1,566 results for Thesis, 2012

  • HIV prevention, treatment, and care in Sub-Saharan Africa

    Crump, Andrew John (2012)

    Post-doctoral thesis
    University of Otago

    Description: xi, 296 pages : illustrations, map ; 30 cm. Notes: Thesis (M. D.)--University of Otago. Includes bibliographical references.

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  • The angler's catch

    Martyn, Geoff (2012-05-29)

    Masters thesis
    Auckland University of Technology

    For detectives, historians, crossword fanatics, quest-seekers and many many more, finding the solution to a puzzle or mystery is a thing most satisfying. Demystifying the mysterious, solving problems and meeting challenges are perhaps the most obvious driving forces behind the novel The Angler’s Catch, the thesis component of this submission. Beyond that, the creative work endeavours to portray social issues and cultural-historical features of small town New Zealand in the early-mid 1970s. A further aim was to explore the personalities of the central characters and to tell a Kiwi story of ordinary people trying their best and persevering and achieving extraordinary results. It is a tale of surmounting obstacles through collaboration and, in the case of the protagonist Amos, of facing up to and overcoming personal flaws along the way. The Angler’s Catch then, is a story of seeking, of solving and of growth. The exegesis, entitled Seeking, Solving and Growth, attempts to place The Angler’s Catch in context, by exploring the detective novel genre and by identifying the author’s motivations, intentions, and methodologies. It is suggested that the exegesis be read before the creative work, but this of course is left to the preference of the reader.

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  • Sexual and reproductive behaviour and health in a birth cohort

    Dickson, Nigel (2012)

    Post-doctoral thesis
    University of Otago

    Description: 1 v. (various paging) ; ill. ; 30 cm. Notes: University of Otago department: Paediatrics & Child Health. "January 2012". 50 leaves of current text, followed by reprints of 32 articles by the author published between 1993 and 2010. Thesis (M.D.)--University of Otago, 2012. Includes bibliographical references.

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  • Oral-Health-Related-Quality-of-Life in Cambodian Children

    Turton, Bathsheba (2012)

    Masters thesis
    University of Otago

    Introduction Children in Cambodia are known to have a high burden of dental caries (Chu et al., 2008; Durward and Todd, 1991; Shidara et al., 2007) and very little access to dental care. This thesis examines the validity of an Oral-Health-Related-Quality-of-Life (OHRQoL) instrument for characterising the dental caries experience of Cambodian children. Methods The CPQ8-10 and the CPQ11-14 16 item short-form (CPQ11-14) were cross-culturally adapted for testing. Eight-to-14-year-old children were recruited from those attending mobile dental clinics run by the One-2-One Charitable Trust through various provinces of Cambodia. Each participant was interviewed by a trained interviewer using the cross-culturally adapted instruments. He/she then underwent an intra-oral examination to record the clinical manifestations of dental caries using the DMF and the PUFA indices. Following this, data were analysed using SPSS version 17.0 (SPSS Inc, Chicago, USA). Results The sample comprised 430 participants with approximately equal representation by age group (the 8-10 age group and the 11-14 age group) and sex. There were statistically significant differences in mean CPQ8-10 and CPQ11-14 scores and impact prevalence by global item response, the presence of caries and the presence of pulpally involved teeth. There were also significant positive correlations between instrument scale scores and caries severity measures. Moreover, the Cronbach’s alpha values for each of the scales and subscales were acceptable. In the 8-10 age group, there was a very strong correlation between the CPQ11-14 scores and the CPQ8-10 scores and the distribution of responses from the two instruments. Discussion The participants in this sample had a mean DMF score similar to that reported in the 2011 Cambodian National Oral Health Survey; however, the DMF scores were higher than those seen in other validation samples for the CPQ8-10 and CPQ11-14, apart from the Northland (New Zealand) sample. None of the other validation studies used the PUFA index. The CPQ8-10 was a sound OHRQoL measure in the 8-10 age group; the CPQ11-14¬ was a sound OHRQoL measure in the 11-14 age group and the 8-10 age groups. Conclusion The cross-culturally adapted version of the CPQ11-14 was a sound measure of OHRQoL across both age groups; therefore, it could be used for Cambodian children between the ages of eight and 14. Further investigation into the instrument’s test-retest reliability and responsiveness would add to knowledge of its properties and validity.

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  • The Hawza of Najaf

    Al Tooq, Fadhel Naser Mohamed Abdulla (2012)

    Masters thesis
    University of Otago

    Abstract Under Saddam Hussein the Shi’ites of Iraq lived a sad story; they were politically suppressed and killed in cold blood. After the creation of the Iraqi state they lived as if they were a minority without any rights. Perhaps the main responsible factor was the hawza - the Shi’ite religious leadership - and its interpretation of religion and politics. Senior religious scholars in the hawza sought to isolate Shi’ite from state affairs in the belief that during the Great Occulation of the Twelfth Imam no one could fill the political leadership except the Imam. Therefore, establishing an Islamic state was religiously wrong. Furthermore, involvement in politics was considered as supporting the enemies of the Imam. The clerics and the Islamists who believed in politics were not supported and were left to their bloody destiny. This study seeks to provide a detailed explanation of how the hawza was one of the reasons behind the tragic story of the Shi’ites of Iraq. In addressing this task, an analysis of the political thinking of the Shi’ite is provided in chapter one, before examining the hawza of Najaf in chapter two, in particular its historical background and its political role up to 1920s. Chapter three deals with the role of the hawza from 1958 until 2003, in particular the leadership of Ayatollah Al-Hakeem, Ayatollah Ko’i and Ayatollah Sistani. Chapter four outlines the new role that the hawza has played after the fall of Saddam’s regime and the main obstacles it faces.

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  • IR Studies of the Zirconia-Water Interface

    Scholz, Jan (2012)

    Doctoral thesis
    University of Otago

    The aim of the present work was to contribute to an understanding of the reactivity of hydroxylated zirconia surfaces towards hydration and anion adsorption. IR spectroscopy was used to characterise the structure and bonding of surface functional groups and interfacial water molecules, to study slow surface reconstruction processes and to obtain insights into the specific adsorption of chloride, sulphate, phosphate and tungstate ions. To account for the structural diversity of the zirconia-water interface and hence its spectral complexity, both zirconia nanoparticle films and structurally related materials including crystalline zirconyl chloride n-hydrates, zirconia hydro gels and aqueous zirconia sols were studied spectroscopically. Thermal and isothermal dehydration and humidity-controlled hydration studies of zirconyl chloride octahydrate, zirconia hydro gels and zirconia nanoparticle films as well as anion adsorption studies to zirconia nanoparticle films from aqueous solutions under static conditions were conducted. Further, X-ray single crystal, thermogravimetric, mass spectrometric and calorimetric data as well as electrophoretic mobility measurements were used to infer additional structural information. Vibrational data for hydroxylated zirconia polymorphs, crystalline hydrogen chloride n-hydrates and size-selected water clusters was employed for spectral assignments. The characteristic vibrational signature of stoichiometric zirconyl chloride n-hydrates was obtained and assignments for vibrational modes of discrete Cl-•••H+-O, Cl-H•••O, O•••H+•••O, O-H•••O and Zr-(OH2)3 groups are given. H2O52+- and H3O2--like entities were evident in zirconyl chloride octa and -hexahydrate. A hydrolysis mechanism for the reaction of H2O(g) and HCl(aq) with Zr4+ sites in Zr-O-Zr groups is proposed (chemisorption). The formation of a strongly H-bonded network of surface-bound water molecules at the zirconia surface was observed (physisorption), and the role of continuous yet slow Zr-O-Zr bond cleavage in the formation of a gel-like surface layer is highlighted. The loss in crystallinity of the zirconia surface led to a gradual increase in the positive net surface charge of zirconia particles. The latter seems to be accountable for the embedding of chloride ions into the network of surface-bound water molecules; and a specific chloride adsorption mechanism is suggested. Sulphate, phosphate and tungstate adsorption studies to zirconia nanoparticle films revealed binding motifs of the oxoanions at pH 3 and 1; and their adsorption affinities were compared in view of considerable differences in Langmuir equilibrium constants, Kads.

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  • Synthesis and study of Quaternary Nitrogen Surfactants

    Jordan, Deborah Kay (2012)

    Doctoral thesis
    University of Otago

    The effect of head group modification on the solubility and antimicrobial potency of some quaternary nitrogen surfactants (QNSs) was investigated. Using high yielding Menshutkin reactions, a homologous series of monomeric, dimeric and polymeric QNSs based on aliphatic ammonium and aromatic pyridinium head groups were synthesised. The hydrophilicity of the head groups was increased via hydroxymethyl addition and decreased using ethyl substitution. The tails used were saturated, straight alkyl chains ranging from 6 to 22 carbons in length. The hydrophobicity of the QNSs was established by calculating their predicted partition coefficient in an octanol/water mix (Log P) and by measuring their critical micelle concentration (cmc). As anticipated, the QNSs with longer alkyl tails were more hydrophobic with lower cmc and increased Log P values. Alterations to the head groups showed predictable results for all head groups except the hydroxymethyl addition on the pyridinium head group. The Log P value predicted an increased hydrophilicity, while the cmc suggested an increased hydrophobicity. This difference (lower cmc) was postulated to be due to decreased repulsion of the head groups allowing for micellisation at lower concentrations. This theory was supported by crystal structure analysis which showed that the hydroxymethyl addition caused the QNSs to pack more closely. Measurement of limiting molar conductivity (Λo) also showed that the hydroxymethylpyrdinium compounds were unexpectedly less solvated than the unsubstituted counterparts, and the micelle size was increased by the presence of the hydroxymethyl group. This data as a whole suggested the hydroxymethyl group was not solely acting to decrease the hydrophobicity. The antimicrobial activity of each QNS was assessed against three Gram positive bacteria (Staphylococcus aureus, Listeria innocua, Bacillus subtilis); three Gram negative bacteria (Pseudomonas aeruginosa, Yersinia enterocolitica, Escherichia coli); a fungus (Aspergillus niger); and a yeast (Saccharomyces cerevisiae), using a minimum inhibitory concentration (MIC) assay. The longer chain compounds were generally found to be more effective against the bacteria with a cut-off seen in many cases at the hexadecyl derivative. The charge of the bacteria cell surface (ζ-potential) became increasingly positive at higher concentrations of QNS and transmission electron microscopy (TEM) showed that at concentrations above the MIC the cytoplasmic membrane had been compromised. These studies suggested the primary mode of action of the QNS against the bacteria was due to the attraction of the QNS to the cytoplasmic membrane of the bacterial cell which resulted in its destabilisation. Destabilisation of the bacterial cytoplasmic membrane occurred at lower concentration for QNSs with longer alkyl tails. It was therefore postulated that the hydrophobicity of a QNS could be used to predict its antimicrobial potency. However, when the MIC was related to Log P using a quantitative structure activity relationship (QSAR) it was demonstrated that the relationship was not linear, and that while parabolic and bilinear models provided a better approximation to the observed data no model sufficiently accounted for all the data. The research presented in this thesis has shown that the physical properties and antimicrobial activity of QNSs varies greatly with altered head group hydrophobicity. It has been demonstrated that very small changes to the head group can lead to unexpected physical properties which changes their interactions with micro-organisms. The antimicrobial action of these compounds has been shown to rely on the attraction of the cationic head group to the cytoplasmic membrane which is then destabilised by the alkyl tail. Findings from this project will help in the development of more potent QNSs and a greater understanding of the interaction of QNSs with cytoplasmic membrane.

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  • Design and Implementation of an Efficient and Scalable Software Distributed Shared Memory System

    Yu, Byung-Hyun (2012)

    Doctoral thesis
    University of Otago

    This thesis presents the design and implementation of our novel hybrid software DSM system. We call our system hybrid home-based EAC (HHEAC) since the system implements our novel exclusive access consistency model (EAC) based on the hybrid protocol of the homeless and home-based protocols. HHEAC guarantees only that shared variables inside a critical section are up to date before the accesses. Other shared variables outside a critical section are guaranteed to be up to date after the next barrier synchronisation. Our home-based DSM implementation is different from the previous implementations in that a home node does not receive any diffs from non-home nodes until the next barrier synchronisation. It is also different in that during a lock synchronisation required diffs are prefetched before the critical section, which reduces not only data traffic but also page faults inside the critical section. We also present a diff integration technique that can further unnecessary data traffic during lock synchronisation. This technique is especially effective in reducing data traffic for migratory applications. Finally, we develop a home migration technique that solves the wrong home assignment problem in the home-based protocol. Our technique is different from others in that an optimum home node is decided before updating a home node. To evaluate our system, we performed various experiments with well-known benchmark applications, including a novel parallel neural network application.The performance evaluation shows that HHEAC is more scalable than other DSM systems such as TreadMarks and removes the home assignment problem in the conventional home-based protocol.

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  • Hydro-development and Conflict: The Mekong Basin

    Pearse-Smith, Scott William David (2012)

    Masters thesis
    University of Otago

    Hydro-development of the Mekong Basin is proceeding at an increasing pace. The relatively small-scale hydro-development projects that have taken place to date provide some insight into the expanding environmental and social impacts that can be expected as hydro-development projects increase in number and scale. This thesis explores how these environmental and social consequences of hydro-development might generate violent conflict, both between, and within, Mekong nations. This study adopts a value-added model – based on that of Homer-Dixon – to consider the causal relationship between hydro-development and violent conflict. In doing so, it explores how hydro-development interacts with the unique environmental, social, economic, and political conditions of the Mekong Basin. Two intervening variables between hydro-development and violent conflict are identified as particularly significant: environmental scarcity and social effects. This study reaches two main conclusions. The first is that, despite increasing interstate tensions, violent conflict between Mekong States is unlikely. As well as strategic and historical arguments, this is because regional hydro-development advances economic growth and regional integration, in line with the economic imperative of Mekong nations. The second main conclusion of this study is that, while violent interstate conflict is unlikely, violent intrastate conflict is likely to increase. Hydro-development is predicted to decimate the supply of crucial natural resources, upon which the largely rural Mekong Basin populations depend for their livelihoods. Furthermore, the costs and benefits of hydro-development are not equitably shared, which in combination with the increasing scarcity of key renewable resources, can sharpen existing social divisions. Violent conflict within society is therefore predicted to increase. Protests and civil unrest are also likely to increase, although such movements are unlikely to generate serious attempts at insurgency.

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  • "Let Us Go to Him": The Story of Faith and the Faithfulness of Jesus in Hebrews

    Easter, Matthew Charles (2012)

    Doctoral thesis
    University of Otago

    This thesis investigates faith and the faithfulness of Jesus in Hebrews. Preceding studies have understated the christological dimension of faith or have made Jesus the object of faith. Furthermore, while Käsemann emphasized the corporate motif of the travelling people of God for Hebrews, most interpreters still operate with a largely individualistic concept of faith. I argue that faith in Hebrews is manifested in four dimensions: christological, eschatological, ethical, and ecclesiological. That is, faith is exemplified and enabled by Jesus (christological dimension), who in faith endured suffering to death (ethical) in hopes of postmortem life (eschatological). Humans exercise this faith by persevering with the travelling people of God (ecclesiological). I read Hebrews with an eye to story, and the thesis is organized with these narrative concerns in view. Chapter 2 lays the exegetical and philosophical foundations for such an approach to Hebrews, arguing that Hebrews operates with stories and that human identity is itself a story. Our treatment of Hebrews deals with the two narrative identities the author presents, which are laid out succinctly in Heb 10:39: “but we are not (story 1) of timidity unto destruction, but (story 2) of faith unto the preservation of the soul.” I discuss these two stories in parts 2 and 3 of the thesis. Part 2 of the thesis (chapters 3-5) addresses “the default human story.” We find that the default human story is characterized by unfaithfulness and concludes assuredly in death. Although God intended glory, honor, and dominion for humanity (Heb 2:6-8), we do not at present see this divine intention fulfilled. Instead, humans are shackled by a guilty conscience and are inherently unfaithful. The assured conclusion of death holds true even for Israel’s heroes of faith, who did not receive the promise and are not made perfect (11:13, 39-40). Although these chapters do not address faith per se they are necessary pieces to fill out the whole vision of the understanding of faith in Hebrews. To understand “faith” fully, we need to understand “unfaith.” Part 3 of the thesis (chapters 6-8) discusses the story rewritten in Christ. This story, lived out perfectly by Jesus, is characterized by faith in the face of death and concludes assuredly in postmortem life. Hebrews depicts Jesus in martyrological terms, whose faith is associated with endurance through suffering in hope of postmortem reward. The conclusion to the story of faith is assured because the pioneer of faith is also the perfecter who successfully realized life after death. Part 4 of the thesis (chapter 9) addresses how human beings exercise faith. The question of how a person first participates in the story of faith is difficult, since the author of Hebrews never speaks to this question directly. However, looking at how the author expects humans to exercise faith after they are “in” may offer a glimpse into the way humans can “get in.” I argue Jesus’ faithfulness in sacrifice enables humans to exercise faith, and we subsequently follow the model of Jesus’ faith (christological dimension), moving forward in hope of postmortem life (eschatological). In the present, faith entails endurance to the end (ethical), and this endurance likely involves suffering. Ultimately, we find that the author of Hebrews expects humans to join together with others being faithful (ecclesiological dimension), “going to Jesus outside the camp, bearing his reproach” (13:13).

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  • The burden and management of water related diseases in Maldives

    Saleem, Fathmath Jeehan (2012)

    Masters thesis
    University of Otago

    The study broadly explores water-related disease burden, encompassing drinking-water supply, sanitation, hygiene, climate change and the management of water resources in the Maldives. There have been few studies undertaken which address the burden of water-related diseases in the Maldives. The World Health Organization (WHO) estimates that almost ten per cent of the global disease burden is caused by unsafe water and sanitation; developing countries suffer a disproportionate share of the disease burden. For many small island states like the Maldives, availability of safe drinking water is a factor contributing towards water-related diseases. Most of these islands consist of small, flat low-lying coral islands depending on rain water as their main source of water. The Republic of Maldives consists of small coral islands stretching across 500 miles of Indian Ocean. The unique geography coupled with lack of proper infrastructure for water resources development and management have considerable implications on disease burden, and water related diseases are a major cause of concern in Maldives. A mix of descriptive statistical and qualitative approach was used in the analysis. The quantitative analysis examines the disease burden as indicated by notification data from 1998 to 2008. This was analysed using Excel and Epi Info version 3.4. While this is a broad area of concern the focus of the analysis is on diarrhoea and typhoid as water-borne diseases, malnutrition as a consequence of diarrhoeal disease, and dengue and chikungunya as water-related diseases. Scrub typhus is also examined as a weather-related emerging disease. The findings show that water and sanitation related diseases are prevalent and widespread in both the rural islands and in the urban capital of the country, Male’. Besides, the average rainfall shows strong correlation with disease patterns for diarrhoea, dengue and typhoid. The recent increase in cases of typhoid, which has probably been present historically, the re-emergence of scrub typhus after it was probably introduced in the 1940s and recent establishment of dengue fever and chikungunya have had a considerable impact on the health and well-being of the population. Children are more vulnerable to diarrhoea and dengue while typhoid cases contrast by age of onset. The qualitative investigation was based on semi structured key informant questionnaires. This was conducted on a sample of professionals dealing with water or health issues in the Maldives. The analysis highlights that the atoll populations are disadvantaged not only by geographic isolation, but also in their low level of access to health facilities and basic services. Furthermore, factors such as sanitation, water treatment, water sources, hygiene, extreme weather events, health education and awareness, influence and correlate strongly with disease patterns observed. In addition to this, water supply and infrastructure issues on the atolls also strongly modify the effects. The findings highlight that there is no simple solution to these issues, a combination of multi-sector interventions through policy recognition based on evidence is crucial to reduce the disease prevalence particularly in the atolls.

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  • Regime Transition and Foreign Policy: The Case of Russia's Approach to Central Asia (1991-2008)

    Hazelton, Glen (2012)

    Doctoral thesis
    University of Otago

    In 1991, Russian embarked on an ambitious regime transition to transform the country from communism to democracy. This would be a massive transformation, demanding economic, political, institutional, and social change. It was also expected that the transition would result in significant foreign policy adaptation, as Russia’s identity, direction and fundamental basis for policy-making was transformed. However, it was an unknown quantity how transition in the domestic environment would interact with foreign policy and what the nature of these changes would be. This thesis examines the relationship between regime transition and Russia’s foreign policy. It begins with an examination of literature on regime transition and the types of changes that potentially impact policy-making in a democratising state. It then moves to examining the policy environment and its impact on the contours of policy in each of the Yeltsin and Putin periods, drawing links between domestic changes and their expression in foreign policy. How these changes were expressed specifically is demonstrated through a case study of Russia’s approach to Central Asia through the Yeltsin and Putin periods. The thesis finds clearly that a domestic transitional politics was a determining factor in the nature, substance and style of Russia’s foreign relations. Under Yeltsin, sustained economic decline, contested visions of what Russia’s future should be and where its interests lay, as well as huge institutional flux, competition, an unstructured expansion of interests, conflict, and the inability to function effectively led to an environment of policy politicisation, inconsistency, and turmoil. Tracing relations with Central Asia through this period demonstrates the challenges of transitional foreign policy. Although an apparent ‘consensus’ on a focus on ‘near abroad’ partners emerged in the wake of rising nationalism and political conflict in 1993, it was never consistently implemented. Continued uncertainty, division, and unrestrained political competition, meant Moscow never substantiated opportunities to maintain or increase its influence in the region. This situation changed drastically under Vladimir Putin. Economic recovery, greater agreement on identity and national interests, transformation of the institutional environment and the installation of a more managed, delegative form of democracy stabilised the policy-making context. The political system became more personalised and tightly controlled, while political liberalism and pluralism declined. A smaller range of actors influenced foreign policy and their involvement was more predictable and constructive, though less autonomous. Policy shifted from the previously reactive nature where it catered more to immediate political interests, to demonstrating greater coherence, consistency and long-term, strategic focus. The subsequent change in Russia’s policy towards Central Asia was signficant. Putin saw Russia’s relations with Central Asia as part of an integrated approach to the world. He refocused relations to target economic and security considerations; areas of primary Russian interest and in which he knew Russia had something to offer. The greater coordination of a range of foreign policy actors and the growth of resources at the state’s disposal allowed for more comprehensive strategies. Importantly, it also laid the basis for a more significant future Russian presence, even in spite of the challenges presented by the more vigorous external activity in the region following September 11. Ultimately, Putin’s domestic changes meant that regime transition came to matter less in the formulation and implementation of foreign policy and allowed Russia to pursue a more successful foreign policy in Central Asia.

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  • Marram grass seed ecology: the nature of the seed bank and secondary dispersal

    Lim, Daniel David (2012)

    Masters thesis
    University of Otago

    Marram Grass (Ammophila arenaria), represents a significant threat to the natural values of dune systems in southern New Zealand. Following introduction, marram grass’ primary mode of invasive spread is vegetative. Key studies suggest that sexual reproduction is of lesser importance (Huiskes, 1979; Hertling and Lubke, 1999; Krajnyk and Maun, 1982). In southern New Zealand, observational evidence suggests that seed may play a much more important role in the invasion of marram grass than has been previously thought. This study therefore has two objectives relating to marram grass seed ecology: 1) to investigate the role of secondary seed dispersal in marram invasion in transgressive dune systems; and 2) to determine if marram grass forms viable seed banks in southern New Zealand. The investigation of secondary seed dispersal was investigated along three lines of enquiry. Seed production was estimated for flowering populations of marram grass in six depositional environments at Mason Bay, Stewart Island. This aimed to identify those environments that are important sources of invasion and the potential for invasion via seed. The greatest seed production was found in the exposed populations of the northern and backdune nabkha (17,382.5 and 17,772 seeds m-2 respectively). The lowest production was found in the semi-stabilised and moribund populations on the trailing arms and coppice dunes (196.5 and 39.4 seeds m-2 respectively). Seed production may be related to the input of fresh sand. Understanding which factors affect germination and emergence in marram grass seed was a key factor in the first objective of the study. The effects of light and darkness and burial appeared to play a major role in determining germination. Marram grass seed was shown to be highly sensitive to light and failed to emerge from depths greater than 5 cm.The restriction of light penetration with increasing burial may be the main factor inhibiting germination in marram grass seed. Marram grass seedling distribution data was compared against dune environments at Mason Bay. Previous literature suggests that the deflation surfaces (i.e. stonefields) would provide ideal microsites for emergence of seedlings by increasing soil moisture and protecting from micro-erosion. Analysis of seedling distribution however showed a greater proportion of seedlings concentrated outside of deflation surfaces (68.26%) compared to within (31.74%). This finding may be due to the high rainfall experienced at Mason Bay, the eroding nature of the deflation surfaces or the greater overall area of sandsheets. A unique opportunity was taken to age the marram grass seed bank in two dune systems in southern New Zealand. Viable seed recovered from St Kilda and Allan’s Beach was aged between 0 to 21+ years old. The longest previous estimate of marram grass seed bank longevity is ‘at least 9 years’, making this result particularly significant. The marram grass seed bank may therefore represent a significant threat of re-invasion following control on the foredune. The final outcomes of this research are a conceptual model of invasion by marram grass seed and management recommendations for ongoing and future marram grass control operations. The entire invasion process is expected to take between six to nine years. Empirical information relating to some aspects of marram grass invasion ecology is currently unavailable and is therefore a key area of future research. Future control operations need to monitor the foredune at least 21 years following eradication and bi-annual systematic searches are required to prevent the establishment and flowering of any new seedlings.

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  • FPGA Based Radio

    Scott, Ian Russell (2012)

    Masters thesis
    University of Otago

    This thesis describes a demonstration field programmable gate array (FPGA) based radio intended for high frequency applications. This prototype uses a Xilinx Spartan-3 FPGA to provide many signal processing functions previously executed in a microprocessor or DSP. The FPGA radio described here has separate receive and transmit functions. Operating frequency and channel bandwidth are software configurable. System test frequency was 13.45 MHz corresponding to a University narrow band frequency shift keying licence. The system uses three processes – radio frequency (RF), mixed signal devices (MSD) and FPGA computation. Several Xilinx IP cores are used integrated with Verilog code. The receive path uses direct analogue to digital converter (ADC) signal acquisition using the FPGA system clock at 50 MHz. The transmit path uses a similar approach using a digital to analogue converter (DAC) at the same clock rate. A number of technologies have been used in this implementation. These include direct digital synthesis (DDS), cascaded integrator comb (CIC) decimation, digital frequency down conversion (DDC) to and Q, complex frequency demodulation, software pulse width modulator DACs with 10 bit resolution and parameter tuned digital filters (PTDF). The system has been successfully built and tested. Receive and transmit channels have behaved as predicted. It is shown that low cost, medium resolution mixed signal devices can achieve land mobile radio communication performance standards. From this, increased MSD bit resolution can be expected to exhibit even higher performance.

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  • Dietrich Bonhoeffer's Spatially Structured Ecclesiology. Reconfiguring the Confession of Christ's Presence.

    Fergus, Donald Murdoch (2012)

    Doctoral thesis
    University of Otago

    From the beginning of his career Dietrich Bonhoeffer was invested in describing and then crafting a form of religious community that provided a way of being human, and a form of corporate sociality that was grounded in and grew out of the presence of the person of Jesus Christ. The sanctorum communio was that form of sociality. Bonhoeffer’s ecclesiology was the outcome of his relentless searching for a form of the church that could meet the challenges of National Socialism’s Third Reich and contribute meaningfully to the life of the German nation. A reading of Bonhoeffer reveals the widespread use of spatial metaphors or descriptors in the development of his ecclesiology. Bonhoeffer was always interested in the empirical church and a careful reading shows how his spatially structured ecclesiology underlies and supports the church’s Christological core and its communal nature, giving a concrete form to the ministry of the church in the culture in which it is embedded. Bonhoeffer’s ecclesiology serves to shape the way in which the church structures its confession of Christ’s presence in the world, while at the same time keeping a steady eye on the church as a creation and gift of God. The quest for a vibrant articulation of Christ’s presence becomes a persistent hermeneutic throughout Bonhoeffer’s writing. His robust doctrine of the church based on the images of place and space leads eventually to the form of the suffering servant, Jesus Christ. Collectively, the images build a compelling case for a form of sociality that brings the motifs of self-giving love and of dying and rising in Christ together to shape discipleship in Christ and the theological reflection on that discipleship. Bonhoeffer's use of spatial imagery places the church’s central acts of announcing and bearing witness to the word of God, and its celebration of the sacramental enactments of that word of promise and hope within a particular space in which the church is highly visible. Bonhoeffer called this ‘the living space [Lebensraum] of the visible church-community’. It is from within this living-space that the church is committed to pushing back the boundaries of life until the world is held by Jesus Christ, the Lord of Life.

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  • Nutritional Optic Neuropathy in Papua New Guinean Prisoners

    Gould, Camilla Alice (2012)

    Masters thesis
    University of Otago

    Since 2000, ophthalmologists providing clinical services in Madang, Papua New Guinea, have become aware of local adult prisoners presenting with gradual vision loss. An informal assessment conducted in Beon Jail in 2007 indicated that at least 40 local inmates had a significant level of visual impairment. This was most commonly associated with atrophy of the optic nerves, a result of optic neuropathy (ON) and suspected to be caused by nutritional deficiency. A more detailed assessment of the prison population including clinical characterization of the ON, comprehensive dietary analysis and assessment of toxic risk factors was necessary to help determine disease aetiology and appropriate treatment for prisoners. In May 2010, a collaborative project between the Fred Hollows Foundation and the University of Otago was made to further investigate the occurrence of ON previously documented in Beon Prison. All adult prisoners detained in Beon Prison (264 persons) were invited to participate in the study. Beon prison guards were also invited to participate on the basis of some shared environmental exposures with prisoners. Consenting participants were individually interviewed regarding demography, general and ocular health, diet and lifestyle. Participants underwent a vision and ocular examination as well as a physical examination performed by a team of trained health workers. A 24-hour dietary recall interview was performed on each participant and a venous blood sample was collected by venipuncture for the analysis of nutrients and other biomarkers. As an additional measure of dietary intake, samples (n=30) of prison rations were weighed and analysed for nutrient content. Finally, prison food samples were analysed for lead and cadmium content. Consent was obtained for 158 prisoners and 17 prison guards. Due to a low female contingent in the prison, only data collected from males was analysed. ON was found to be present in the prisoner population. Of the prisoners examined (n=135), 14 had ‘definite’ or ‘likely’ ON and 30 had ‘possible’ ON. No guards had ‘definite’ or ‘likely’ ON. No cases of peripheral neuropathy were found in participants. The prisoner diet predominantly consisted of rice, canned corned beef, canned tuna, water-crackers, tea and water. The fruit and vegetable consumption of the prisoners was low - 66% reported to never or rarely consume fruit and vegetables whilst in prison. Nutrient intake data generated from the 24 –hour recall suggested that less than 25% of prisoners met the estimated average requirement (EAR) for vitamin A, folate, vitamin C, vitamin E, potassium and calcium. Biochemical assessment indicated that over half of the prisoners fell below the cut-offs values of deficiency for biochemical indicators of vitamin A, folate and vitamin C. An elevated plasma homocysteine concentration was also found in 79% of prisoners. Blood concentrations of α-tocopherol, thiamin, B12 and selenium predominantly fell within normal ranges (<5% below recommended cut-offs). Both age and time of incarceration in Beon Prison were significantly correlated with ON severity. A significant inverse trend between ON severity was found with both whole blood folate and red blood cell folate concentrations using linear regression when adjusted for age and time of incarceration. Investigation into possible toxic causes of the disease showed a low exposure of prisoners to common risk factors of ON including alcohol, cassava, and lead. Other risk factors including tobacco and the use of certain pharmaceutical drugs were not correlated to disease risk. Our findings suggest that folate deficiency has a likely aetiological role in the ON found in this prisoner population. The involvement of other B-vitamins, nutrient deficiencies or toxic agents may however be causal or contributing to the onset and development of ON. This investigation highlighted nutritional ON in prisoners of Beon jail, Madang. As a response to these findings recommendations for multivitamin supplementation and dietary changes including the addition of fruit, leafy green vegetables and milk powder to the prison diet have been made to the prison authorities in order to correct nutritional deficiencies and to prevent further cases of ON.

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  • Optimal design methods that are robust to uncertainty

    Foo, Lee Kien (2012)

    Doctoral thesis
    University of Otago

    Assumptions are usually made when optimising design for an experiment. Unexpected departure from the assumptions may result in suboptimal design. This thesis aims to address the issue of optimal design under uncertainties. Various optimisation methods were proposed to locate optimal design that is efficient even if the assumptions do not fully hold. A hypercube optimal design (HClnD) was proposed to address the issue of uncertainty in the parameter space, where D-optimal design for nonlinear models has an issue of dependency on the parameter values. The HClnD criterion is presented in Chapter 2 and was compared to other robust design criteria in terms of efficiency, relative errors and computational cost with simulation studies. The performance of HClnD was further evaluated in Chapter 3 where the optimality criteria in this chapter are solved analytically whenever possible and numerically otherwise for two simple nonlinear models. HClnD was shown to be as efficient as other robust methods and consumed less computational cost. This robust criterion was applied prospectively to design a three arm double blind pharmacokinetic (PK) clinical study for two drugs (midazolam and droperidol). The design was evaluated in Chapter 4. An adaptive optimal design method was proposed in Chapter 5 to design experiments for PK bridging studies. In a PK bridging study the researcher uses knowledge of the PK model from a prior-population to design the experiment for a target-population. The design is suboptimal if the PK profile of prior and target-populations are widely diverged. The proposed adaptive optimal design was compared to optimal design for target-population based solely on the prior-population information. The proposed method was superior in the estimation precision when the PK profiles of the two populations are widely divergent and comparable precision when the PK profiles are similar. Sampling windows is used to ensure certain degree of design efficiency under execution uncertainty, where samples may not be collected following exactly the optimal design. Two methods to construct sampling windows for nonlinear mixed effects models were proposed in Chapter 6. Initially a naïve adaptive method that determines the window for the next sample when the previous and current samples become available was proposed. Another method is a recursive random sampling method that is based on the Gibbs sampling techniques. Both methods were applied to locate sampling windows for a population PK study and tested via simulation. Finally, an optimal design method to minimise the cost for phase II PK clinical studies was proposed in Chapter 7. An additional level of uncertainty when designing phase II clinical study based on the population PK estimates from healthy volunteers in phase I study was incorporated in the form of hyperprior distribution. In this design, the expected cost is minimised. The resulted optimal design accounts for both cost of the study and the probability of study failure. The proposed optimisation method was shown to locate designs that attained high power, without the need to define the power a priori, and without the need to define upper constraints in the design space.

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  • Spatial ecology of introduced mammalian predators in New Zealand: using satellite technology to quantify resource selection

    Rodríguez Recio, Mariano (2012)

    Doctoral thesis
    University of Otago

    Introduced predator mammals have caused significant impact on New Zealand’s native species, typical of the global phenomenon of biodiversity loss caused by biological invasions. Introduced predators need to find the required resources across a hierarchy of spatial and temporal scales to survive in recipient ecosystems. Improved understanding of the ecological and behavioural processes mediating resource selection can be used to improve strategies to control introduced mammal populations using traps and poison baits. Areas of high-use by predators can be related to specific microhabitat characteristics, and ultimately the distribution and availability of suitable microhabitats patches within selected macrohabitats will determine home range establishment and thus species distribution. Hence, identifying and quantifying the landscape configuration and composition of high-use areas of target species at fine-scale can inform trap or bait station placement so as to maximise likelihood of encounter within managed areas. Spatial ecology research is being facilitated by current technical advances in remote sensing, spatial analysis tools and methods, and wildlife tracking systems. This project applies Global Positioning System (GPS) tracking and remote sensing techniques to quantify fine-scale resource selection by two introduced predators, the feral cat (Felis catus), the largest introduced carnivore in New Zealand, and the European hedgehogs (Erinaceus europaeus) one of the smaller predators. Both species represent different behavioural patterns, require different designs of lightweight GPS-devices, and pose a threat to ground nesting birds, such as the critically endangered black-stilt (Himantopus novaezelandiae) in braided rivers of the central South Island. Technical advances now make it possible to track medium-to-small mammals using GPS devices. However, limitations of the new technology have been assessed only for applications on large mammals and thus an evaluation for smaller species, with different behaviours and use of microhabitat features, is required. This research demonstrates through stationary, movement and on-animal tests, that lightweight GPS-collars perform on average similarly to the larger and heavier collars deployed on larger mammals. Models of animal movement and resource selection at fine-scale require the collation of landscape covariates with higher spatial details than those available from most resource maps currently in use. The combination of very high spatial resolution (VHSR) satellite imagery, including spectral-rich multispectral bands and spatial rich panchromatic band, and classification techniques on object-based imagery analysis (OBIA) was used to derive resource maps from which were extracted landscape cover and metrics at fine-scale. The classification of a Quickbird image covering the selected study area (Godley Valley) using OBIA reveals that heterogeneous patchy landscapes can be more accurately classified and small features (e.g., shrub clumbs) better identified by using these techniques. The level of accuracy required depends on the ecological question and whether this question can justify the extra cost of incorporating the panchromatic band. Analyses on the spatial ecology of feral cats revealed that the species mainly establish home ranges conditioned by rabbit (Oryctolagus cuniculus) abundance, including mosaics of pastures and shrubs at low elevation, and other variables such as presence of boulders on scree slopes for den sites. Core areas of high use are mainly composed of pasture and shrub mosaics. Hedgehogs establish home ranges in landscape mosaics most likely supporting high invertebrate abundance (i.e., high productivity vegetation such as green pastures), habitat edges for dispersal movement, near tracks and avoiding proximity to gravel roads. Core areas of high use are mainly mosaics of green pastures, tussocks (to provide food and dry nesting materials) and shrubs (shelter). Traps and poison bait stations used for lethal control of these two introduced mammalian pest species are recommended to be placed according to the specific landscape patterns identified as important for each respective species. The satellite-based techniques presented in this thesis have been shown to provide data suitable for analysis using current methods to study the resource selection of medium-to-small mammals. Applications of this technology could be extended to address more mechanistic approaches to studies of individual activity patterns, movement behaviour, and intraspecific interactions.

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  • Prefrontal cortex delay activity: Sample code or reward code?

    Browning, Rebecca (2012)

    Masters thesis
    University of Otago

    Prefrontal cortex (PFC) delay activity found in working memory tasks has been said to be a neural correlate of memory. However, similar PFC delay activity has been found in reward tasks. Given that a reward usually follows a correct response in a working memory task, it is unclear whether delay activity found in these tasks is actually a memory trace. We examined whether delay activity in the avian equivalent of the prefrontal cortex represents a neural correlate of a to-be-remembered sample or an upcoming reward. Birds were trained on a directed forgetting paradigm in which sample stimuli (red and white) were either followed by cues to remember (high tone) or a cue to forget (low tone). In addition, the task also incorporated a differential outcomes procedure in which a correct response on the memory test following a red (remember) sample was rewarded with food, but correct responses on the memory test following the white (remember) sample were not. If delay activity represents a sample code, then it should be seen on both red-remember and white-remember trials. On the other hand, if delay activity represents a reward code, then delay activity should be seen only on red-remember trial, but not white-remember trials. The findings suggest that activity in the avian prefrontal cortex represents the outcome associated with each sample (reward or no reward) rather than memory for the sample itself.

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  • Logic and Normativity

    Olsen, Elizabeth (2012)

    Masters thesis
    University of Otago

    What is the relationship between logic and thought? One view is that logic merely describes how people think. But this view – called 'psychologism' – cannot be quite right. Logic cannot describe how people reason, because although people can reason well, they can also reason badly. The obvious response is to say that logic does not describe how people do think, but rather prescribes how they ought to think. If logic describes how people ought to reason, then if the premises of a logical argument imply the conclusion of that argument and you believe the premises, then you ought to believe the conclusion. According to classical logic the premise, 'grass is green' implies the conclusion, 'the sky is blue or the sky is not blue', but it seems absurd to say that because I believe that grass is green, I ought to believe that the sky is blue or the sky is not blue. What has gone wrong here? Should the principle, 'if the premises imply the conclusion and you believe the premises, then you ought to believe the conclusion' be changed? If so, perhaps it would be more correct to say, 'if the premises imply the conclusion and you believe the premises, then you have reason to believe the conclusion'. Or is classical logic to blame? Are we mistaken in thinking that 'grass is green' implies 'the sky is blue or the sky is not blue'? I examine a number of arguments that relate to this question. I argue that classical logic deserves a philosophy of logic that does not imply that classical logic is not proper logic.

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