14,602 results for Doctoral

  • The Epidemiology of Cervical Cancer in Ghana

    Nartey, Yvonne (2017)

    Doctoral thesis
    University of Otago

    INTRODUCTION: Cervical cancer is a significant health issue worldwide. It is the fourth most common cancer among women with more than 85% of new cases of the disease occurring in low- and middle-income countries. Cervical cancer is the most common cancer among women in Ghana. Incidence and mortality rates are unknown due to an absence of a national-based population cancer registry. HPV positivity has been shown to be a necessary initiator of cervical cancer but the infection progresses to cancer only in a small number of women. Cofactors associated with the disease progression are not well understood. The study was designed to assess the epidemiology of cervical cancer in Ghana. AIMS: • Estimate the regional cervical cancer incidence and mortality using data from two large referral hospitals in Ghana. • Use results from the above study to estimate national incidence and mortality rates of the disease. • Estimate the 1, 3 and 5 year disease-specific survival rates of Ghanaian women diagnosed with invasive cervical cancer. • Determine the HPV DNA prevalence and prevailing HPV types present in Ghanaian women with and without cervical cancer. • Determine the associations between cofactors and a woman’s risk of developing cervical cancer in Ghana. METHODS: Medical records and other hospital data of women diagnosed with cervical cancer from January 2010 to December 2013 were reviewed at Korle-Bu Teaching Hospital, Accra, and Komfo Anokye Teaching Hospital, Kumasi, in Ghana. Telephone interviews were also conducted for patients and relatives to gather further information. To assess the risk factors for cervical cancer in Ghana, a hospital-based case-control study was undertaken. Women aged 18-95 years with a new diagnosis of invasive cervical cancer that had been histologically confirmed were considered for inclusion as cases. Controls were a random selection from the same hospitals as the cases. A structured questionnaire was administered to the women after which a request for a cervical smear was made for the reporting of cytological abnormalities and laboratory detection of HPV DNA to establish the HPV types present. RESULTS: Using the data from review of medical records and telephone interviews, the incidence, mortality and survival rates of women diagnosed with invasive cervical cancer in Ghana were estimated. An increased risk of cervical cancer with age was found. The incidence rate of cervical cancer was highest for women aged 75-79 years and decreased at older ages. Incidence and mortality rates were higher in the Greater Accra and Ashanti regions of Ghana than for other regions. At three years from diagnosis, overall disease-specific survival was 39%. Unsurprisingly, stage at presentation and histological type were strong predictors of cervical cancer survival. Some forms of treatment were also associated with better survival than others. A total of 206 women with incident cervical cancer and 230 controls were recruited for the case-control study to identify possible risk factors and cofactors for cervical cancer in Ghana. The results of the case-control study confirmed many known established risk factors associated with cervical cancer. These included age, an increased number of pregnancies, higher parity and oral contraceptive use. In addition, use of firewood for cooking, use of homemade sanitary towels and having a polygamous husband was associated with an increased risk of cervical cancer in this study after adjustment for the presence of highest oncogenic HPV types. High prevalence of HPV was detected among women with cervical cancer (80.1%). HPV types 45, 16, 18, 35 and 52 were the most common types detected among cases. Knowledge of HPV and cervical cancer was very low overall among women with and without cervical cancer. CONCLUSIONS: In addition to the presence of high-risk oncogenic HPV DNA, parity and oral contraceptive use was associated with an increase risk of cervical cancer in Ghana. The results of the research suggest that the identification of factors associated with the progression of HPV positivity to invasive cervical cancer may help reduce the burden of cervical cancer in Ghana. In addition, the development of a cancer control programme that takes into consideration the social and cultural factors for the prevention, early detection and diagnosis, treatment and palliative aspects of cervical cancer is needed to combat the disease.  

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  • Exploring undergraduate students’ perceptions of factors influencing their engagement and alienation in higher education

    Asare, Samuel (2017)

    Doctoral thesis
    University of Otago

    Student engagement has been identified as having a positive influence on learning and retention. This has attracted much research on how to enhance engagement in higher education. Studies have considered the role of student motivation and various environmental factors that affect engagement. However, these studies are concentrated in Western countries including US, Canada, UK, Australia and New Zealand. The few done in Africa have been in South Africa. Drawing on Mann’s (2001) framework of engagement and alienation, this study explores undergraduate students’ perceptions of factors influencing their engagement and alienation in a public university in Ghana. The study adopted a case study design underpinned by an interpretive approach to provide a broad and in-depth understanding of how student motivation interacts with factors relating to teachers, family and peers to produce engaged and alienated experiences. Three data sources were drawn upon in this study: survey, diary and interview. The survey included 469 Humanities students selected by quota sampling from main campus, city campus and distance learning across all year levels. Of the 469 students surveyed, 225 agreed to keep a diary of their learning experiences for two days and participate in a one-on-one interview. Purposive sampling was used to select 17 students for diaries and interviews by considering both male and females, year of study, mode of study (distance learning, city campus and main campus) as well as respondents’ availability for interviews. This ensured that data were collected from a wide range of perspectives. The analysis was in two forms. First, survey data were analysed with Statistical Package for the Social Sciences (SPSS) to find percentages and means of the responses. In addition, ANOVA (Analysis of Variance) and t-tests were conducted to determine any differences among students’ perceptions at the time of the survey. In some instances, where there were differences, a post hoc test was conducted to determine which groups were different from each other. Second, data from diaries and interviews were analysed using the general inductive approach to develop themes relating to the objectives of the study. The analysis was guided by a framework that highlighted students reported engaged and alienated experiences. The study resulted in a new conceptual framework that brings the various parts of the findings together. This study suggested that students’ need for belonging, competence and autonomy spurred them on to invest more time and effort in their learning. However, autonomy and belonging had different influences depending on the year of study. First year students reported the highest level of influence compared with students of other year levels. Engagement was influenced by students’ desire to achieve goals: to be knowledgeable; for postgraduate study; and to gain a high-paying job. In addition, students reported engaged and alienated experiences resulting from four teacher factors: level of knowledge; teaching approaches; relationships with students; and support. Also, almost all students received support from their family and most of them thought that family support had a lot of influence on their engagement. Engagement was influenced by financial and social support as well as the monitoring of their academic performance by their parents. Interactions with peers influenced engagement in academic and social ways. For instance, students shared learning material such as textbooks, lecture notes and computers. Furthermore, students reported improved self-confidence and a better understanding of their subject by interacting with their peers in formal and informal contexts. Despite the positive influence of peers, a small number of students reported feeling pressured by their peers to spend most of their study time partying, and some members not contributing during group study. The findings add an alternative voice to the growing literature on student engagement by presenting data from a context that has not been explored in this way before. It has shown the usefulness of engagement and alienation as a framework to investigate students’ learning in higher education. The few existing studies that have applied the framework did not analyse data as has been done in this study. Thus, this study has provided new insights. In addition, the findings revealed that students have the desire to work hard to achieve their goals, but these desires will need positive contributions from the environment to achieve much results. Summarising, the implications of the findings include the need for higher education institutions to invest in teacher professional development and to seek ways to collaborate with families of students who may be struggling academically, to enhance their engagement.

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  • Three Essays on Equity, Volatility and Commodity Derivatives

    Xu, Yahua

    Doctoral thesis
    Auckland University of Technology

    This thesis provides a comprehensive study on option markets, with a focus on Leveraged Exchange Traded Fund (LETF) options, volatility options and crude oil options. Study of LETF option market is carried out using a parametric framework. A stochastic volatility framework for the LETFs is proposed and a systematic pricing formula for options on equity and volatility LETFs is further developed by employing Fast Fourier Transform (FFT). In contrast, research on volatility and crude oil option markets is conducted under a nonparametric framework. We extract variance and skew risk premiums from VIX options, which the first study on higher moment risk premiums for the volatility market and explains how they are related to VIX index returns as well as to S&P 500 index returns. When analysing higher moment risk premiums in the crude oil market, we decompose the risk premiums conditional on the market return sign. One key finding is that the decomposed risk premiums contain more predictive information about market excess returns. All the results contribute to a better understanding of the option market, and provide comparison with equity market.

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  • Healthcare-seeking behaviour for sexually transmitted infection testing in New Zealand: A mixed methods study

    Denison, Hayley (2017)

    Doctoral thesis
    Victoria University of Wellington

    Sexually transmitted infections (STIs) are a global public health problem. Sequelae for infected individuals can be serious and STIs impose a substantial financial burden on healthcare systems. Duration of infection is one factor influencing transmission rates, and is modifiable through secondary prevention methods, namely ‘test and treat’. For this approach to be effective, at-risk individuals must choose to present for testing. New Zealand provides a useful case-study to investigate healthcare-seeking behaviour for STI testing, as incidence rates of common STIs are especially high. The aims of this thesis were to quantify healthcare-seeking behaviour for STI symptoms and assess the risk of transmission in this period, to identify the barriers to STI testing, to understand the personal drivers for getting an STI test, to examine how STI knowledge is associated with testing behaviour, and finally, to collate and critically evaluate the published evidence regarding the incidence of a lesser known sequela of STI, reactive arthritis. This thesis took a mixed method approach, employing both qualitative and quantitative methods to address the research aims. The results showed that delays in healthcare-seeking for STI symptoms were common among patients attending an inner-city Sexual Health Clinic (SHC). Almost half of people with symptoms waited longer than seven days to seek healthcare, although there were no identified predictors of delayed healthcare-seeking. Around a third of people with symptoms continued to have sex after they first thought they may need to seek healthcare. Among these individuals, infrequent condom use was reported more by those who had sex with existing sexual partners than by those who had sex with new partners. Having sex while symptomatic was statistically significantly associated with delaying seeking healthcare for more than seven days (odds ratio (OR) = 3.25, 95% CI 1.225 – 8.623, p = 0.018). Analysis of qualitative interview data revealed three types of barriers to testing. These were personal (underestimating risk, perceiving STIs as not serious, fear of invasive procedure, self-consciousness in genital examination and being too busy), structural (financial cost of test and clinician attributes and attitude) and social (concern of being stigmatised). This work also revealed several drivers for testing including crisis, partners, clinicians, routines, and previous knowledge. Knowledge of the incidence, asymptomatic nature and sequelae of STIs featured prominently in the explanations of those who undertook routine testing. However, at the same time, many of the participants felt they did not have a good knowledge base and that their school-based sex education had been lacking. STI knowledge was investigated further using quantitative methodology. Levels of STI knowledge were generally good and did not differ between a Student Health Service population and an SHC population. Individuals who had tested before had significantly better knowledge than those who were attending for testing for the first time (U = 10089.500, Z = -4.684, p < 0.001). In addition, total knowledge score was an independent predictor of having had a previous test (OR = 1.436, 95% CI 1.217-1.694, p < 0.001). Reactive arthritis can be triggered by STI, thus STI screening patients who present with reactive arthritis has the potential to identify undiagnosed infection. This thesis provides the first assessment of the international literature regarding the incidence of reactive arthritis after STI. The systematic review found only three published studies which had prospectively examined the incidence of reactive arthritis after STI. The studies reported an incidence of reactive arthritis after STI of 3.0% to 8.1% and were found to be of low to moderate quality. In conclusion, this thesis provides healthcare service providers, policy makers and clinicians with data to inform practice and public health interventions aimed at improving healthcare-seeking behaviour for STI testing. It illustrates that delayed healthcare-seeking for STI symptoms is a common behaviour in New Zealand and could potentially be contributing to STI transmission and downstream burden on the health system. This work provides evidence of the drivers of STI testing that can be promoted, and the barriers that need to be removed. Specifically, improving STI knowledge may positively impact on testing rates. Lastly, this research indicates that there is a need for more studies assessing the incidence of reactive arthritis after an STI.

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  • Becoming aware: A study of student teachers' personal and professional values

    Vermunt, Jenny (2017)

    Doctoral thesis
    University of Otago

    Student teachers’ personal and professional values have received passing attention in the educational literature, despite assertions that their values influence their perceptions, pedagogical decisions and actions. This study explores the professional learning of a sample of secondary student teachers. It aims to understand the role played by their personal and professional values while they participate in a year-long initial teacher education programme. Framed by social constructivist and interpretivist theory, this qualitative study uses semi-structured interviews and journal entries to capture the perspectives of five secondary student teachers about their learning-to-teach experiences. Constant comparative data analysis methods are used to reveal patterns of themes within and across the five case studies. Findings from the research reveal that personal and professional values underpin the learning and teacher identity of student teachers in the sample. They are influenced by values and experiences in their families and communities, and their core values are behind their sense of purpose, awareness and resilience. Findings reveal how professional values and structures at play in school organisations conflict or align with their own personal and professional values and impact on their commitment to the profession. The research shows that student teachers vary in the opportunities they are afforded in university and school environments to participate in critical dialogue in communities of practice that develop their self-awareness, acquisition of professional values and understanding of their contexts. The study concludes by proposing a model of personal and professional learning that aims to develop student teachers’ critical reflection and awareness of the impact of their personal and professional values when learning to teach.

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  • The Nutritional Implications of Partner Switching in the Cnidarian-Dinoflagellate Symbiosis

    Matthews, Jennifer (2017)

    Doctoral thesis
    Victoria University of Wellington

    Reef-building corals form a symbiosis with phototrophic dinoflagellates of the genus Symbiodinium. Specificity in the host-symbiont partnership is widespread, despite the potential for flexibility in endosymbiont community composition to provide a mechanism of environmental acclimatisation and adaptation. The potential for partner switching may be linked to the nutritional flux between the two partners, with optimal nutritional exchange determining success. Further research is therefore necessary to determine how novel symbiont types (i.e. not originally detected in the host) affect the nutritional biology of the cnidarian host, and ultimately the capacity for the evolution of novel associations in the cnidarian-dinoflagellate symbiosis. The specific objectives were: 1) to design an effective method of providing aposymbiotic host organisms for experimental symbiont colonisation studies; 2) to determine how colonisation with a novel symbiont affects the gene-to-metabolite response of the host; 3) to deduce how the quantity and identity of translocated photosynthetic products from symbiont to host is affected by the symbiont type; 4) to determine whether natural differences in the Symbiodinium community composition affect the metabolite profile of the same cnidarian host. Chapter 2 demonstrates that menthol-induced bleaching effectively and efficiently provides experimental aposymbiotic (i.e. symbiont-free) sea anemones (Aiptasia sp.) for colonisation studies. The menthol treatment produced aposymbiotic hosts within just 4 weeks (97–100% symbiont loss), and the condition was maintained long after treatment when anemones were held under a standard light:dark cycle. The ability of Aiptasia to form a stable symbiosis appeared to be unaffected by menthol exposure, as demonstrated by successful reestablishment of the symbiosis when anemones were experimentally re-colonised with the homologous Symbiodinium (i.e. originating from the same host species). Furthermore, there was no significant impact on photosynthetic or respiratory performance of re-colonised anemones. A novel application of statistically integrated transcriptomic and metabolomic analyses was applied in Chapter 3 to explore the molecular and metabolic pathways underlying symbiosis specificity in the cnidarian-dinoflagellate symbiosis. Aposymbiotic individuals of the sea anemone Aiptasia generated by the methods optimised in Chapter 2 were colonised with either the homologous Symbiodinium type B1 or the novel Symbiodinium type D1a. RNA-seq gene expression analysis and gas chromatography-mass spectrometry-based metabolite profiling were conducted on the isolated host tissues. Analysis of the gene and metabolite expression profiles revealed that a novel symbiont confers an expression pattern intermediate between hosting a homologous symbiont, and having no symbiont. Although the formation and autotrophic potential of the novel association was similar to the homologous association, as determined by O₂ flux measurements, the novel association resulted in an increase in the catabolism of metabolic stores (glycogen, lipid and protein), presumably in order to meet the energy requirements associated with the maintenance of cellular homeostasis. Integrated pathway analysis revealed reduced energy storage, an increased catabolism of stores, metabolic signalling and cellular redox homeostasis were molecular processes involved in the hosts’ response to a novel symbiont type. This raised interesting questions as to how differences in the composition of symbiont-derived metabolites might feature in the specificity of the symbiosis. Metabolite profiling was subsequently coupled with ¹³C-labelling in Chapter 4, to identify the specific differences in the identity and quantity of photosynthetic carbon products translocated to the Aiptasia host when in symbiosis with the novel Symbiodinium type D1a versus the homologous Symbiodinium B1. A reduction in the diversity and quantity of net translocated products was observed in the novel association, despite achieving a similar autotrophic potential to the homologous association, as determined by O₂ flux measurements. Interestingly, however, there was a continued fixation and translocation of carbon products to the host, suggesting that novel associations are, at least in part, metabolically functional in terms of photosynthate provision. Nevertheless, the decreased diversity and abundance of translocated products were associated with modifications to biosynthesis, increased catabolism of host energy stores, and oxidative stress-related signalling pathways in hosts colonised with the novel Symbiodinium type D1a.The impact of symbiont type on the host’s metabolite profile in an experimental setting raised the interesting possibility that the metabolite profiles of a cnidarian that forms natural flexible associations with different Symbiodinium types may also have dissimilar metabolite profiles, with implications for the nutritional physiology of the symbiosis. This was tested in Chapter 5. An in situ field survey of the metabolite profiles of Montipora capitata, a dominant reef-building coral in Hawai’i that forms homologous symbioses with Symbiodinium in clades C and clade D, revealed the metabolite pools of a coral host were not affected by Symbiodinium community composition. Given prior evidence that clade D can be less nutritionally beneficial to the coral host than some other symbiont types, the reasons for the similarity in metabolite profiles remains unclear. However, possible explanations are: 1) host heterotrophic compensation for the presence of a less beneficial symbiont; 2) modifications to the abundance and identity of metabolites exchanged in the symbiosis, perhaps via host selection of its symbiont community over time to provide an optimal state; or 3) adjustment to the host’s metabolic pathway activity in response to different host-symbiont interactions, that produces similar free-metabolite profiles in the host. Nevertheless, this served to highlight that a coral host in a naturally flexible association, and under ‘normal’ environmental conditions, may maintain a steady metabolite profile irrespective of its Symbiodinium community composition. Notably, this contrasts with the findings that heterologous symbionts (i.e. those not usually associated with a particular host species) may have negative nutritional implications for the host that could ultimately restrict the success and persistence of novel host-symbiont pairings. This study provides important evidence that optimal nutritional exchange and mechanisms of coping with oxidative stress in both partners are important determinants in the evolution of novel cnidarian-dinoflagellate symbioses. However, it also raises the possibility that such novel pairings, should they persist, may evolve over time to a more beneficial symbiotic state; this is worthy of further study. Indeed, we need to continue our efforts to understand the molecular and physiological mechanisms underpinning the adaptation of the cnidarian-dinoflagellate symbiosis to climate change, to facilitate the development of robust management strategies to safeguard the world’s coral reefs.

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  • Drifting 3D Underwater Wireless Sensor Networks for Pollution Monitoring

    Ren, Yu (2017)

    Doctoral thesis
    Victoria University of Wellington

    Increasing demands by a growing population for food and oil have resulted in synchronous rises in the past 40 years of aquaculture and offshore oil drilling. Growth in these industries has highlighted the potential crippling impacts of coastal pollution, with marine farms likely to be susceptible to damage from harmful algal blooms and oil platforms to cause oil spills, as headlined by the 2010 Deepwater Horizon incident in the Gulf of Mexico. Drifting underwater wireless sensor networks (UWSNs) represent a technology that can greatly enhance our understanding of such processes. Consisting of a swarm of untethered sensor nodes, an UWSN can be deployed over a large segment of the feature. The feature is carried through to different positions by underwater currents, the nodes, also drifting with the currents, are able to follow it and track it. To enable UWSNs, work is proceeding at multiple laboratories throughout the world on the design of localization, medium access control and routing protocols that can adapt to the problem that a drifting network topology has over short time intervals: frequent neighbour changes. However, the long-term impact that current drift has on 3D drifting UWSNs is poorly understood. Current mobility models used to generate the motion of drifting nodes in simulation do not reflect how devices in real-life will disperse in water. At present, UWSN protocol schemes are evaluated in simulations where the current mobility of nodes is generated by unrealistic land-based random waypoint and other stochastic mobility models, or coarsely resolved numerical ocean models. Recently, a physically-inspired current mobility model known as MCM has been proposed. This is only defined along the water's surface, in 2D, however, and 3D extensions of this model have been simplistic and arbitrary. The lack of realistic 3D current mobility models motivates this thesis to develop one so that the simulated evolution of UWSNs can more accurately reflect real-life. A consideration of the oceanographic data on which MCM is based is used to derive a 3D extension of the model that reflects observed features of the Gulf Stream current. The speed of the current declines with depth. This model is utilized to advect a drifting UWSN in an oil plume monitoring scenario and study the performance of two pressure routing protocols, Depth Based Routing (DBR) and HydroCast, over time. Previously, these schemes had only been validated in unrealistic stochastic and depth-invariant mobility models and their time-averaged performances were only reported. Our findings show that 3D UWSNs cannot expect to stay connected and functioning if nodes only passively drift with the currents, with results demonstrating that a fully connected network can be so dispersed after three hours that no paths to sinks exist at all. Nodes must be equipped with some form of mobility to prevent their being separated and carried out of the monitoring region. Autonomous underwater vehicles (AUVs) capable of omnidirectional motion are expensive however, and instead UWSNs consisting of pro ling floats are considered in this thesis. Floats can move up and down by adjusting their buoyancy, which also allow them to move in 3D by exploiting water layers that are flowing in different directions to proceed along a desired heading. Recently, promising results in 2D path planning and formation control of floats have been presented. However, these works consider the floats to have infinite vertical velocity whereas in reality this is around 0:3 metres per second. In this thesis, a practical node movement scheme is proposed for extending the coverage lifetime of a 3D UWSN consisting of floats. By accounting for the finite profiling velocity of floats, the scheme is able to position nodes at coverage holes with greater precision than existing 2D strategies. The scheme's performance is analysed by simulations. The results support the use of floats for achieving partial coverage, which can achieve similar levels of coverage as an AUV strategy while requiring less cost to deploy. In determining the lifetime of the network, we find that both energy and dispersion limit the lifetime of the network. Without propulsion, the nodes are carried out of and cease to cover the monitoring region. Using mobility to remain with the region, at the end of a 5 day mission duration floats have had to use up some or almost all of their battery capacity in profiling.

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  • Politics as creative pragmatism: rethinking the political action of contemporary university students in Aotearoa New Zealand

    Nissen, Sylvia Esther (2017)

    Doctoral thesis
    University of Canterbury Library

    This thesis reconsiders the political action and agency of contemporary university students in Aotearoa New Zealand. Although the twenty-first century has witnessed a global growth in student protest (Brooks 2017), there does not seem to have been a noticeable increase in political activism among New Zealand students, with critics variously labelling students as apathetic, selfish, distracted or disinterested (Green 2015; McClennen 2015). However, this thesis argues there is more to contemporary New Zealand student political action and attitudes than has been previously understood. The political attitudes of New Zealand students are examined through 70 in-depth interviews with students at New Zealand’s eight universities, supplemented by observation in the period 2014 to 2015. The thesis provides a conceptual framework of ‘3 Ds’ for understanding the experiences of contemporary students that inform their political action: desires for different types of politics, demands of contemporary university environments and doubts in an era of political ambiguity. This framework challenges and extends dominant theoretical explanations of student political action in the early twenty-first century, specifically theories of agency, political economy and social network analysis. In advancing a ‘3 Ds’ framework, this thesis also identifies a particular form of political agency emerging among New Zealand students that can be synthesised and understood through a concept of ‘creative pragmatism’. Creative pragmatism is a term advanced here to describe a ‘realistic’ orientation among students towards their social world, and their creative but cautious negotiation of political environments. The term also acknowledges a willingness amongst students to rethink how they engage politically, while retaining a strong ideal that a ‘different politics is possible’.

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  • Novel N-heterocyclic carbene ligands for use in asymmetric catalysis

    Kerr, Will (2017)

    Doctoral thesis
    University of Canterbury Library

    This investigation sought to establish new and adaptable methods for incorporating an enantiomeric component into NHC ligands and to develop novel precatalyst prototypes capable of asymmetric induction for use in transition metal mediated catalysis. This thesis details the fulfilment of these objectives through the design, synthesis and characterisation of forty‐eight previously unreported compounds including twenty‐six new NHC proligands and fourteen NHC complexes. NHC derivatives of the chiral mono‐terpene camphor are explored in Chapter 2, primarily through the synthesis of a series of bornyl‐acetamide linked NHC proligands, demonstrating expedient incorporation of an enantiomeric moiety by acetamide linkage. Bornyl‐acetamide NHC complexes of Ag(I), Pd(II), Pt(II) and Ru(II) are studied and structural elucidation supported by comparison with the Pd(II) and Pt(II) complexes of an achiral cyclohexyl‐acetamide analogue (Chapter 3). Chapter 4 introduces metallo‐ NHC proligands derived from imidazo[4,5‐f][1,10]phenanthroline, capable of backbone coordination of a ruthenium‐polypyridine component. Alternatively, use of an acetamide‐tether provides metallo‐NHC proligands of 5‐acetamido‐1,10‐ phenanthroline and 4‐acetamido,2,2’‐bipyridine (Chapter 5). Also outlined is the synthesis of several remarkable hetero‐dinuclear NHC complexes in addition to the effective enantiomeric resolution of a metallo‐NHC proligand. The performance of selected systems in an asymmetric Suzuki coupling is examined in Chapter 6. Several of the organic‐NHC ligands elicit comparable activity to reported systems, however, product formation is not observed when using an acetamide‐linked metallo‐NHC ligand. This is most likely related to amide‐group coordination which occurs readily for the metallo‐NHC ligands compared with the bornyl and cyclohexyl analogues. Such conclusions are supported by the comprehensive structural elucidation of all NHC complexes prepared in this thesis, providing evidence for the behaviour of catalytic intermediates involving these ligands.

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  • Fostering incidental vocabulary uptake from audio-visual materials: The role of text comprehension

    Nguyễn, Chí Đức (2017)

    Doctoral thesis
    Victoria University of Wellington

    This research project explores various factors that may influence the rate of incidental foreign/second language (L2) vocabulary acquisition from audio-visual materials, with a special focus on procedures that enhance learners’ comprehension of these input materials. Informed by relevant theories and research findings in the fields of L2 listening comprehension and incidental vocabulary acquisition, I investigate the effects of having learners (a) view a TED Talks video twice rather than once, (b) sum up the content of the video before watching it a second time, (c) watch TED Talks videos on the same subject in order to increase familiarity with that subject, and (d) exchange summaries of TED Talks videos with peers so as to assist each other’s subsequent processing of those videos. As these interventions are all deemed to facilitate L2 listening comprehension, they are also expected to create favourable conditions for incidental vocabulary uptake to occur. The effects on incidental vocabulary acquisition of the above interventions were gauged in a series of classroom experiments with Vietnamese EFL learners. Although vocabulary uptake was generally far from spectacular, all of the tested procedures were found to result in statistically significant vocabulary gains. The insertion of the output tasks (i.e., the summary activities) was particularly useful. First, they helped to enhance the learners’ text comprehension. Second, they created opportunities for the learners to use newly met words and thus consolidate their knowledge of these lexical items. A thread through the experimental data is the strong association between the learners’ vocabulary uptake and their comprehension of the input content. The findings from this research project are consistent with several established notions, models and theories in the fields, including Ausubel’s Advance Organizer (1978), Hulstijn and Laufer’s Involvement Load Hypothesis (2001), Krashen’s Input Hypothesis (1985), Nation’s Vocabulary Generation (2013), Swain’s Output Hypothesis (2005), and Wittrock’s Model of Generative Teaching of Comprehension (1991). However, there are also findings that go beyond the core tenets of these, and that can further our understanding of how learners process new lexical items in meaning-focused input and output tasks. Regarding pedagogical implications, this research project confirms that fostering L2 listening comprehension creates favourable conditions for incidental vocabulary acquisition to happen, and that the aforementioned classroom procedures are facilitative in this regard, albeit to different degrees.

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  • "Getting it": Successful intercultural teaching practicum

    Murray, Sara Rosalind (2017)

    Doctoral thesis
    University of Otago

    New Zealand’s population is becoming increasingly diverse, particularly with new arrivals from the Asian continent. With this, comes the increased need for early childhood education professionals to respond authentically to children and their families from minority ethnicities. One way to do so is to employ a wide range of culturally and ethnically diverse early childhood professionals to help respond to this diversity. However, a significant body of research has suggested that Asian-born early childhood student teachers may have difficulty during initial teacher education (ITE) in Aotearoa New Zealand, especially during the practicum component. Working within an educational context completely at odds with their own personal experience appears to place additional stress upon an already potentially-stressful situation. As a result, student teachers may struggle to meet required ITE learning outcomes for practicum. This research investigates what makes for a successful practicum experience for both Asian-born student teachers and their supervising associate teachers. Using symbolic interactionist theoretical underpinnings, it explores the experiences of three Asian-born early childhood education student teachers and their associate teachers during one of the final practicums of the students’ teaching qualification. Interviews with each of the six participants were conducted prior to, and after, the practicum to determine their changing views of success. In addition, video-stimulated discussions occurred during the practicum to gain a deeper sense of what each participant viewed as successful practice. The findings indicate that themes of mutual respect, professional identity development, student confidence, alignment of understanding around appropriate pedagogical practice, supervision in response to student need, English language competency, and sufficient time, are all seen to contribute to success in practicum. As a result of these findings, a conceptual model of success is proposed. It shows success involves more than simply passing the externally-imposed learning outcomes of the ITE institution. Instead, success is conceptualised as occurring along two continuum; formative and summative, and internally-experienced and externally-demonstrated. With this broader understanding of success in mind, a model of a successful intercultural practicum is proposed which incorporates the key success themes. Subsequent implications for the length of practicum, support structures in place for Asian-born students and associate teachers, practicum assessment processes, and the focus of initial teacher education are discussed.

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  • Teenagers' perspectives on the Canterbury earthquakes : an insight into their needs and experiences : a thesis presented in partial fulfillment of the requirements of the degree of Doctor of Clinical Psychology, Massey University, Wellington, New Zealand

    Pine, Nicola Stacey (2015)

    Doctoral thesis
    Massey University

    Natural disasters inflict physical, psychosocial, and economic impacts on individuals and their communities. Although a substantial number of disaster survivors are teenagers (13-19 years), this population group has not been widely investigated, especially regarding their views on their post-disaster needs and received supports. Such information would be important when planning post-disaster supports for current and future disaster-exposed teenagers. The aim of this research therefore, was to explore teenagers’ experiences and retrospective views of their needs, supports, and recovery following the Canterbury, New Zealand earthquakes. The first study surveyed 398 Christchurch secondary school students (aged 16-18 years [male = 169; female = 229]) who had experienced at least one of the major Canterbury earthquakes between September 2010 and June 2011. The survey’s purpose was to obtain an overview of teenagers’ experiences (including their needs and supports received), using both qualitative and quantitative data. Content analysis of this data revealed nine overall themes, including: physical basics, secondary stressors, social support, psychological impact, coping, school, support figures, gender, and recovery. Decile 2 school participants reported a need for physical basics significantly more than deciles 3, 9 and 10, and decile 10 reported a need for social support significantly more than decile 2. With gender, females reported a need for social support significantly more than males, and males reported a need for physical basics significantly more than females. Also, participants reported that their parents/caregivers understood their needs better than their siblings and friends, and their teachers were of greater help to them following the earthquakes compared to other students in their class. The second study extended the enquiry and involved six focus groups, each containing three to six students aged 16-18 years (male = 13; female = 18). Findings from the first study informed these focus group discussions, the aims of which were to gain deeper insights into disaster-exposed teenagers’ experiences, needs, and supports. The discussions were transcribed and analysed via thematic analysis. This analysis revealed seven major areas of importance, including participants’ advice for future planning and six others: individual, family, school, community, national and international. The latter six areas were incorporated into an ecological model combined with a timeline spanning from 2010 till 2013. The model demonstrated a number of notable points - for instance, immediately after the earthquakes many of the participants’ most important needs was to be in the presence of family, to know that family members were safe, and to receive comfort from them; however, three years later, participants’ concern had shifted to the rebuild of their city and their need for not only the pace to quicken, but also for youthfocused areas to be built (e.g., for recreational and leisure activities). The main recommendations from the research include: addressing acute post-disaster psychological responses early on and arranging preventative interventions; incorporating parental mental health support into youth-focused interventions; individually tailoring supports that address differences in gender, living conditions, and damage; encouraging youth to talk but not forcing them; having schools resume structured routines as soon as possible; providing psychoeducation to teachers, parents and guardians regarding typical disaster reactions and coping strategies for youth; and providing teenagers with accurate information. It is also recommended that communities provide or facilitate entertainment for youth post-disaster; that they organise youth-focused volunteer groups; involve youth in rebuild consultations; commence the rebuild of a disaster-struck city as soon as possible, and maintain gains in progress; distribute important information in multiple languages; and try to ensure that media coverage maintains a balance between both positive and negative content. Possible areas for future research include a deeper investigation into the experiences of disaster-exposed international students, the impact of the duration and permanency of relocation, and longitudinal studies into the recovery and adaptation of youth.

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  • Tree-based models for poverty estimation : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Statistics at Massey University, Manawatu

    Bilton, Penelope A (2016)

    Doctoral thesis
    Massey University

    The World Food Programme utilises the technique of poverty mapping for efficient allocation of aid resources, with the objective of achieving the first two United Nations Sustainable Development Goals, elimination of poverty and hunger. A statistical model is used to estimate levels of deprivation across small geographical domains, which are then displayed on a poverty map. Current methodology employs linear mixed modelling of household income, the predictions from which are then converted to various area-level measures of well-being. An alternative technique using tree-based methods is developed in this study. Since poverty mapping is a small area estimation technique, the proposed methodology needs to include auxiliary information to improve estimate precision at low levels, and to take account of complex survey design of the data. Classifcation and regression tree models have, to date, mostly been applied to data assumed to be collected through simple random sampling, with a focus on providing predictions, rather than estimating uncertainty. The standard type of prediction obtained from tree-based models, a \hard" tree estimate, is the class of interest for classification models, or the average response for regression models. A \soft" estimate equates to the posterior probability of being poor in a classification tree model, and in the regression tree model it is represented by the expectation of a function related to the poverty measure of interest. Poverty mapping requires standard errors of prediction as well as point estimates of poverty, but the complex structure of survey data means that estimation of variability must be carried out by resampling. Inherent instability in tree-based models proved a challenge to developing a suitable variance estimation technique, but bootstrap resampling in conjunction with soft tree estimation proved a viable methodology. Simulations showed that the bootstrap based soft tree technique was a valid method for data with simple random sampling structure. This was also the case for clustered data, where the method was extended to utilise the cluster bootstrap and to incorporate cluster effects into predictions. The methodology was further adapted to account for stratification in the data, and applied to generate predictions for a district in Nepal. Tree-based estimates of standard error of prediction for the small areas investigated were compared with published results using the current methodology for poverty estimation. The technique of bootstrap sampling with soft tree estimation has application beyond poverty mapping, and for other types of complex survey data.

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  • The development of L2 Arab writers' proficiency : autonomy, online self-access centres, and advisement : a dissertation presented in partial fulfillment of the requirements for the degree Doctorate of Education at Massey University, Manawatu, New Zealand

    Denekamp, Carmen (2016)

    Doctoral thesis
    Massey University

    Autonomy has been identified as a contributing factor to language development and may affect the use and effectiveness of self-access centres (SACs). Numerous universities in non-English speaking countries have adopted English as the language of instruction with Western academic writing being a main form for assessment. SACs have been funded in many tertiary institutes to promote language proficiency through autonomous learning. The general purpose of writing SACs is to make a wide portfolio of resources available to aid L2 writers with the place of advisors an emerging field. The use of technology at SACs has been extended with some going completely online. This action research study involved the development of an online SAC for second language (L2) academic writers at a university in Qatar. The SAC provided volunteer students with out-of-class help in the form of multiple resources and tools. Additional help could also be accessed in the form of advisement both synchronously and asynchronously. The purpose of this study was to investigate the form of the L2 students’ individual autonomy to determine how this might be fostered and implemented online to develop their academic writing proficiency. The online research SAC was designed to offer aid with grammar, vocabulary, and writing skills and to be responsive to the needs and demands of the students. Interactions between participants and the researcher were available via email, chats, revisable assignments, and forums. Diverse data sources were integrated and analyzed, including questionnaires and interactive dialogues, to understand deeply the cultural dimension and situated perspective of the participating Arab students. The findings revealed that, contrary to expectations, the Arab participants manifested multi-dimensional autonomy. Most preferred to receive help with their writing via 1-1 advisory sessions together with some use of the online resources. Advisory sessions evolved into multiple dialogues whereby reactive autonomy could gradually become proactive. The addition of a structured component to the advisory sessions enhanced autonomy and writing development. The success of the SAC depended on various factors, such as aiding students’ language development and academic writing in a way that capitalized on the participants’ desires and perspectives without imposing Western ideologies. This study contributed to the body of research on developing academic writing proficiency in an under-researched context of Arab learners and with a special emphasis on autonomy, online SACs, and advisement. In doing so it broadened existing paradigms of constructivism and critical theory in the arena of education, and challenged the use of established concepts in the setting of the Arab world.

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  • The Experience of Living With Bowel Cancer for Maori in Taranaki

    Ruakere, Brian Thomas

    Doctoral thesis
    Auckland University of Technology

    The title of this study is: The experience of living with bowel cancer for Māori in Taranaki. Research methods for this study have been adapted from research approaches collectively known as Kaupapa Māori. The study is also informed by Gadamerian hermeneutic interpretive methodology which unpacks the nature of how we understand and interpret. However, the lens through which understanding is expressed, is from a Māori worldview. Ten Māori patients, diagnosed with bowel cancer were interviewed and their narratives analysed using Gadamerian hermeneutic methodology. The concepts of whakapapa, mauri and tapu were fundamental to the analysis process. Whakapapa in the context of this study examined the stories substance or origin about participant experiences and initial signs that not all was right with their health. The concept of mauri shed light on ways of experiencing bowel cancer that came to reveal how participant stories fell into one of three perspectives: mauri moe; mauri oho and mauri ora. Signs archetypal of mauri moe were evident where participant behaviours remained grounded in responses framed within the notion of mamae and its negative elements of neglect, hurt, pain, anguish, and sorrow. Mauri oho revealed distinct changes in behavioural patterns that signified an upsurge in motivation by participants who were committed to overcome their dilemma and be well again. Mauri ora signified actions that revealed successful outcomes when participants became highly motivated, felt good about their health and were committed to keeping good health. The concept of tapu was utilised to examine the underlying principal issues that determined participant existence in the present. The findings showed that participants had no understanding of bowel cancer before they were diagnosed. Some participants experienced shame and embarrassment at the prospect of having to live the rest of their lives with a stoma. Recognition of tapu through the proper exercise of mana was an important factor in participant recovery. Violation of tapu through the wrongful exercise of mana also manifested as having negative effects on participant recovery. Based on the findings from this study the following recommendations for further research are proposed: a Kaupapa Māori action research study in conjunction with introducing the inflatable colon to the community working with a group of stakeholders to educate Māori about bowel cancer and; a Kaupapa Māori action research study with a group of stakeholders to devise a treatment pathway that integrates the concepts of whakapapa, mauri and tapu when assessing Māori who present to healthcare providers with a suspected prognosis of bowel cancer.  

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  • Theory & Observation of High-Order Radio Recombination Lines

    Alexander, Jordan

    Doctoral thesis
    Auckland University of Technology

    This dissertation resolves a mystery in cosmic radio recombination line observations reported by Bell et al. (2000). This is accomplished by rigorously “reverse-engineering” the novel data processing technique they used and through independent observations of high-order RRLs (radio recombination lines) of cosmic origin to test the theory of Stark broadening in plasmas. The findings of this dissertation are summarized in two papers published during the dissertation and reproduced in Chapter 4. I discovered that the apparent hydrogen RRL narrowing first reported by Bell et al. is an artifact of their data processing. I accomplished this by creating a theoretical model of the multiple FS (frequency shifting) technique, originally developed by Bell (1997), which I then implemented as a computer simulation. This technique copies a spectral line bandpass, shifts it in frequency by an offset, and adds it to the unshifted bandpass. The output of this process is then fed back to itself multiple times. I then co-created a theoretical model of the Orion nebula which includes mechanisms of spectral line broadening and non-equilibrium thermodynamics effects. This model is used to numerically solve the radiative transfer problem to simulate hydrogen RRLs. These simulated lines are then processed through the multiple FS model, the results of which are called “processed” lines. Finally, I used Monte Carlo simulation to estimate how noise influences the processed line widths and amplitudes. From these models and simulations, I discovered that multiple FS does not preserve broadening when the original line width is greater than the FS-offset. In this case, I find the processed results manifest the narrowing reported by Bell et al., by reducing broad spectral wings characteristic of Stark broadened RRLs. I also discovered that the S/N of processed lines reduces weakly with the number of overlaps as a result of adding dependent samples. This means the S/N of processed lines as a function of ∆n (transition-order), at fixed frequency, decreases faster than for unprocessed lines, such that a given statistical insignificance level is reached more quickly. Given this analysis, I argue Bell et al.’s ∆n > 11 lines are artifacts of their technique. I conclude that their reported findings, upon re-examination of their novel data processing technique, do not indicate a need to change Stark broadening theory. I present original observations of high-order RRLs from the Orion nebula to test the theory of Stark broadening in cosmic plasmas. I use a wide 1 GHz bandpass centered at 6 GHz to significantly improve the accuracy of measurements by stacking up to eleven hydrogen RRLs of the same ∆n and find no evidence of spectral line narrowing. I show that all statistically significant data from my observations and four-sets of previous observations of high-order hydrogen RRLs (Smirnov et al., 1984; Bell et al., 2011) are in agreement and demonstrate how Stark broadening theory is consistent with these observations. I find that Lockman and Brown (1975)’s RRL model of the Orion nebula over a large range of radio frequencies and ∆n ≤ 2 requires the addition of small-scale density inhomogeneities (clumps) and turbulence to adequately predict my observed hydrogen RRLs for ∆n ≤ 5. I demonstrate that the power law predicted by electron-impact Stark broadening theory is consistent with the five-sets of high-order hydrogen RRLs analyzed here. My data do not allow distinguishing between two approaches to the cut-off parameters (nearest neighbor versus Debye radius) when predicting line broadening from electron impacts. Specifically, the data does not allow an unambiguous choice between the theoretical results of Griem (1967); Gee et al. (1976) and Watson (2006); Peach (2015). This ambiguity arises from small differences in the radiative transfer nebula model parameters. It is currently impossible to independently determine turbulent velocities and other physical & geometric parameters of the Orion nebula with enough accuracy to choose between the two predications of electron-impact broadening theory. This situation represents an ill-posed inverse problem that is currently unsolvable (Brown et al., 1978). However, I am able to show that Peach’s model for electron-plus-proton impacts significantly deviates from the Lorentz-width trend in my data.

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  • The Power of Robot Groups with a Focus on Persuasive and Linguistic Cues

    Brandstetter, Jürgen (2017)

    Doctoral thesis
    University of Canterbury Library

    Today the HRI community generates a lot of knowledge on how one robot affects one human, and how one robot affects multiple human listeners. Much less knowledge is available on how robots affect the human language and how this language change can affect human attitudes and behaviours. This language effect is of particular interest for when we get into a situation where a major part of the human population has robots, as we are now experiencing with the ubiquity of smartphones. In this case, the questions are: What happens if all robots were to use the same words? For example, when they all use the same source as their dictionary. Will robots be able to affect the word choices of the human population, and what are the implications of connotation-laden vocabulary? Even more interesting, will this word choice affect the attitudes and behaviours of the human population? Through all those questions a central question for this thesis emerged: "Are Robots able to influence a group of people via the usage of language?" To find out if this might be possible, we developed three connected experiments. In the first, the effect of peer pressure on humans created by robots is explored, focusing on how this peer pressure affects the language of a person. To see if and how this influence of robots works, the effect of the robots was compared against that of human actors. The results of the ex- periment showed that the actors could indeed influence the participants as predicted, however, no such influence could be shown by the robots. It was concluded that the reason the robots did not affect the humans was that the participants did not feel that they belonged to the robots group. In the second experiment, a robot and human group setting was created. In this experiment, the robot tried to influence the human language. Important here to mention is that the experiment measured if the language of participants was affected by the robot influence, even after the interaction and without any robot in the room. It was also mea- sured if the word chosen by the robot had an influence on how a person would perceive the discussed object. The outcome of the experiment was successful, and showed that the group building worked and the robot was able to affect the human language, even after the interaction was over. It further showed that robots were able to affect the hu- mans attitude toward objects simply by using positive or negative connoted synonyms for a particular object. In the third and last experiment, the question was: Can many robots affect the language of a whole human population? To answer this, different parameters were measured: How many humans need robots so that the robots could manipulate the whole human populations language? And does it matter which persons in the human population will get a robot - whether it be a person who is very well connected or a person who is poorly connected, for example? Since we are currently not in a time where a huge number of people actually have robots, a simulation was created. The outcome of the simulation was that on average only 11% of the human population needed robots to affect the language of 95% of the human population. Finally, to further deepen the knowledge on how simple language change can affect human attitude and behaviour a literature review is added. This review focuses particularly on persuasion via language, which includes effects like gender neutral versus non-gender neutral language. The conclusion of this thesis is that in certain situations, a group of robots is able to affect the language, and in turn the behavioural responses, of the majority of the human population.

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  • Conquest, Kingship, Calamity: Demetrius Poliorcetes After Ipsus

    Dunn, Charlotte Marie Rose (2017)

    Doctoral thesis
    University of Otago

    Demetrius Poliorcetes (336-282 BC), was one of the extraordinary figures of the Hellenistic Age, whose career began in wake of the chaos that followed the death of Alexander the Great. His father was Antigonus Monophthalmus, one of the greatest of the Successors, and under Antigonus’ guidance Demetrius achieved some of the standout accomplishments of his career. The pair’s ceaseless and energetic campaigning enabled them to jointly claim the royal title in 306 BC, something which quickly prompted the other Successors to follow suit. They continued to consolidate and expand their empire in the years that followed; however, the Antigonids’ dominant position eventually saw the other dynasts conspire to eliminate them. In 301 BC, Demetrius suffered a violent reversal of fortune, when the coalition that had formed against the Antigonids defeated them in battle, and his father was killed. This misfortune saw Demetrius fleeing from the battlefield with a small band of followers, now the heir to a piecemeal and much threatened empire.

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  • Planning to develop land returned under Treaty settlement in Waikato, Aotearoa New Zealand : an institutional ethnography : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Health at Massey University, SHORE & Whāriki Research Centre, Aotearoa New Zealand

    Livesey, Brigid Te Ao McCallum (2017)

    Doctoral thesis
    Massey University

    This research investigates planning to develop land returned as settlement for breaches of Te Tiriti o Waitangi (the Treaty of Waitangi). Using institutional ethnography methodology, I explore a case study of the relationship between an iwi authority, Te Whakakitenga o Waikato, and a local authority, Hamilton City Council. In 1995, significant areas of land were returned to Waikato-Tainui through Treaty settlement. This research focuses on processes to develop planning regulation for land owned by Waikato-Tainui at Te Rapa, site of ‘The Base’ retail development and Te Awa shopping mall, and Ruakura where an inland port and associated activities are proposed. Iwi planning documents describe a vision to develop land returned under Treaty settlement. Commercial property development to regain ‘economic sovereignty’ is a critical element in the ‘integrated development agenda’ for Waikato-Tainui. However, critical discourse analysis and intertextual analysis illustrate that this vision is not well-reflected in local government planning documents. Relations between Hamilton City Council and Waikato-Tainui have changed from generally adversarial in 2009 during planning processes to restrict development at Te Rapa through Variation 21, to more collaborative during planning processes to approve the Ruakura Plan Change in 2014. Complementing data from interviewing practitioners with analysis of texts created through these planning processes, I consider control, timing, and trust as key factors in this changing relationship. This research provides evidence for dual planning traditions in Aotearoa New Zealand. Communal ownership of land and inalienability are characteristics of land returned under Treaty settlement which have influenced development decisions made by Waikato-Tainui. Planners and the planning profession can ‘transform’ planning practices to create new relationships between local government and iwi authorities. Interviews suggest that crosscultural planning can be a challenging and emotional experience. Iwi planning documents articulate a vision for future relationships based on mana whakahaere (affirming Māori authority) and mātauranga Māori (valuing Māori knowledge). In response, I highlight the need for changes to the New Zealand Planning Institute Code of Ethics to support planners working to decolonise planning. I conclude by ‘mapping’ the institution of planning for Treaty settlement land, and identifying levers which planners can use to support Māori goals for land development and economic self-determination.

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  • Molecular epidemiology of waterborne zoonoses in the North Island of New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science (Epidemiology and Public Health) at Institute of Veterinary, Animal and Biomedical Sciences (IVABS), Massey University, Palmerston North, New Zealand

    Shrestha, Rima Devi (2016)

    Doctoral thesis
    Massey University

    Campylobacter, Cryptosporidium and Giardia species are three important waterborne zoonotic pathogens of global public health concern. This PhD opens with an interpretive overview of the literature on Campylobacter, Cryptosporidium and Giardia spp. in ruminants and their presence in surface water (Chapter 1), followed by five epidemiological studies of Campylobacter, Cryptosporidium and Giardia spp. in cattle, sheep and aquatic environment in New Zealand (Chapters 2-6). The second chapter investigated four years of retrospective data on Campylobacter spp. (n=507) to infer the source, population structure and zoonotic potential of Campylobacter jejuni from six high-use recreational rivers in the Wanganui- Manawatu region of New Zealand through the generalised additive model, generalised linear/logistic regression model, and minimum spanning trees. This study highlights the ubiquitous presence of Campylobacter spp. in both low and high river flows, and during winter months. It also shows the presence of C. jejuni in 21% of samples containing highly diverse strains, the majority of which were associated with wild birds only. These wild birds-associated C. jejuni have not been detected in human, suggesting they may not be infectious to human. However, the presence of some poultry and ruminant-associated strains that are potentially zoonotic suggested the possibility of waterborne transmission of C. jejuni to the public. Good biosecurity measures and water treatment plants may be helpful in reducing the risk of waterborne Campylobacter transmission In the third study, a repeated cross-sectional study was conducted every month for four months to investigate the source of drinking source-water contamination. A total of 499 ruminant faecal samples and 24 river/stream water samples were collected from two rural town water catchments (Dannevirke and Shannon) in the Manawatu- Wanganui region of New Zealand, and molecular analysis of those samples was performed to determine the occurrence of Campylobacter, Cryptosporidium, and Giardia spp. and their zoonotic potential. The major pathogens found in faecal samples were Campylobacter (n=225 from 7/8 farms), followed by Giardia (n=151 from 8/8 farms), whereas Giardia cysts were found in many water samples (n=18), followed by Campylobacter (n=4). On the contrary, Cryptosporidium oocysts were only detected in a few faecal (n=18) and water (n=3) samples. Cryptosporidium and Giardia spp. were detected in a higher number of faecal samples from young animals (≤ 3 months) than juvenile and adult animals, whereas Campylobacter spp. were highly isolated in the faecal samples from juvenile and adult ruminants. PCRsequencing of the detected pathogens indicated the presence of potentially zoonotic C. jejuni and C. coli, Cryptosporidium parvum (gp60 allelic types IIA18G3R1 and IIA19G4R1) and Giardia duodenalis (assemblages AII, BII, BIII, and BIV) in cattle and sheep. In addition, potentially zoonotic C. jejuni and Giardia duodenalis assemblages AII, BI, BII, and BIV were also determined in water samples. These findings indicate that these three pathogens of public health significance are present in ruminant faecal samples of farms and in water, and may represent a possible source of human infection in New Zealand. In the fourth study, PCR-sequencing of Cryptosporidium spp. isolates obtained from the faeces of 6-week- old dairy calves (n=15) in the third study were investigated at multiple loci (18S SSU rDNA, HSP70, Actin and gp60) to determine the presence of mixed Cryptosporidium spp. infections. Cryptosporidium parvum (15/15), C. bovis (3/15) and C. andersoni (1/15), and two new genetic variants were determined along with molecular evidence of mixed infections in five specimens. Three main Cryptosporidium species of cattle, C. parvum, C. bovis and C. andersoni, were detected together in one specimen. Genetic evidence of the presence of C. Anderson and two new Cryptosporidium genetic variants are provided here for the first time in New Zealand. These findings provided additional evidence that describes Cryptosporidium parasites as genetically heterogeneous populations and highlighted the need for iterative genotyping at multiple loci to explore the genetic makeup of the isolates. The C. jejuni and C. coli isolates (n=96) obtained from cattle, sheep and water in the third study were subtyped to determine their genetic diversity and zoonotic potential using a modified, novel multi-locus sequence typing method (“massMLST”; Chapter 5). Primers were developed and optimised, PCR-based target-MLST alleles’ amplification were performed, followed by next generation sequencing on an Illumina MiSeq machine. A bioinformatics pipeline of the sequencing data was developed to define C. jejuni and C. coli multi-locus sequence types. This study demonstrated the utility and potential of this novel typing method, massMLST, as a strain typing method. In addition to identifying the possible C. jejuni/coli clonal complexes or sequence types of 68/96 isolates from ruminant faeces and water samples, this study reported three new C. jejuni strains in cattle in New Zealand, along with many strains, such as CC-61, CC-828 and CC-21, that have also been found in humans, indicating the public health significance of these isolates circulating on the farms in the two water catchment areas. Automation of the massMLST method and may allow a cost-effective high-resolution typing method in the near future for multilocus sequence typing of large collections of Campylobacter strains. In the final study (Chapter 6), a pilot metagenomic study was carried out to obtain a snapshot of the microbial ecology of surface water used in the two rural towns of New Zealand for drinking purposes, and to identify the zoonotic pathogens related to waterborne diseases. Fresh samples collected in 2011 and 2012, samples from the same time that were frozen, and samples that were kept in the preservative RNAlater were sequenced using whole-genome shotgun sequencing on an Illumina MiSeq machine. Proteobacteria was detected in all the samples characterised, although there were differences in the genus and species between the samples. The microbial diversity reported varied between the grab and stomacher methods, between samples collected in the year 2011 and 2012, and among the fresh, frozen and RNAlater preserved samples. This study also determined the presence of DNA of potentially zoonotic pathogens such as Cryptosporidium, Campylobacter and Mycobacterium spp. in water. Use of metagenomics could potentially be used to monitor the ecology of drinking water sources so that effective water treatment plans can be formulated, and for reducing the risk of waterborne zoonosis. As a whole, this PhD project provides new data on G. duodenalis assemblages in cattle, sheep and surface water, new information on mixed Cryptosporidium infections in calves, a novel “massMLST” method to subtype Campylobacter species, and shows the utility of shotgun metagenomic sequencing for drinking water monitoring. Results indicate that ruminants (cattle and sheep) in New Zealand shed potentially zoonotic pathogens in the environment and may contribute to the contamination of surface water. A better understanding of waterborne zoonotic transmission would help in devising appropriate control strategies, which could reduce the shedding of Campylobacter, Cryptosporidium, and Giardia spp. in the environment and thereby reduce waterborne transmission.

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