3,587 results for ResearchSpace@Auckland, Doctoral

  • Truth and Physics Education: a Heideggerian Analysis

    Shaw, Robert Keith, 1948- (2010)

    Doctoral thesis
    The University of Auckland Library

    This thesis develops a hermeneutic philosophy of science to provide insights into physics education. Modernity cloaks the authentic character of modern physics whenever discoveries entertain us or we judge theory by its use. Those who justify physics education through an appeal to its utility, or who reject truth as an aspect of physics, relativists and constructivists, misunderstand the nature of physics. Demonstrations, not experiments, reveal the essence of physics as two characteristic engagements with truth. First, truth in its guise as correspondence enables a human being to prepare for the distinctive event of physics. Second, the event of physics occurs in human perception when someone forces a hidden reality to disclose an aspect of itself. Thus, the ground of physics is our human involvement with reality achieved by way of truth. To support this account of physics, the thesis reports phenomenological investigations into Isaac Newton‘s involvement with optics and a secondary school physics laboratory. These involve interpretations of Heidegger‘s theory of beings, schema and signification. The project draws upon, and contributes to, the hermeneutic phenomenology of modern physics, a tradition in continental philosophy that begins with Immanuel Kant, and advances particularly from Martin Heidegger to Patrick Heelan. The thesis advocates an ontological pedagogy for modern physics which has as its purpose each individual student‘s engagement with reality and truth. Students may achieve this through demonstrations of phenomena that will enable them to dwell with physics, an experience that contrasts with their embroilment in modernity, and which perpetuates nature‘s own science.

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  • DNA testing for cancer susceptibility : the needs of Maori

    Port, Ramari Viola (Waiora) (2007)

    Doctoral thesis
    The University of Auckland Library

    An inherited predisposition to cancer may result from constitutional mutations in a number of tumour suppressor genes. Knowledge of the specific mutations with a family which render the individuals susceptible to bowel, breast or stomach cancer facilitates genetic testing. Genetic testing is a relatively new technology, and New Zealand society is still coming to terms with its ethical implications and informational potential. Maori people are the indigenous people of Aotearoa New Zealand. As a consequence of a colonial history that has had a major impact on Maori health, New Zealand is struggling to reduce significant disparities in the health status of Maori. With the exception of one high profile case, Maori people have not readily engaged in genetic testing or genetic counselling services. This thesis set out to examine Maori perspectives about this state. Drawing on a Kaupapa Maori approach to research, a group of Maori cultural commentators (Pukenga), Maori families (whanau), and health professionals who work with families (Interfacers) were interviewed for this study. The thesis discusses the different world views that Maori have in regards to health, wellbeing and human society. These world views help explain Maori cultural perspectives about predictive/presymptomatic DNA testing. The thesis draws on the notion of two worlds which may stand apart in terms of world view, but which have the potential to come together at the level of individual and family health and well-being. The thesis draws on the interviews and suggests pathways forwards in the area of genetic counselling and other services. While these pathways are relevant to Maori and the New Zealand context the study shows how other cultural groups with alternative world views may seek their own solutions and responses to the technologies available through predictive/presymptomatic DNA testing.

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  • The organisation and management of clinical research in academic medical centres

    Pettus, Candace Gale (2003)

    Doctoral thesis
    The University of Auckland Library

    Clinical research is a traditional function of academic medicine and is vital to the development of new therapies and therapeutics. Most clinical research takes place within academic medical centres (AMCs), which are complex organisations operating at the juncture between clinical care, teaching and research. However, the environment in which academic medical centres operate has experienced significant turbulence over the last l0 years. Concerns have been raised about how clinical research is being managed in this dynamic environment. The question arises: what elements of organisational structure are important in the management of clinical research in academic medical centres? Working within the framework of organisational theory, this study employed a multimethod investigative process to explore the context of clinical research management in AMCs in five countries: the United States, the UK, Canada Australia and New Zealand. Archival data, a survey questionnaire and key informant interviews were analysed to develop a description of the context and structure of modern clinical research management. The results describe four structural models for clinical research management: (1) the established university-based model; (2) the hospital-based model; (3) the research institute model; and (4) the UK-NHS trust hospital model. In addition to formal organisational structures, this study has found that the use of informal structures, such as liaison devices and other integrative mechanisms are important to facilitate communications, co-ordinate complex activities and mitigate tensions between professionals and managers, and between the hospitals and universities that comprise academic medical centres. The findings from this study contribute to the body of knowledge on complex organisations in general and AMCs in particular. Moreover, it is anticipated that the findings from this study might be useful in the planning and development of clinical research management practices in academic medical centres as well as other professional research organisations.

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  • The effectiveness of medicines : the relationship between patient and prescriber expectations of effectiveness of medicines and compliance

    Ware, Gail Jocelyn (1997)

    Doctoral thesis
    The University of Auckland Library

    Effectiveness of medicines as reported in the literature can be difficult to interpret and explain to patients in clinical practice. A patient-orientated measure of effectiveness, the Category of Effectiveness (COE) was developed in 1988 by Dr Holford, Department of Pharmacology and Clinical Pharmacology, University of Auckland, School of Medicine. This was designed to examine the effectiveness of medicines in terms of easily understood patient-orientated outcomes which may influence the patient's daily living or quality of life. As part of their pharmacology training, third-year medical students were assigned two medicines to evaluate in terms of COE and asked to calculate a rate/1000 treatments or rate/1000 treatment years i.e. a Rate of Effectiveness (ROE). Interviews with three health professionals to obtain their opinions of the assigned medicines in terms of COE and ROE were recorded. An ordered scale of effectiveness, the Likelihood of Effectiveness (LOE), was developed by Dr Holford and the author in order to review these student projects. A review by the author of 201 of these projects over a five year period, suggests that health professionals expectations of some commonly prescribed medicines are over-optimistic. A literature search to obtain effectiveness information in terms of COE and LOE of twelve commonly prescribed medicines, Augmentin, cefaclor, beclomethasone, salbutamol, atenolol, captopril, enalapril, ranitidine, paracetamol, diclofenac, aspirin, and triazolam was undertaken. Such information was found to be limited in the literature as clinical trial results are seldom expressed in such terms. Opinions of patients and prescribers about The Category of Effectiveness (COE) and Likelihood of Effectiveness (LOE) of commonly prescribed medicines have not been examined in clinical practice. The influence these may have on medicine use was therefore surveyed for the twelve medicines listed above. One hundred and fifty-three patients received 247 prescriptions for one or more of these medicines. Expectations of patient and corresponding prescriber were similar in terms of COE, but LOEs differed significantly for 8 of the 12 medicines. Neither COE nor LOE were significantly related to patient compliance which was measured after 5-10 days. Most compliance-failure was seen in patients whose medicine was newly prescribed for short-term treatment. Information other than basic instructions was received by <25% of patients from either the prescriber or the pharmacist. At the surgery/hospital only 19% of patients remembered receiving written information about their medicine, which increased to 22% at the home visit. Of the patients who completed the medicines information questionnaire, only 59/152 (38.6%) would like more general information about their medicines. Despite this, 139/152 (91.4%) patients would like more specific information on how their medicine works, and 130/152 (85.5%) want to know how well it can be expected to work. This information has not been given to patients in the past. It was hypothesised that providing effectiveness information to patients may have some effect on compliance. The influence on compliance that providing written medicine effectiveness information as pamphlets from community pharmacists may have, was examined for 211 patients in a double-blind controlled trial. Patients who presented a prescription for beclomethasone for asthma or enalapril for hypertension were invited to participate. Each patient received one of three pamphlets, 1. specific medicine information pamphlet, 2. specific medicine information plus effectiveness information, 3. a control pamphlet containing general medicine information. Medicine knowledge was significantly increased by both the medicine information pamphlet (p=0.028) and the medicine and effectiveness information pamphlet (p=0.016) compared to control. Significantly more beclomethasone than enalapril patients showed compliance-failure (p=0.001) although this was independent of the pamphlet given. Expectations of LOE were related to patient compliance for beclomethasone patients, but not for enalapril patients. Significantly more beclomethasone patients with higher expectations of LOE were compliant (p=0.017). Satisfaction with the information contained in the pamphlet had a positive effect on patient compliance with beclomethasone individually. Patient-orientated measures of effectiveness such as COE (Category of effectiveness) and LOE (Likelihood of effectiveness) can identify patient expectations, increase patient knowledge and may provide some insight into patient compliance failure.

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  • Improving the immunogenicity of recombinant adeno-associated virus

    Ussher, James Edgeworth (2010)

    Doctoral thesis
    The University of Auckland Library

    Recombinant adeno-associated virus (rAAV) has many attractive features as a T cell vaccine vector, however disappointing immunogenicity was seen in a phase I clinical trial. Subsequent in vivo studies showed that several pseudotypes of rAAV elicited a dysfunctional CD8+ T cell response in mice that may reflect poor priming, lack of CD4+ T cell help or persistence of the vector. Dendritic cells are the key antigen presenting cells that prime a naive T cell response. Therefore, in this study multiple pseudotypes of rAAV were screened for their ability to transduce human monocytederived dendritic cells (MoDCs) and rAAV2/6 identified as the optimal pseudotype. Further improvements in transduction efficiency were achieved by mutation of surface-exposed tyrosine 731; analogous mutations in the capsid of AAV2 have previously been shown to decrease proteasomal degradation and increase nuclear trafficking of rAAV. Lysine 531 was identified as a key residue in the tropism of pseudotype 6 for MoDCs. Interestingly, while this residue is critical for the interaction with immobilised heparin, soluble heparin did not inhibit the transduction of MoDCs by AAV6. rAAV is a poor maturation stimulus of MoDCs therefore the development of immunoreactive vectors was a major goal of this project. One strategy adopted was the generation of vectors that encode MAVS, a signalling molecule in the RIG-I/MDA-5 pathway whose expression led to robust activation of NFκB and IRF-3 signalling pathways. However yields of vector encoding MAVS were greatly reduced due to reduced viability of the producer cell line. Therefore alternative means of vector production were sought. As rAAV has previously been successfully produced in insect cells and insects lack a homologue of MAVS, a baculovirus production system was developed for the production of pseudotype 6 rAAV. Successful production of rAAV was demonstrated, however further optimisation is required to allow production of high titres of rAAV necessary to facilitate further assessment of self-adjuvanting pseudotype 6 rAAV as a vaccine vector.

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  • ChronoMedIt : a computational quality audit framework for better management of patients with chronic disease

    Mabotuwana, Thusitha (2010)

    Doctoral thesis
    The University of Auckland Library

    Chronic disease is a leading cause of death worldwide accounting for around 60% of all deaths. An important aspect of successful chronic disease management is quality audit and feedback to clinicians. However, due to the complex temporal relationships inherent in chronic disease, formulating clinically relevant queries is difficult using the querying tools often built into commercial practice management systems. The onset of this PhD research involved working with staff of a general practice clinic to develop a set of explicit quality audit indicators for blood pressure control. Eight indicators were identified as most relevant to the practice. The ability to compute these indicators reliably from routinely collected electronic medical records (EMRs) was validated by clinical panel assessment. These eight indicators informed formulation of a model of chronic disease audit with four broad classes of indicators: (1) persistence to indicated medication; (2) timely measurement recording; (3) time to achieve target; and (4) measurement contraindicating therapy. The four broad indicator classes have been implemented within the ChronoMedIt (Chronological Medical audIt) framework as an extensible and configurable architecture. The main components of the ChronoMedIt architecture are: an XML based specification for indicator formulation (with an associated XML-Schema), a drug and classification knowledge base maintained using Semantic Web technologies, a C# based criteria processing engine, a SQL-Server based patient database with related stored procedures and a graphical user interface to formulate queries and generate reports. ChronoMedIt can produce patient-specific audit reports as well as reports to benchmark an entire practice for a given evaluation period. A visualisation tool has been developed to provide an alternate representation of patient prescribing and measurement histories. By modifying the indicator specification and knowledge base an analyst can address a wide array of chronic disease management queries as specific instances of the four broad indicator classes. The framework's core computation has been verified using redundant query implementations on a battery of simulated case data and is illustrated against the EMRs of several practices. ChronoMedIt has been applied in several real-world settings; notably, identifying patients with poor antihypertensive medication adherence profiles for a feasibility study of nurse-led adherence promotion.

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  • AC Processing Controllers for IPT Systems

    Wu, Hunter (2009)

    Doctoral thesis
    The University of Auckland Library

    Inductive Power Transfer (IPT) technology allows electrical energy to be transferred between two loosely coupled inductors over relatively large air gaps. An IPT system can be divided into two sections - a primary supply and one or more secondary pickups and controllers. Currently, IPT applications have been used in a variety of industrial and commercial applications. This thesis proposes a novel AC processing controller which directly regulates power in AC form, hence producing a controllable high-frequency AC source. The pickup has significant advantages in terms of increasing system efficiency and reducing pickup size compared to traditional pickups that also produce a controlled AC output using complex AC-DC-AC conversion circuits. The parallel AC processing pickup employs switches operating under Zero Voltage Switching (ZVS) conditions to clamp parts of the resonant voltage across a parallel tuned LC resonant tank to achieve a controllable AC current source. The derivation of key power electronic specifications such as component ratings, output harmonic content and power factor are shown along with the pickups normalized characteristics. Practical implementation aspects such as a new synchronization scheme using clamp time, series and parallel connection of switching devices to achieve higher ratings and a new PWM control technique to reduce conduction losses are investigated. By adding a rectifier, a controlled DC output can be produced. Practical examples including a lighting system and an EV charging system have shown the pickup to achieve very high operating efficiencies above 96%. The series AC processing pickup uses an AC switch operating in series with a resonant network to produce a controllable AC voltage source. When a rectifier is cascaded onto this pickup, it can also produce a precisely controlled DC voltage. The circuit is analytically analyzed and the maximum efficiency for a 1.2kW prototype is measured to be 93%. A direct AC-AC IPT system which takes 50Hz mains input and has 50Hz mains output without requiring a DC link is also proposed. This technique is based on the AC processing concept with matrix converters giving it the advantage of high efficiency. Other AC-AC systems at the track frequency are also proposed to enable controllable intermediate IPT links suitable for powering separate IPT tracks. Both of these later systems, appear to have significant future potential but need much further study to understand and overcome practical limitations which could form the basis of separate Ph. D. studies in their own right.

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  • Unleashing the Power of Human Genetic Variation Knowledge: New Zealand Stakeholder Perspectives

    Gu, Yulong (2010)

    Doctoral thesis
    The University of Auckland Library

    This thesis reports a qualitative study that collected multiple perspectives of New Zealand genetic services stakeholders concerning genetic information management issues. With the rapid development of human genetic variation knowledge and medical testing technologies, the demand for clinical genetic services is expanding in many healthcare systems. There are, however, many challenges in managing genetic testing and understanding test results. Taking a grounded theory approach, semi-structured interviews were conducted with 48 participants in order to understand their experiences, expectations, and concerns. The interview data were triangulated with our field notes, literature, and by applying a semantic space modelling technique - hyperspace analogue to language. The data analysis took a general inductive approach with a constant analytic comparison strategy. Three themes emerged from the data that identify gaps in the use of information relating to genetic services. Firstly, four service delivery models were identified in operation, including both those expected models involving genetic counsellors and some variations that do not route through the formal genetic services program. Secondly, a number of issues were perceived by the participants as barriers to sharing and using genetic information, including technological, organizational, institutional, legal, ethical, and social issues. Thirdly, the wider use of genetic testing technology is also impeded by the mixed understanding of genetic test utilities, particularly among clinicians, and is limited by the capacity of clinical genetic services. Due to the effect of these three themes, the potential of human genetic variation knowledge to enhance healthcare delivery has been put on a "leash." Targeting these problems, information technologies and knowledge management tools may support key tasks in genetic services delivery, improve knowledge processes in the domain, and enhance knowledge networks. Promising technologies include decision support systems, electronic referral systems, electronic health record or personal health record systems, data submission and other knowledge processing tools, ontology, and knowledge networking tools. The establishment of effective ethics and policy frameworks is also important in leveraging the power of genetic information for better healthcare outcomes.

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  • The structure of epithermal deposits of the Coromandel Peninsula : dynamic processes and three-dimensional strain

    Irwin, Marion Ruth (2004)

    Doctoral thesis
    The University of Auckland Library

    The many epithermal deposits of the Coromandel Peninsula, ('Hauraki volcanic zone') display a range of structural characteristics at a number of scales that illustrate the varied processes involved in their formation. Structural information synthesised from existing literature, including the theses on different parts of the Coromandel Peninsula suggests that there is widespread tilting towards the east and south throughout the region. Blockfaulting in the basement influences trends within the overlying volcanics. On a large scale, deposits may exhibit plane strain (e.g. Karangahake) or three dimensional strain in an orthorhombic fashion (e.g. Kapanga) or in a fashion akin to the model proposed by Harding for strike slip systems (e.g. Golden Cross underground). Other deposits have a more complex three-dimensional structure (e.g. Hauraki). Linked deposits, such as those seen underground and in the open pit at Golden Cross, may have quite different characteristics (Harding 3-D and plane-strain respectively). At an outcrop scale, vein opening processes are reflected in the patterns of veining and shape of individual veins. There are several very common vein shapes in Coromandel epithermal deposits. The influence of pre-existing planar features, including columnar jointing, is important, with veins often following their precursors. The main processes which influence vein patterns and shapes are shearing (pre, syn, alternating with and post vein opening), oblique opening ('shear opening') and perpendicular opening ('dilational opening') of veins. Rotation between adjacent blocks causes tapering veins. Other, non-dilational, processes resulting in vein opening or widening include erosion, dissolution and desiccation. The influence of folding on individual patterns is not clear. Jigsaw breccias are gradational with vein networks. Vein fill material gives information about some opening processes -such as cyclic opening and sealing- as well as filling processes that are influenced by such factors as fluid composition, hydrology, kinetics (which may in tum be influenced by factors such as seismic activity) and sedimentology within the veins. There are a variety of breccia types, probably reflecting a number of brecciation processes. A mathematical model is developed for ascertaining opening vectors for systems of three intersecting veins. Careful study of one level of a deposit can reveal a great deal of information about the whole deposit (e.g. Golden Cross underground workings. Golden Cross open pit). Old mine plans, used in conjunction with modern field studies, are a valid and valuable additional source of information (Kapanga).

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  • The Role of Oestrogen Receptor ß in Ovarian Granulosa Cell Tumours

    Cohen, Paul (2010)

    Doctoral thesis
    The University of Auckland Library

    Ovarian granulosa cell tumours (GCTs) are a specific subtype of malignant ovarian neoplasm which account for 5% of all ovarian cancers. GCTs are rare tumours which most commonly present in the early post-menopausal period. Although GCTs have a better short term prognosis than the more common epithelial ovarian carcinomas, in the longer term approximately 50% of patients will have tumour recurrence and 80% of these patients will die from their disease. Currently women with ovarian GCTs receive similar treatment as those with epithelial ovarian cancer, but given the unique biology of granulosa cells, GCTs are likely to respond differently to the more common epithelial ovarian tumours. Alternative GCT-specific treatments and prognostic markers are needed if outcomes are to be improved. The aim of this thesis was to characterise the role of oestrogen receptor ß (ERß) in ovarian granulosa cell tumours, in order to determine its potential as a GCT-specific prognostic marker and treatment target. Specific objectives were: to investigate the hypothesis that ERß inhibits cell proliferation in the ovarian GCT-derived cell lines COV434 and KGN-T, and to determine what genes and gene pathways are uniquely expressed in ovarian granulosa cell tumours compared to other ovarian cancers. ERß has been identified as a potential tumour suppressor in many human malignancies, and its effect on proliferation in two GCT-derived cell lines was studied with the aid of an ERß-specific agonist, diarylpropionitrile (DPN), and by silencing expression of ERß using small interfering RNAs (siRNA). Treatment of the GCTderived cell lines with DPN inhibited growth, and silencing expression of ERß with siRNA resulted in a significant increase in cell proliferation.

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  • Caesarean birth: too posh to push, or punished for not pushing? Exploring women's experiences of caesarean birth

    Taylor-Miller, Leanne (2010)

    Doctoral thesis
    The University of Auckland Library

    Caesarean birth is the mode of delivery for almost a quarter of births in New Zealand (NZ), and as the rate steadily rises, the expectation of a “natural birth” remains ubiquitous in society. Research investigating the impact of caesarean birth has previously demonstrated mixed findings regarding psychological outcomes, and recently caesareans have become topical with the addition of the idiom “too posh to push” to our lexicon. This implies that caesarean is an easy option, and may have shaped a sense of stigma against caesareans, particularly elective caesareans. The previous research demonstrating differences in psychological outcomes between planned and unplanned caesareans was conducted when caesarean birth was less common, and tended to be quantitative in design. The purpose of this qualitative research was to investigate the experiences of 32 women, including both first-time and non-first time mothers, who have undergone caesarean birth, half planned and half unplanned, in order to gain insight into their perceptions of their experiences and identify aspects that contributed to positive and negative experiences. Semi-structured interviews were used to explore their perceptions, including how they and others have reacted to their caesarean experience. These interviews were analysed using thematic analysis to identify themes to help to understand their experiences. This research supported a number of previous findings regarding caesarean birth including increased rates of induction associated with caesarean birth; differences in initial interaction between mother and infant for planned or unplanned caesareans; trust in medical experts; low occurrence of 'maternal' request for caesarean; and perceptions of societal attitudes towards caesarean. In addition, this research identified themes regarding the roles of expectations and preferences with the actual caesarean or breast feeding experience, influenced by individual and social factors. Negative outcomes were associated with a lack of reconciliation between actual experience, expectations and preferences; while positive outcomes were associated with effective reconciliation, through the development of rationales, applied both prospectively and retrospectively.

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  • Novel Statistical Methods For Analysing Proteomic And Clinical Data Associated With Pregnancy-Related Diseases

    Wu, Steven (2010)

    Doctoral thesis
    The University of Auckland Library

    The SCOPE (Screening for Pregnancy Endpoints) Project is a large scale international project which aims to screen first time mothers for pregnancy-related diseases. Several statistical methodologies have been developed to address issues associated with large datasets in the SCOPE project. Two dimensional polyacrylamide gel electrophoresis (2D PAGE) is used to identify differentially expressed which may be applied to biomarker discovery. A limitation of 2D PAGE is the inability to detect proteins if its expression level falls below the limits of detection. A likelihood model was proposed to address this issue by incorporating a mixture model which takes into account both detected and non-detected proteins. Simulation analyses showed that the likelihood model has higher statistical power than the standard statistical analyses. A global Bayesian model extended from the likelihood model was proposed which is able to identify groups of differentially expressed proteins simultaneously. Several global distributions are used to model the underlying relationship between individual spot parameters and these parameters are estimated by Markov chain Monte Carlo (MCMC) technique. The simulation analyses showed that the global model is able to accurately recover the underlying global distributions and identifies more differentially expressed proteins than the likelihood model. Several prediction models for uncomplicated pregnancy and preeclampsia were constructed using the clinical features in the SCOPE database. These models were constructed using either logistic regression or linear discriminant analysis with various variable selection procedures. Most of the clinical risk factors that the model selected had previously been reported in other studies. The performance of the models was measured by the area under the Receiver Operating Characteristic curve and there were no significant differences between these models. Two versions of hierarchical prediction frameworks were proposed which attempted to boost the accuracy of the prediction. A different disease endpoint was classified at each stage and different sets of variables were used for each stage of the hierarchy. The structure of the hierarchical framework was predetermined based on the clinical relationship between these disease endpoints. Despite partitioning the database, there were no significant improvements to the prediction performance over the non-hierarchical model.

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  • Simulation, Fabrication, and Control of Biomimetic Actuator Arrays

    O'Brien, Benjamin (2010)

    Doctoral thesis
    The University of Auckland Library

    Ctenophores are small sea creatures that achieve propulsion using thousands of locally controlled ciliated paddles. The human heart is a flexible network of actuators coordinated with electro-chemo-mechanical waves of contraction. Stomata are self-controlling variable apertures that work together to solve the gas exchange problem for plants. It can be seen that flexible networks of actuators coordinated using distributed intelligence and sensing provide robust and adaptable performance in the face of complex and varied challenges. This thesis aims to create networks of flexible actuators with distributed sensitivity and intelligence that realise the robust and adaptable performance seen in nature. Dielectric Elastomer Actuator(s) (DEA) were identified as ideal for achieving this goal, however, their implementation into biomimetic arrays was limited by a lack of modelling tools for engineering design; the fact that DEA self-sensing has never been used to underpin a control strategy; and rigid and bulky sensor, logic, and driver circuitry. The objectives of this thesis were to overcome these three problems: Firstly, a novel low degrees-of-freedom modelling approach was developed and experimentally validated using dielectric elastomer minimum energy structures. The approach was rapid and robust and applied as a virtual experimentation tool where it reduced prototype development times by an order of magnitude. Secondly, biomimetic distributed control using capacitive self-sensing was explored and applied to a variety of DEA arrays including a ctenophore inspired mechano-sensitive artificial cilia array. Actuator coupling, multilevel control, travelling waves of actuation, and performance under partial failure were explored. Finally, Dielectric Elastomer Switch(es) (DES) were invented. DES enable distributed sensor, driver, and logic circuitry to be integrated directly into a biomimetic array and substantially reduce the need for rigid, heavy, and expensive external circuitry. DES were used to create NAND gates, smart oscillator circuits, and memory elements. These contributions have led to two journal articles, three conference papers, two provisional patent applications, and should substantially accelerate progress towards the development and control of large scale biomimetic actuator arrays. Future work involves applying modelling and control techniques to micro-scale systems and developing DES applications, materials, and fabrication techniques further.

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  • Ecological and dendrochronological studies on Agathis australis Salisb. (kauri)

    Ahmed, Moinuddin (1984)

    Doctoral thesis
    The University of Auckland Library

    Quantitative stand descriptions, multivariate analyses, population structures and dendrochronological aspects of kauri were explored during the present studies. Twenty-five stands of mature kauri, throughout its natural range, were sampled by the point-centred quarter (p.c.q.) method and described separately. Multivariate data on density, basal area and frequency were then subjected to TWINSPAN (a polythetic method of classification) and DECORANA (detrended correspondence analysis ordination). On the basis of these analyses four overlapping kauri forest types were recognised. No significant correlation occurred between stand groups (defined by TWINSPAN and DECORANA) and dendrochronological attributes. This implies that the vegetation composition of stands does not provide information about dendrochronologically sensitive sites. Density, basal area, frequency and size class distribution provided information about the structure of the kauri population in each stand. The study suggests that kauri does not compete with associated canopy species in its later life. Regeneration gaps were not evident in mature kauri forests, indicating that they are not unstable. These characteristics increase the suitability of kauri for tree-ring investigations. Structural variability is related to variability in growth rate and age and these are discussed for various kauri forests. Dendrochronological methods were applied to 19 kauri stands, and dated chronologies (with maximum period from 1580 to 1981 AD) from eight sites were obtained. Ring-width sequences of cross-matched sites were standardised using INDEX and the various chronology and sample statistics are discussed. These chronologies show from 20 to 35 percent common chronology variance ('Y' in ANOVA; due to climate). Noncross-matched sites were treated the same way for comparison. It is indicated that high sensitivity does not reflect dendrochronological suitability unless the cores are properly cross-matched, and this emphasizes the need for better site selection and cross-matching techniques in forests such as those in New Zealand. Highly significant correlations (P<.001) between dated chronologies (from 1790 to 1976 AD) and similar patterns of correlation between cores among various sites suggested that all sites were influenced by similar climatic factors. A master chronology was constructed, but found to be less useful than the separate chronologies. It is concluded that north-facing, steep slopes are most suitable for tree-ring studies. These were the only sites from which dated chronologies were developed; other sites showed various problems which are discussed. Kauri growth-climate relationships were evaluated by running various types of response functions. Seventy four response functions are presented and their results are discussed. Variance due to climate ranged from 21 to 53 percent, and is comparable with other studies in New Zealand. Overall, in all sites growth-climate response is similar; at the beginning and end of the growing season low rainfall promotes growth while in the middle of the growing period it may reduce growth. It is concluded that, despite the limitations discussed, these results may be used in dendroclimatic reconstruction.

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  • Does early exercise affect the midcarpal joint of young Thoroughbreds? An investigation into the influence of exercise on lesion prevalence, matrix swelling & histomorphometric changes in the cartilage and subchondral bone of the equine midcarpal joint.

    Kim, Woong (2010)

    Doctoral thesis
    The University of Auckland Library

    The aim of this investigation was to investigate the possible influence of early conditioning exercise on the 18-months old Thoroughbreds in terms of lesion development, extracellular matrix and histomorphometric changes in the cartilage and subchondral bone of the midcarpal joint. 12 Thoroughbreds were divided equally into two groups; a treatment (CONDEX) and a control group (PASTEX) at birth. Both were raised in free pasture conditions from birth for 18 months before euthanasia with the CONDEX only receiving the additional imposed exercise from birth. At the end of the trial, both the CONDEX and PASTEX horses were euthanized and their midcarpal joints were harvested. The investigation involved i) mapping and characterising the gross lesions in the midcarpal joint with respect to known sites of high stress and vulnerability, ii) measuring swelling strains in the cartilage matrix with respect to depth from different topographical regions, iii) histomorphometrically quantifying the area and thickness of hyaline and calcified cartilage and vasculatures, while also measuring the preferential angles of the collagen fibrils in these zones, and counting the number of vascular channels proximal to the cement line as well as measuring the cement line irregularity itself. Both the CONDEX and PASTEX were found to contain five different categories of lesions with similar levels in each category. However, the number of sites affected by mild traumatic osteochondrosis was lower in the CONDEX. There was no detectable exercise effect in the extracellular matrix swelling behaviour (P = 0.795) and neither was the overall histomorphometry (P = 0.4271). Conversely, in the CONDEX, the vascular channel area (VCa) showed a significant exercise effect (P = 0.0461) while the histomorphometric variables were found to be highly correlated to each other (P = 0.052). These findings suggest that the imposed early exercise may have resulted in a lower number of mild osteochondrosis lesions in the dorsal region of third carpal bone while significantly increasing the overall subchondral vascular activity and the development of a coherent tissue response between the hyaline cartilage, calcified cartilage and the vascularity. In conclusion, the findings of this study together with those of others [1-3] suggest that early exercise induced a positive response in the CONDEX without increasing deleterious changes in the midcarpal joint when compared with the PASTEX. It is thus recommended that potential benefits of early exercise should be further explored.

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  • Wood-decaying Fungi and Beetles: A Multilateral Approach to Studying Fungus-insect Communities

    Kadowaki, Komei (2010)

    Doctoral thesis
    The University of Auckland Library

    Fungus-insect interactions permeate through the intricate tapestry of terrestrial ecosystems, but remain a persisting mystery in ecology. The wood-decaying basidiomycete Ganoderma produces perennial sporocarps (fruiting bodies) that provide food (spores) and habitat (hymenial surface) for three endemic beetles; Zearagytodes maculifer (Leiodidae) and two Holopsis species (Corylophidae) that occur in sympatry in the Waitakere Ranges, Auckland, New Zealand. Ganoderma spore release from individual sporocarps undergoes density fluctuations of two orders of magnitude that are neither clearly associated with temperature and humidity nor spatially synchronous. Such resource dynamics did not exert a strong effect on spore-feeding beetles since they use a minute percentage of spores discharged from the hymenial surface and are therefore not resource-limited. Competition at sporocarp patches is pervasive in the beetle community, as beetles range over a restricted area on the hymenial surface to feed and are likely to be space-limited. The three spore-feeding beetles display different host specificity, spore consumption patterns, dispersal behaviour, and seasonality. Remarkably, the two Holopsis species differ in their ontogenetic niches. The long rostrum of Holopsis sp. 1 gives it competitive superiority. All these factors combined to create a complex competitive network among the three species, but competitive coexistence is likely to occur as Z. maculifer and Holopsis sp. 2 evade competition with Holopsis sp. 1 via different colonisation strategies across sporocarp patches. There was no evidence for a fungus-insect mutualism: Z. maculifer does not disperse Ganoderma spores as passage through the beetle gut destroyed the spores and virtually none germinated. Altogether, the unique lifestyles of spore-feeding beetles "living on the surface" in long-lasting, exposed habitats dictate much of this tiny but extraordinary ecosystem of the fungus-insect community, characterised by the structuring forces of weak fungus-insect interactions and strong insect competition.

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  • Rates of Molecular Evolution and Phylogenomic Inference

    Li, Wai Lok (2010)

    Doctoral thesis
    The University of Auckland Library

    Genome studies have become an integral aspect of modern biology. As a result, there has been a need for methods to analyse genomic data. One aspect of genomic research is the analysis of variation in rate of evolution, both across a genome and between the genomes of species. In this study we explore the relationship between different types of rate heterogeneity. We develop several statistical methodologies to address issues associated with the phylogenomic analysis of genomic data. Developments were made to the area of lineage-specific variation in evolutionary rates, with improvements in more efficient computational implementations of relaxed molecular clock models and the proposal of new models of rate changes across branches. The practical application of relaxed molecular clock models was further examined with the proposal of methods of model averaging and model selection for relaxed molecular clock models using Bayesian stochastic search variable selection. Results show that our method identifies the most appropriate model for the underlying distribution of rates across branches in both simulated and real data. Our method of model averaging is particularly useful for preventing poor inference when the correct model is not known. We examined the correlation in rates of substitution between functionally related genes that are caused by co-evolution of genes. Previously, this correlation was thought to only exist between genes with physically interacting gene products. We demonstrate that these correlations are not limited to genes with protein interactions but often extend to functionally related genes. Such patterns of co-evolution are of concern for the multi-gene analysis of genomic data and how species distances are estimated. Finally, an attempt was made to develop a high-throughput method for detecting lineage-specific selection through identifying changes in rate of substitution. Results on simulated data indicate that our method had some success in characterising the variation in rate which occurs as a consequence of selection. Our methods were shown to provide significant speed benefits towards phylogenomic analyses. The outcome of this research has been a progression in methodologies for phylogenomic analysis. Computer software has been developed to allow these methods to be used for understanding rate variations on a genomic scale.

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  • 'All in a day's work' The lifeworld of older people in New Zealand rest homes

    Kiata-Holland, Elizabeth (2010)

    Doctoral thesis
    The University of Auckland Library

    This doctoral thesis contributes to critical gerontology research by investigating the lived experiences of residents in the everyday world of New Zealand rest homes. There is a need to understand how frail rest home residents experience "age". This study focuses on describing and understanding residents lived experiences. As the New Zealand population is ageing, this phenomenological focus adds clarity to the poorly understood lived experiences about being aged in rest homes. Policy initiatives such as the Positive Ageing Strategy with its emphasis on keeping older people living in the community largely ignore the life practices of the increasing proportions of frail older people who require long-term residential care. My mixed-methods modified framework approach draws on the lifeworld as understood by Max van Manen (1990) and Alfred Schütz (1972). The lifeworld is made up of thematic strands of lived experience: these being lived space, lived time, lived body and lived relations with others, which are both the source and object of phenomenological research (van Manen, 1990). These strands are temporarily unravelled and considered in-depth for 27 residents who took part in audio-recorded interviews, before being interwoven through a multiple-helix model, into an integrated interpretation of the residents‟ lifeworld. Supplementing and backgrounding the interviews with these residents, are descriptive data including written interview summaries and survey findings about the relationships and pastimes of 352 residents living in 21 rest homes, which are counted and described. The residents day-to-day use of rest home space, mediated temporal order, self-managed bodies and minds, and negotiated relationships are interpreted. The mythology of the misery of rest home life is challenged, and a more constructive critical gerontology approach is offered. Findings of this research reveal how meanings around daily work practices are constructed by the residents. These elders participate in daily rest home life, from the sidelines or not at all, as they choose or are able, and this always involves work for the residents. They continue to actively manage satisfactory and fulfilling pastimes and relationships, because in their ordinary, everyday lifeworld it is “all in a day‟s work”.

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  • Synthetic Studies Towards Berkelic Acid

    Wilson, Zoe (2010)

    Doctoral thesis
    The University of Auckland Library

    This thesis describes the synthetic endeavours towards berkelic acid, an extremophile derived bioactive natural product. Penicillium sp. Pitna 4 is a fungus isolated from Berkeley Pit Lake, a metal laden, pH 2.5 lake which formed when an abandoned copper mine in Butte, Montana filled with infiltrating ground water. Berkelic acid is one of several bioactive natural products isolated from this unlikely source and has been found to have desirable selective activity against the ovarian cancer cell line OVCAR-3, as well as inhibitory activity against caspase-1 and matrix metalloprotease-3. Synthetic access to this molecule is highly desirable due to its bioactivity and novel tetracyclic structure as well as the fact that the planned bioremediation of Berkeley Pit Lake may eliminate its natural source. The synthetic studies undertaken have focused on developing a flexible strategy for the synthesis of berkelic acid that allows for future modification to structure to allow investigation of biological activity. The strategy is based on the use of a novel one-pot Horner-Wadsworth-Emmons/oxa-Michael cascade to couple two advanced intermediates – a phosphonate and a lactol. A final deprotection/spiroketalisation step then furnishes the spiroketal moiety. Careful functional group manipulations and key introduction of chirality were pivotal in the successful synthesis of a series of coupling partners which allowed the successful synthesis of a series of tricyclic analogues of berkelic acid as well as the entire tetracyclic core, with and without full substitution on the aromatic ring. The formal total synthesis of berkelic acid faltered at the penultimate step, but this project has none the less established a sound approach to this molecule which will build the foundations for a future total synthesis.

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  • Parallelisation of desktop environments

    Giacaman, Nasser (2010)

    Doctoral thesis
    The University of Auckland Library

    The objective of this research was to investigate the parallelisation of desktop environments in light of multi-core processors becoming mainstream. In contrast to the parallelisation of typical high performance computer applications, parallel computing for desktop applications involves further challenges. Although improving performance is the primary aspect of parallel computing, a vital focus of this research was on the software engineering approach. In particular, this included developing an object-oriented solution to desktop parallelisation. To address these issues, two concepts were developed in this research. The first concept, the Parallel Iterator, is an object-oriented solution for data parallelism. The Parallel Iterator is the parallel extension to the standard sequential iterator, to support parallel traversal of elements in an arbitrary collection. The second concept, Parallel Task, is an object-oriented solution for task parallelism. An important design aspect of Parallel Task was its semantic integration with the structure of typical desktop applications. Both of these concepts have been successfully implemented. The solutions provide ease of use by following familiar programming approaches and encapsulating parallelisation details away from programmers. The results for both the Parallel Iterator and Parallel Task concepts show superior performance compared to standard parallelisation approaches. This research has made a vital contribution to parallel computing on mainstream desktop systems. By identifying challenges specific to the parallelisation of desktop applications and their current structure, the concepts developed are in line with object-oriented programming and the software engineering approach. The concepts and tools developed not only ease the programming effort, but also enhance the user's desktop experience by promoting responsive and interactive applications.

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