Macrophages are present in virtually all tissues and account for approximately 10% of all body mass. Although classically credited as the scavenger cells of innate immune system, ridding a host of pathogenic material and cellular debris though their phagocytic function, macrophages also play a crucial role in embryogenesis, homeostasis, and inflammation. De-regulation of macrophage function is therefore implicated in the progression of many disease states including cancer, arthritis, and atherosclerosis to name just a few. The diverse range of activities of this cell can be attributed to its exceptional phenotypic plasticity i.e. it is capable of adapting its physiology depending on its environment; for instance in response to different types of pathogens, or specific cocktail of cytokines detected. This plasticity is exemplified by the macrophages capacity to adjust rapidly its transcriptional profile in response to a given stimulus. This includes interferons which are a group of cytokines capable of activating the macrophage by interacting with their cognate receptors on the cell. The different classes of interferons activate downstream signalling cascades, eventually leading to the expression (as well as repression) of hundreds of genes. To begin to fully understand the properties of a dynamic cell such as the macrophage arguably requires a holistic appreciation of its constituents and their interactions. Systems biology investigations aim to escape from a gene-centric view of biological systems. As such this necessitates the development of better ways to order, display, mine and analyse biological information, from our knowledge of protein interactions and the systems they form, to the output of high throughput technologies. The primary objectives of this research were to further characterise the signalling mechanisms driving macrophages activation, especially in response to type-I and type- II interferons, as well as lipopolysaccharide (LPS), using a ‘systems-level’ approach to data analysis and modelling. In order to achieve this end I have explored and developed methods for the executing a ‘systems-level’ analysis. Specifically the questions addressed included: (a) How does one begin to formalise and model the existing knowledge of signalling pathways in the macrophage? (b) What are the similarities and differences between the macrophage response to different types of interferon (namely interferon-β (IFN-β) and interferon-γ (IFN-γ))? (c) How is the macrophage transcriptome affected by siRNA targeting of key regulators of the interferon pathway? (d) To what extent does a model of macrophage signalling aid interpretation of the data generated from functional genomics screens? There is general agreement amongst biologists about the need for high-quality pathway diagrams and a method to formalize the way biological pathways are depicted. In an effort to better understand the molecular networks that underpin macrophage activation an in-silico model or ‘map’ of relevant pathways was constructed by extracting information from published literature describing the interactions of individual constituents of this cell and the processes they modulate (Chapter-2). During its construction process many challenges of converting pathway knowledge into computationally-tractable yet ‘understandable’ diagrams, were to be addressed. The final model comprised 2,170 components connected by 2,553 edges, and is to date the most comprehensive formalised model of macrophage signalling. Nevertheless this still represents just a modest body of knowledge on the cell. Related to the pathway modelling efforts was the need for standardising the graphical depiction of biology in order to achieve these ends. The methods for implementing this and agreeing a ‘standard’ has been the subject of some debate. Described herein (in Chapter-3) is the development of one graphical notation system for biology the modified Edinburgh Pathway Notation (mEPN). By constructing the model of macrophage signalling it has been possible to test and extensively refine the original notation into an intuitive, yet flexible scheme capable of describing a range of biological concepts. The hope is that the mEPN development work will contribute to the on-going community effort to develop and agree a standard for depicting pathways and the published version will provide a coherent guide to those planning to construct pathway diagrams of their biological systems of interest. With a desire to better understand the transcriptional response of primary mouse macrophages to interferon stimulation, genome wide expression profiling was performed and an explorative-network based method applied for analysing the data generated (Chapter-4). Although transcriptomics data pertaining to interferon stimulation of macrophages is not entirely novel, the network based analysis of it provided an alternative approach to visualise, mine and interpret the output. The analysis revealed overlap in the transcriptional targets of the two classes of interferon, as well as processes preferentially induced by either cytokine; for example MHC-Class II antigen processing and presentation by IFN-γ, and an anti-proliferative signature by IFN-β. To further investigate the contribution of individual proteins towards generating the type-I (IFN-β) response, short interfering RNA (siRNA) were employed to repress the expression of selected target genes. However in macrophages and other cells equipped with pathogen detection systems the act of siRNA trasfection can itself induce a type-I interferon response. It was therefore necessary to contend with this autocrine production of IFN-β and optimise an in vitro assay for studying the contribution of siRNA induced gene-knock downs to the interferon response (described in Chapter-5). The final assay design incorporated LPS stimulation of the macrophages, as a means of inducing IFN-β autonomously of the transfection induced type-I response. However genome-wide expression analysis indicated the targeted gene knock-downs did not perturb the LPS response in macrophages on this occasion. The optimisation process underscored the complexities of performing siRNA gene knockdown studies in primary macrophages. Furthermore a more thorough understanding of the transcriptional response of macrophages to stimulation by interferon or by LPS was required. Therefore the final investigations of this thesis (Chapter-6) explore the transcriptional changes over a 24 hour time-course of macrophage activation by IFN-β, IFN-γ, or LPS and the contribution of the macrophage pathway model in interpreting the response to the three stimuli. Taken together the work described in this thesis highlight the advances to be made from a systems-based approach to visualisation, modelling and analysis of macrophage signalling.

This study is an interpretive investigation of the life-career histories of 53 women in engineering; and a case study of one woman's account of present-lived career and her quest for identity in engineering over an eight year period (1992-1999). This study had two broad aims. First, it aimed to give voice to women's stories derived from their own reflective accounts, and to compare and contrast their perspectives with feminist writers' reviews of non-traditional girls' and women's career experiences, and with the organisational career story of itself. Second, it aimed to evaluate the adequacy of my convergence of a socialist feminist "unified systems" theory of social relations (Jaggar, 1983, 1989; Jaggar & Rothenberg, 1984, 1993) with Super's segmental life-span, lifespace theory (Super, 1980, 1990, 1994) to explain women's career and personality development. Further to this theoretical convergence, I elaborated on Super's original models and evaluated their usefulness for my gender analysis of career from four perspectives. I conceptualised "career" as both "subjective" and "organisational" (Dale, 1972; Hughes, 1937) and, using Benhabib's (1986b) terminology, created four perspectives by further differentiating career into either "generalised other" or "concrete other" (see Figure 1.1). Drawing on the findings of my exploration of the women's careers, I extended the range of Jaggar's/Super's explanatory theories of career and personality development (Figure 2.2) in an elaboration of Supers archway model (Figure 8.1). I found that my combined Jaggar/Super career archway and spider web model (Figure 2.3) represented the life-space tensions in each individual woman's career decision-making in engineering. / The life-career rainbow was a valuable subsidiary model (Figure 2.4) in highlighting the complexities of gender as an overarching socio-cultural factor for theoretical and conceptual analyses of career and its effect on salient role relationships and personality development at each life-stage. My convergence career ladder represented the organisational career statuses and the successive development of the subjective career and identity through the completion of developmental tasks (Figure 2.6). My case study Cecilia, in common with other participants, I found to be an accomplished "feminine ambivalent" (Douvan & Adelson, 1966) and "paver of the way" (Josselson, 1987), yet she (like several others) floundered in the milieux of engineering. Her story indicates the continued need for engineering educators: to acknowledge the significance of women's subjective constructs of career to effect transformative change by promoting equity and excellence; to recognise ways in which the subjective and the organisational constructs of career can complement one another; and to implement changes which facilitate such complementarity. This study fills a space in the research literature on non-traditional girls' and women's career development. It also has potential to assist those who wish to gain a better understanding of the career pathways of women in engineering.

The significant standpoint in this study was that schools’ key role was to educate and yet this process would be severely impeded when a student receiving the education was at-risk. Agencies external to the school provide support in various forms to these individuals with the view of decreasing their at-risk status, thus providing an environment conducive to learning. Communication was posited to be a fundamental process essential to the provision of support and education to these at-risk individuals. The conceptual framework in this study acknowledged the complexity of school and organisational environments and was founded upon four key theoretical perspectives; organisational communication theory; a psychological orientation provided by Maslow’s hierarchy of needs; a social reconstructionist perspective; and constructs underpinning at-risk status causal factors. This research study sought to identify communication patterns existing within a selected school, and between the school (in this case) and associated agencies that were supporting the at-risk individuals. The results of this study, derived from in-depth interviews and questionnaires with agency personnel and school staff, demonstrated that although formal patterns of communication did exist they were inefficient and cumbersome. Formal patterns of communication were subsidiary to informal networks between colleagues. In this study, the school was frequently excluded from informal and formal agency communication patterns. Intra-agency and intra-school communication patterns were characterised by a top-down orientation with administrators tending to control the flow of information. A major finding was that there were considerable barriers to developing more effective communication patterns. / The greatest impediment to communication was case workers’ fear of breaching the Commonwealth Privacy Act 1988, even when dealing with such serious issues as children’s safety. Other less serious, but still substantial barriers, included agency territorialism, poor marketing of services, and individuals’ biases against particular support agencies. A surprising finding was that case workers’ and educators’ conceptualisations of the causal factors which contribute to an at-risk status were well aligned. The family factors, which included drug addicted, alcoholic, violent, criminal, disinterested and/or neglectful parents, problematic siblings, and coming from an English-as-a-second-language background were deemed to have the most significant influence towards creating an at-risk status. School-based factors such as stressed, intolerant, inexperienced, and/or non-supportive teachers, an inadequate and/or violent school environment, and a lack of individualised support were deemed to have the least impact on developing an at-risk status. As a result of this research a model has been proposed which outlines the creation of a State Support Brokerage Authority whose mandate would be to centralise, coordinate, and ensure quality of service to at-risk individuals across the state. This body would utilise a technological solution to enhance and coordinate the communication patterns between all potential stakeholders to facilitate appropriate and timely interventions.

In Australia the homeless population has become more diverse over the last 20 years with more young people, women and families experiencing homelessness. It is also evident that there is considerable variation in the length of time people remain homeless. How these changes relate to movements into and out of the homeless population is not well understood. This research asks: 'Is there a connection between how people become homeless, how long they remain homeless and how they 'get out' of homelessness?' A review of the literature identified two gaps directly relevant to the issue of movement in and out of homelessness. First, it is not well understood why people experience homelessness for different lengths of time when they face similar structural conditions. Second, the prevalence of substance use and mental illness reported in the homeless population has led some to conclude these factors cause homelessness. However, researchers have generally been unclear about whether such problems precede or are a consequence of homelessness. In addition, research has generally presumed a relationship between the amount of time a person is homeless and patterns of behavioural and cognitive adaptation to a homeless way of life. Yet recent research suggests that people's biographies play a significant role in the duration of homelessness. How these different findings relate to each other remains unclear. This thesis investigates these issues through a longitudinal study of homeless households. Data was gathered in two rounds of semi-structured interviews. In the first round 103 interviews were conducted. Approximately one year later 79 of these households were re-interviewed. The process of, and connections between becoming, being and exiting the homeless pathway are analysed using the 'pathways' concept. While on these pathways homeless people actively produce and reproduce social structures including both embracing and rejecting the stigma and subculture associated with homelessness. This complex world of homelessness is then analysed by extending the pathways concept by distinguishing five ideal type pathways based on the main reason for becoming homeless. They are a mental health pathway, a domestic violence pathway, a substance use pathway, a housing crisis pathway and a youth pathway. The research indicates that people on each pathway respond to the experience of homelessness differently and this has implications for the amount of time they spend in the homeless population. People on the substance use and youth pathways commonly describe themselves as 'homeless', focus on the 'here and now', use the welfare service system, are very mobile, and over time, many start to sleep rough. Their embrace of the homeless subculture commonly 'locks' them into the homeless population for long periods of time. In contrast people on the domestic violence and housing crisis pathways generally do not identify themselves as homeless and resist involvement with other homeless people. These homeless careers tend to be shorter. Then there are those who enter homelessness on the mental health pathway. They were frequently exploited in the early stages of their homeless careers and most sought to avoid exploitation by isolating themselves which then increased their marginalisation. These were the longest homeless careers. The use of the pathways concept also helps to understand how the circumstances of homeless people can change while they are homeless. The research found that some homeless people changed pathways. In particular the study found that two thirds of the people who reported substance use problems developed these problems after they became homeless. Most of these people entered the homeless population on the youth pathway. The research also found that three quarters of the people with mental health issues developed these issues after they became homeless, and that for some this was also connected to drug use. Overcoming homelessness is never easy and individuals manage the process in different ways. Again the pathways concept proved useful to understanding how homeless people accomplished this. The findings show that people travelling the different pathways require different levels and types of assistance to resolve their homelessness. The research concludes that the process of re-integration can take a long time but, given the right social and economic support, every homeless career can end.

"April 2003" / Bibliography: leaves 124-144. / xvii, 144 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, School of Molecular and Biomedical Sciences, Discipline of Physiology, 2003

Thesis (Ph. D.)--University of Hong Kong, 2007. / Title proper from title frame. Also available in printed format.

Thesis (M. Sc.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.

Genes can be associated in numerous ways, e.g. by co-expression in micro-arrays, co-regulation in operons and regulons or co-localization on the genome. Association of genes often indicates that they contribute to a common biological function, such as a pathway. The aim of this thesis is to predict metabolic pathways from associated enzyme-coding genes. The prediction approach developed in this work consists of two steps: First, the reactions are obtained that are carried out by the enzymes coded by the genes. Second, the gaps between these seed reactions are filled with intermediate compounds and reactions. In order to select these intermediates, metabolic data is needed. This work made use of metabolic data collected from the two major metabolic databases, KEGG and MetaCyc. The metabolic data is represented as a network (or graph) consisting of reaction nodes and compound nodes. Interme- diate compounds and reactions are then predicted by connecting the seed reactions obtained from the query genes in this metabolic network using a graph algorithm. In large metabolic networks, there are numerous ways to connect the seed reactions. The main problem of the graph-based prediction approach is to differentiate biochemically valid connections from others. Metabolic networks contain hub compounds, which are involved in a large number of reactions, such as ATP, NADPH, H2O or CO2. When a graph algorithm traverses the metabolic network via these hub compounds, the resulting metabolic pathway is often biochemically invalid. In the first step of the thesis, an already existing approach to predict pathways from two seeds was improved. In the previous approach, the metabolic network was weighted to penalize hub compounds and an extensive evaluation was performed, which showed that the weighted network yielded higher prediction accuracies than either a raw or filtered network (where hub compounds are removed). In the improved approach, hub compounds are avoided using reaction-specific side/main compound an- notations from KEGG RPAIR. As an evaluation showed, this approach in combination with weights increases prediction accuracy with respect to the weighted, filtered and raw network. In the second step of the thesis, path finding between two seeds was extended to pathway prediction given multiple seeds. Several multiple-seed pathay prediction approaches were evaluated, namely three Steiner tree solving heuristics and a random-walk based algorithm called kWalks. The evaluation showed that a combination of kWalks with a Steiner tree heuristic applied to a weighted graph yielded the highest prediction accuracy. Finally, the best perfoming algorithm was applied to a microarray data set, which measured gene expression in S. cerevisiae cells growing on 21 different compounds as sole nitrogen source. For 20 nitrogen sources, gene groups were obtained that were significantly over-expressed or suppressed with respect to urea as reference nitrogen source. For each of these 40 gene groups, a metabolic pathway was predicted that represents the part of metabolism up- or down-regulated in the presence of the investigated nitrogen source. The graph-based prediction of pathways is not restricted to metabolic networks. It may be applied to any biological network and to any data set yielding groups of associated genes, enzymes or compounds. Thus, multiple-end pathway prediction can serve to interpret various high-throughput data sets.

The ubiquity of circadian systems has allowed their characterization in a broad range of model systems, which has greatly improved knowledge of how these systems are organized and the vast range of cellular and organismal processes under circadian control. Most of the advances, however, have come in describing the central oscillators of these systems, and, in some cases, the input pathways used to coordinate these oscillators to external time. Very little progress has been made in understanding the output pathways that allow circadian systems to regulate the breadth of processes shown to be clock-controlled. A genetic selection was designed to obtain mutations in genes involved in circadianregulated expression of the Neurospora crassa ccg-1 and ccg-2 genes. Some, but not all, of the strains obtained display altered regulation of more than one ccg as well as an ‘Easlike’ appearance on solid media, and altered circadian period on race tubes. The data suggest a model in which output from the clock to these two genes is through a single, bifurcated pathway. The cloning of the gene mutated (rrg-1) in one of the strains from the above selection led to the first molecular description of a circadian output pathway in Neurospora, the HOG MAP kinase pathway. The HOG pathway has been previously described with regard to its role in the osmotic-stress response. The discovery of the involvement of rrg-1 in circadian regulation of ccg-1 and ccg-2 led to the discovery of regulation of the HOG pathway by the circadian clock. The data indicate that osmotic stress information and time-of-day information are transduced through the HOG pathway and implicate a role for the clock in preparing the organism for daily occurrences of hyperosmotic stress associated with sun exposure. The genetic selection, and the description of the HOG pathway with regard to circadian output, provide a basis for further characterization of circadian output in Neurospora. The ubiquity of MAP kinase pathways, such as the HOG pathway, and the observed similarities in the mechanisms of circadian clock function across multiple phyla, indicate that these findings may well be applicable to other model systems.

Nowadays, the hospital managers are facing increasing financial difficulties, because of the global budget policy from the national health institute. Patient-oriented services, good manner of the care providers, and the rapid response of the hospital to the medical environment are among the important factors for hospital survival. Therefore, many medical care providers had designed the clinical pathway for standardized medical treatment to control the medical costs, but they also allowed some extra-services for attracting and recruiting more patients. In this study, by way of participating management and job enrichment, we try to improve the quality and the patient satisfaction of the pelvic sonography provided by Obs/Gyn department. The study was proceeded in 2 ways. First, we designed a standardized obstetrical and gynecological sonography service pathway, which include a standard flow chart, customer encounter, and a checklist. Second, we measured the total service time duration, including those of pre-service consultation, actual sonography performing, and the post-service consultation. The measurements were performed before and after the application of the standardized sonography pathway. The measurement results were used to analyze and evaluate the validity and efficiency of the originally designed pathway. The study results demonstrate that after application of the sonography pathway, the total service time duration is reduced in Gyn sonography, but increased in Obs sonography. For Gyn sonography, the duration of pre-service consultation and post-service consultation were significantly reduced after application of standardized pathway. Further analysis revealed that thorough pre-service consultation not only made our patients more comfortable, but also reduced the post-service consultation time. However, the actual sonography performing time was increased, because of the adding of the standardized conversation. For obstetrical sonography, the duration of the actual sonography performing time was decreased, possibly due to the adding of standardized conversation, which answered most of the questions that the pregnant patients want to know about. In conclusion, by way of establishment and repeated reassessment/correction of the standardized sonography pathway, the quality of the sonography services can be greatly improved, and the patient¡¦s satisfaction can be even greater. The same experience can be applied to other fields. The quality of medical care can be more stable by the application of standardized clinical pathway. Besides, through the efforts of quality control, the medical cost can be limited, and the financial burden of the hospital and medical care providers can be reduced, making a double-win medical environment. Key Word: service pathways,total service, Obs/Gyn sonography