function. The study design incorporated new analytical approaches to investigate fatiguerelated alterations in knee function during landing. Participants (N = 16) were measured during multiple pre-fatigue baseline trial blocks prior to the fatigue model. A final block of landing trials was recorded once the participant met the operational fatigue definition that was identified in Study 1. The analysis revealed that the effects of fatigue in this context are heavily dependent on the compensatory response of the individual. A continuum of responses was observed within the sample for each knee function measure. Overall, preimpact preparation and post-impact mechanics of the knee were altered with highly individualised patterns. Moreover, participants used a range of active or passive pre-impact strategies to adapt post-impact mechanics in response to quadriceps fatigue. The unique patterns identified in the data represented an optimisation of knee function based on priorities of the individual. The findings of these studies explain the lack of consensus within the literature regarding the effects of fatigue on knee function during landing. First, functional fatigue protocols lack validity in inducing fatigue-related changes in mechanical output and spectral compression of surface electromyography (sEMG) signals, compared with isokinetic exercise. Second, fatigue-related changes in knee function during landing are confounded by inter-individual variation, which limits the sensitivity of group-level analysis. By addressing these limitations, the 3rd study demonstrated the efficacies of new experimental and analytical approaches to observe fatigue-related alterations in knee function during landing. Consequently, this thesis provides new perspectives into the effects of fatigue in knee function during landing. In conclusion: • The effects of fatigue on knee function during landing depend on the response of the individual, with considerable variation present between study participants, despite similar physical characteristics. • In healthy males, adaptation of pre-impact muscle activity and postimpact knee mechanics is unique to the individual and reflects their own optimisation of demands such as energy expenditure, joint stability, sensory information and loading of knee structures. • The results of these studies should guide future exploration of adaptations in knee function to fatigue. However, research in this area should continue with reduced emphasis on the directional response of the population and a greater focus on individual adaptations of knee function.