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Improving patient safety and quality of care are among the most important challenges facing hospital executives, not the least because of recent changes in hospital reimbursement. The usual tactic is to reduce medical treatment conditions, ensure proper drug dosage, and develop and enforce standards of care. While these efforts are important, the research here has considered one of the less obvious but critical operational issues as variation in patient flow. Patient flow and the reduction of waiting times is a subject of great discussion across all healthcare providers, underpins many waiting time improvement techniques. In healthcare, flow is the movement of patients, information or equipment between departments, staff groups or organisations as part of their care pathway. Ideally they would move from one ward in their care to the next without delay. Patient flow through an Emergency Department (ED) is complex with several changes in the pathway being produced by many decisions made at various points. However, variation in patient flow occurs throughout a hospital and contributes to different problems e.g. increasing in demand, a need for interactive care pathway or delivery of care solutions to measure different types of variability on patient flow and capacity management, extended waiting times, overcrowding and boarding in the emergency department (ED) bumped and late surgeries, lack of available routine and beds, overburdened nurses, and exasperated physicians. Not only does this threaten patient safety and quality of care, but it also causes enormous stress in the institution, making it increasingly difficult for hospitals to recruit and retain physicians and nurses. Healthcare delivery improvement techniques such as Lean allow providers to improve systems by reducing waste and highlighting the non-value added activities in the process. There are many possible process improvement solutions that can only be validated by implementation and understanding the whole process. Therefore, healthcare providers are turning to innovative technologies such as patient flow simulation in order to identify non-added activities, bottlenecks and to test Lean and more radical solutions before actually implementing them. The research will aim at proving that by adding simulations a radical thinking to improve the efficiency of flow of patients by reducing waiting time and get the best utilisation. Patient flow simulation allows you to immediately see the benefits of process changes with real time data and graphical visualisations. A novel approach is introduced within this research through the integration of simulation modelling techniques along with Taguchi analysis to investigate 'what if' patient variation scenarios. Such scenarios reflect the different combinations of the variability that can affect waiting time in one flow of patients and/or more than one patient at once. In addition, the research has adopted the concept of lean thinking to develop an automated Decision Operations Heuristic Analysis-Quick Response (DOHA-QR). The model acts in an iterative manner which investigate the different levels of variability by identify constraints that may affect the waiting and different performance outputs. Optimisation routines have been developed to get the best of senior medical resource scheduling to achieve best utilisation, reducing waiting time and react to the different levels of variability. Therefore, the developed method: (i) Concentrated on using customers and resources information to improve the quality of services while improving the productivity of the resources used in ED. (ii) Its principles can be extended and applied to different healthcare departments and other types of service granting organizations. (iii) Integrate with the simulation model that will have a real time picture of flow of patients' system load, condition, and behaviour i.e. different level of variability. It will act as a quick response tool that can provide a rationale to decision makers of small-business clinics to structure the right blend of medical resources, thereby maximizing profitability and patient satisfaction. (iv) Simulate different patient acute flow conditions i.e. emergency, urgent, non-urgent flow lines where senior medical resources can be best utilized, and (v) Additionally it will look at moving senior medical resources where and when needed between different patient acute flow lines.

Bacterial bioluminescence has been shown to be an accurate real-time reporter of bacterial internalisation and a valid alternative to viable counts. A self-bioluminescent strain of the bacterial pathogen Neisseria meningitidis was used to develop and optimise an internalisation assay with a range of cell lines including ECV-304, C6 and Caco-2 as an alternative to traditional indirect methods such as viable counting. The use of bioluminescence as a reporter of bacterial internalisation did not produce any robust evidence of internalisation of N. meningitidis C751 pGLITE within cell lines suggesting that internalisation is short lived, does not occur or is below the minimum level of detection. The traditional approach of using a gentamicin protection assay followed by viable counts to investigate internalisation of N. meningitidis suggested evidence of very low level internalisation, the reliability and reproducibility of which remains questionable due to methodological limitations. Although studying bacterial-cell interactions in internalisation assays using monolayers can provide useful insight into bacterial pathogenesis, when infecting the human host, bacteria are required to react with more than a monolayer of cells. The human blood-brain barrier (BBB) is considered to be the main physiological barrier controlling entry and exit from the brain parenchyma of molecules and bacteria. Knowledge of the exact mechanisms by which pathogens invade the brain remains incomplete for two main reasons; most of these pathogens are restricted to humans, limiting the relevance of any animal models and there are few good in vitro models of the BBB. It has been shown, that upon co-culture with C6 cells, ECV-304 cells demonstrate many of the key features of the BBB in vivo including an upregulation of endothelial tight junctions. This continuous co-culture model was further developed and adapted to enhance transendothelial electrical resistance (TEER), indicative of tight junction formation and adapted for use with bioluminescent strains of bacterial pathogens capable of crossing the BBB and entering the CNS to cause meningitis. Penetration of lux-expressing N. meningitidis, Pseudomonas aeruginosa, Staphylococcus aureus and pathogenic Escherichia coli across the BBB model was studied and subsequent effects on TEER and cell viability were also measured. Breaching of the BBB co-culture model by bioluminescent P. aeruginosa was observed after only 6 hours for 106 cfu whereas the other pathogens were not observed to cross the BBB model until in excess of 20 hours. For all pathogenic bacteria tested BBB penetration was associated with high bacterial numbers and all pathogens were observed to have a significant effect on TEER. The effect on cell viability was more variable. By combining the use of bioluminescence and a continuous cell culture model of the BBB, further investigation into breaching of the BBB by bacterial pathogens could be made that would be difficult or impossible to carry out in vivo. This study has resulted in the development of a robust system which has the potential to significantly enhance our understanding of bacterial translocation of the BBB and possible preventative measures.

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Biodiversity loss is occurring at an unprecedented rate and most of this loss is due to human induced pressure. This loss in biodiversity had led to concerns that the provision of ecosystem services that humans depend upon might be negatively affected. As such much modern conservation science focusses on preserving biodiversity whilst protecting priority ecosystem services. However, there may be spatial and temporal trade-offs between these services and the biodiversity that is considered important. Characterisation of such the relationships between biodiversity and ecosystem services is vital in order to improve management and policies which aim to protect and restore both biodiversity and ecosystem services. The broad aims of the thesis were to explore biodiversity-ecosystem service relationships in (1) ecosystems invaded by non-native plant species and (2) tropical forests affected by human exploitation and disturbance. Specifically this thesis aimed to answer the questions: 1. What effect do non-native plant invasions have on aboveground carbon storage, belowground carbon storage, carbon sequestration, water quality and water provision? 2. How do changes in species richness affect this ecosystem service provision? 3. How do these changes relate to the woodiness and traits of invasive and native dominant species, and the type of ecosystem invaded? 4. What factors drive differences in residual stand damage, biomass loss and species richness change following selective logging? 5. After deforestation how long do carbon stocks and plant biodiversity take to recover in tropical forests? 6. Do carbon and plant biodiversity differ in their recovery rates? 7. Which areas are priorities for restoration of tropical carbon? All chapters in this thesis make use of large datasets that I collated from the literature and other authors in order to draw broad conclusions about trade-offs and relationships between services and biodiversity In the section concentrating on invasive species my results suggest that non-native invasive plants generally increase the storage of carbon, whilst reducing water quality and availability. This may indicate a fundamental trade-off between services where increased biomass of plants results in higher evapotranspiration and thus water loss, while also enhancing the carbon cycle and nitrogen production of microorganisms. In addition my results suggest that aboveground carbon storage increases as species richness is reduced, showing the opposite relationship to that shown in many biodiversity ecosystem functioning experiments. This is the first time any such relationship has been found between community change and ecosystem level impacts in the context of species invasions. However, it seems likely that this relationship depends on the identity and traits of the species, with invasions in open habitats by woody species likely to drive a negative relationship between richness change and biomass change with the opposite true when grassy species invade woodlands. This result presents a trade-off between conservation priorities that managers will need to consider. In Chapter 3 I investigated the possibility of predicting the impact of non-native invasive plant impacts on ecosystem services by using characteristics and functional traits of both invasive and native species. This work suggested that aboveground carbon storage is most easily predicted by traits and characteristics of native and non-native species, with few other ecosystem services well explained by models. Results suggested that transition from woody to non-woody dominant species resulted in most dramatic changes in aboveground carbon storage. However, interestingly aboveground carbon storage also tended to increase where native species were replaced by species of similar woodiness. Similarly, given that woodiness and size of species are related, there was a positive relationship between the invasive species height and increases in aboveground carbon storage. However, all other ecosystem services were poorly predicted by species traits and characteristics. This work suggests that the most dramatic changes in carbon storage may result from shifts in ecosystems that resemble regime shifts. Future work addressing invasive species from this perspective is warranted as many invasions resemble such shifts. In Chapter 4 I investigated the relationships between logging intensity and methods and residual stem damage, biomass loss and species richness change in tropical logged forests. Many syntheses of the logging literature have made little distinction between logged sites, and only one has explored any of the mechanisms that may drive heterogeneity in logging impacts. This is particularly surprising given that Reduced Impact Logging (RIL) has been implemented relatively widely principally to reduce carbon loss from logged forests. My results from this chapter suggest that the principal driver of logging impacts is the intensity at which logging is carried out, showing broadly negative relationships with biomass and tree species richness change and a positive relationship with residual stem damage. Interestingly, RIL appeared to reduce residual stem damage slightly but evidence for this effect was weaker in other analyses. These analyses also suggest a slight increase in tree species richness at low logging intensities, showing some similarities to intermediate disturbance hypothesis type relationships. This is suggestive of a complex relationship between tree species richness and biomass changes during logging that deviated substantially from that suggested in grassland biodiversity-ecosystem function experiments. This is as far as I know the first time this relationship has been suggested in the context of logged forests. The result from this chapter also suggest that there is weak support that RIL reduces logging damage at low intensities but little evidence that this is reflected by changes in biomass. Further studies are needed to discern the effect of RIL over a wide range of logging intensities. Chapter 5 investigates tropical forest recovery following agricultural clearance. In this chapter I aimed to identify the recovery times of different above and belowground carbon pools and tree and epiphyte species richness as well as tree species composition using studies that had paired mature forest sites as comparators. Surprisingly this chapter represents the first attempt to generalise about this recovery rate. The results suggest that following clearance carbon and species richness of plants recovers relatively quickly (<100 years), but species indicative of old forests are rarely present in recovering forests and show few signs of recovery. Thus, while carbon recovery goals may be achievable full recovery of plant biodiversity may require centuries. This slow recovery may be aided by active restoration. Finally in Chapter 6 I investigated which areas should be considered as priorities when restoring tropical forests for carbon storage and bird biodiversity. In this chapter I found evidence of spatial trade-offs between carbon storage and bird species recovery. Empirical models suggested that carbon is accumulated most rapidly in forests with long growing seasons, while probability of bird species presence was primarily driven by habitat specificity, range size and forest cover. Model projections suggested that areas that should be considered a priority for restoration targeting carbon storage are found in the wet tropics while priorities for restoration of bird biodiversity are found in mountainous areas. These analyses indicated that there was no relationship between the two goals, but that by using model projections it was possible to identify areas that maximised both. In summary work in this thesis provides the best synthesis of the relationships between biodiversity and ecosystem services in the context of non-native invasive plants, and selective logging and recovery from tropical forest clearance to date. This is of particular value because such relationships have rarely been explored in these contexts despite widespread and of global importance for conservation.