27,490 results for The University of Auckland Library

  • Smart functionalized catalytic films for drinking water purification

    Ismail, Nabilah (2015)

    Doctoral thesis
    The University of Auckland Library

    This thesis which is entitled ???Smart functionalized catalytic films for drinking water purification??? is a stepping stone towards overcoming this problem. This thesis evolved around designing new polymers that can be used to make membrane films which can anchor oxidation catalysts such as Fe-(TAML)s, concentrate pollutants and deliver hydrogen peroxide and base to the catalyst centres in a systematic and efficient way so that large volumes of water can be purified without having to contaminate the bulk water solution. In the first chapter green chemistry, oxidation chemistry, the use of hydrogen peroxide chemistry as an oxidant, and common contaminants found in wastewater are discussed, and in addition an overview of homogeneous and heterogeneous catalysts is given. In the second chapter details about the development of the special polymer that was used to form the smart catalytic films (SCFs) in this project is covered. In particular, details of how the polymer was formed, cast, cured, crosslinked and functionalized are discussed as well as the methods used to anchor the catalyst to the polymer film. Details of the mechanism by which the iron-TAML oxidation catalysts operate are presented since most of the subsequent studies involved the use of these compounds. Finally, preliminary studies of the performance of the SCFs in simple catalytic dye bleaching reactions are presented. These studies were carried out so that the most promising SCFs could be selected for further more detailed studies. In the third chapter details of the more comprehensive tests carried out on the selected SCFs is covered. Catalytic oxidation experiments were carried out using water soluble organic dyes as surrogate pollutants with the smart catalytic film used in 3 different configurations; (i) simply suspended in solution in a beaker, (ii) as part of a ???U-tube??? device that uses the catalytic film to separate the hydrogen peroxide solution from the substrate (pollutant) solution and (iii) a ???cross-flow??? device that uses the catalytic film to separate the static hydrogen peroxide solution from the flowing substrate solution. In these three configurations the effects of changes to parameters such as pH, types of catalyst, catalyst loading and turbulent flow on the performance of the SCFs were investigated. Finally, in chapter 4, the results of studies aimed at using the smart catalytic films to reduce or completely remove actual contaminants such as 17??-ethynylestradiol (EE2), Bisphenol A (BPA) and Triclosan (TCS) are presented. In these studies the catalytic films were used in the three different configurations detailed above under the semi-optimized conditions that were discussed in chapter 3. In the case of the studies with BPA and EE2, some preliminary tests of the estrogenicity of the oxidation products formed after catalytic oxidative treatment with the SCFs were carried out using a yeast estrogen assay (YES) test to confirm that with the oxidative removal of these compounds from solution there was a corresponding drop in estrogenicity characteristics.

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  • Choreographing through an expanded corporeality

    Cowan, Suzanne (2017)

    Doctoral thesis
    The University of Auckland Library

    This practice-led research explores the potential for an expanded corporeality through choreography and a posthuman ethics. Engaging somatechnics (body technologies) such as rope tying and Contact Improvisation I develop techniques that seek to rupture the binaries of nature/culture and dis/ability through performance. These techniques establish somatic processes for sharing weight, experiencing suspension and torsion through the body and a tactile exchange with the environment and participating audience. They take shape through rhizomatic rope structures that create complex interconnected systems of support. Through using these techniques to investigate our relationality, I reveal a permeable, porous subjectivity and an erotics of connectivity. My position is that we are always already extended: we lean, touch, and absorb the surfaces surrounding us which can allow us to experience ourselves as dynamic, fluid identities. Throughout this thesis the process of exploring dynamic identities is led by a part-real, part mythical entity called Ethico Super-Girl. She introduces each chapter including the final performance submission, Knot Just Body, a culminating experiment in intimacy, relationality, and ethics. The notion of an expanded corporeality is inspired by ontologies of vulnerability and permeability. It unfurls its choreo-philosophy through engaging with theoretical insights such as Margrit Shildrick???s concept of the distributive body, Rosie Braidotti???s posthuman ethics, and Karen Barad???s theory of queer entanglements. The diacritical cut, introduced by Ann Cooper-Albright and Gabriele Brandstetter (2015), is used as an analytical tool to reveal the potentially transformative space between the ???dis??? and the ???ability???. In referencing the work of other artists such as Claire Cunningham, Bob Flanagan, and Rita Marcalo, I demonstrate how queer transformations taking place through contemporary performance trouble assumptions about the boundaries of the body and relations between performer and audience. While dance studies has a well theorised frame of expanded choreography (Harvey, 2011), little attention has been paid to the possibilities inherent within an expanded corporeality. This research offers an original conception of how an expanded corporeality can both reimagine and construct through performance how we inhabit space and specifically our response to dis/ability, through performance. It calls for more pluralistic understandings of embodiment. The techniques and theoretical positions developed in this thesis are relevant to practitioners and scholars in disability studies, dance studies, queer theory, posthumanism, and new materialism.

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  • Energy Minimisation by Concurrent Propagation with Applications to Stereo Matching

    Gong, Rui (2017)

    Doctoral thesis
    The University of Auckland Library

    Classical energy minimisation paradigm based on probabilistic models of input and output data, employs an energy functional which combines the weighted prior energy of output, with a conditional energy of the input given the output. The regularising weight controls an adequacy of solutions establishing the correspondence between input and output data, to select a unique goal solution out of a multiplicity of these solutions for most frequent ill-posed problems. Such a weight is usually chosen by hand, and different choices may affect the output in unpredictable ways. This thesis proposes an alternative Two-Stage energy minimisation paradigm by treating separately both the energy terms. The First-Stage employs a very simplistic prior to obtain and store a whole set of minimisers of the ill-posed and non- regularised initial problem. Then the second stage selects an adequate solution only within the stored set of minimisers. The proposed Two-Stage paradigm needs no regularising weight, which implicitly pursues two different goals: to choose a suitable solution amongst the set of energy minimisers and include to this set not only primary but also secondary minimisers of the unregularised energy to account for unavoidable random deviations (noise) of the input data.

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  • Effects of grain boundary structure in discrete simulations of multiscale dislocation dynamics

    Burbery, Nathaniel (2017)

    Doctoral thesis
    The University of Auckland Library

    This research develops a multiscale approach to study the defect-driven evolution of the microstructure in polycrystalline FCC metals, by using atomic-informed models to reproduce multi-grain, microscale simulations with discrete dislocation dynamics (DD). The dynamically evolving dislocation and grain boundary (GB) microstructure dictate the non-linear ???plastic??? response of polycrystalline metals during deformation. The processes of intercrystalline plastic coupling are generally a consequence of multi-dislocation pile up interactions with GBs, however such effects are beyond feasible limits of conventional atomic simulations or experimental studies. More accurate computational models of the discrete micro-macro scale dislocation and GB dynamics could be applied to elucidate the fundamental mechanisms and reduce the dependence on costly experimental testing. This work expands upon the physics-based single crystal DD framework by using molecular dynamics simulations to develop structure-property models that compensate for the variable characteristics of GB interfaces. This research involved studies with a broad set of equilibrium, non-equilibrium and metastable atomic bicrystals. The results showed that the intercrystalline strength was strongly influenced by the ???GB shape??? characteristics of the structural free volume, in addition to the intrinsic energy. Defect interaction studies verified the realistic conditions for the observation of structural multiplicity, and showed the significance of intermediate ???transitory??? GB states. Observation of the slip transmission process showed that the GB dislocations acted as pinning sites, so that the intercrystalline plasticity resembled Orowan-type obstacle bypassing. A novel multi-orientation approach was developed to provide a control routine for modelling atomistic dislocation dynamics that enabled a self-consistent multiscale comparison with DD simulations. Insights regarding dislocation core construction and Burgers vector analysis played an integral role in the development of atomically accurate DD representations of the GB dislocation structures. A world-first 3D polycrystal DD approach was implemented to provide a discrete representation of the dislocation structure of high angle GBs, through the culmination of the atomistic insights and many years of concerted code development. This robust, versatile implementation enables tailor-made polycrystal simulation specimens with arbitrary shape, grain orientation and size to be generated from common .stl files. The unique, comprehensive modelling framework provides a realistic reproduction of key intercrystalline slip mechanisms including GB sliding, dissociation and absorption, dislocation transmission and reflection. As such, the present work provides a novel contribution of relevance, particularly, to the developing sector of GB engineered nanocrystalline materials.

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  • ???True of Voice????: The speech, actions, and portrayal of women in New Kingdom literary texts, dating c.1550 to 1070 B.C.

    Crowhurst, CJ (2017)

    Doctoral thesis
    The University of Auckland Library

    This thesis will examine texts from the corpus of ancient Egyptian love songs, narrative tales, and funerary literature (The Book of the Dead, specifically that of Anhai, Chantress of Amun), dating to the New Kingdom, c.1550 to 1070 B.C. I shall focus on the presentation and speech of women within these three literary genres, analysing not just what women say and do, but also what is said about them and their actions. However, this thesis does not aim to give an Essentialist account of women, as a homogenous group, in New Kingdom Egypt. Instead, I will discuss some of the constructs of gender and gendered identity in ancient Egypt as revealed by these texts, constructs that go beyond an overly simplified male vs. female binary opposition that is based on biological sex alone. In order to do this, I will use intersectional analysis in conjunction with a close reading of the texts, and concepts of transformations, liminality, and transfigurations in relation to individual identity will be addressed. One of the central concerns of this thesis is that of gender ventriloquism, the act of somebody putting their own words into the mouth of someone or something of a different gender to the original ???speaker.??? This ???speaker??? may be a fictional constructed character or a historically attested individual. In this study, these words must, out of necessity, be examined in written form, as ancient Egyptian is a dead language. The writer of these words must therefore be taken to be exactly that: someone who has written them down and not necessarily composed or invented them. Indeed, we do not have a named ???author??? in the modern sense for any of the texts analysed in this thesis, although in some cases we do have the name of the ???owner??? of the source, or the scribe who wrote the words down. These factors lend themselves to a post-structuralist analysis of the texts, wherein I will consider them to be the product of a specific cultural milieu rather than only as the individual creation of a single person. The transmission as well as genesis of the texts therefore relies on both collective understanding and social reception to impart a desired message that may be accepted, altered, or rejected by the receiver(s), both ancient and modern. Although the content of the sources is largely culture-specific, certain aspects can be regarded as perennial, or at the least able to cross cultural borders. In the case of the texts analysed, I will argue that their transmission would be at least partly in oral form, most likely performative and potentially mutable to a degree. This then gives a physicality to the ventriloquism, a way of verbally actualising another???s speech, and a means of vocally performing and even manipulating gender constructs. Feminist theory therefore plays a substantial part in my reading of the texts; both Anglo-American, regarding the performativity of gender, as well as French, in terms of linguistic expressions of gender. Lastly, performance theory relating to the suspension of disbelief is considered, particularly in terms of creating a connotative non-literal identity through specific usages of the literature that often overrides, or at least modifies, the denotative identity of the gendered individual. Here, the themes of liminality and transformation already presented will be discussed alongside modern discourse from this discipline. My overall aim is to present a new reading of texts that are already familiar to Egyptologists, using modern theory in a way that can lead us to re-evaluate and deepen our understanding of gender constructs in New Kingdom Egypt. In this way, we are able to recover the lives and experiences of individuals who most often exist only on the peripheries of our extant literary evidence and in academic studies.

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  • Maternal Matters: A Narrative Analysis of Mother-Daughter Family Business Dyads

    Kilkolly-Proffit, Michelle (2016)

    Doctoral thesis
    The University of Auckland Library

    The literature on parent-adult child family business dyads is traditionally focused on father-child led firms. These studies are predominantly concentrated on intergenerational transfers in family firms and include both father-son dyads and a growing body of father-daughter literature (cf. Davis, 1982; Davis & Tagiuri, 1989; Dumas, 1990; Hollander & Bukowitz, 1990; Humphreys, 2013). Less visible are mother-son family business dyadic studies (cf. Kaslow, 1998). Higginson???s (2010) recent contribution examining relational factors and knowledge transfer in mother-daughter businesses and Vera and Dean???s (2005) comparative study of succession in father-daughter and mother-daughter led firms are among the very few examining the mother-daughter family business dyad. This study examines four mother-daughter family business dyads who own their firms. Each daughter is also a mother. Using the life story interviewing techniques and tools of Atkinson (1998) and McAdams (2008), and an adapted family history method (Miller, 2000), this research takes an interpretive, narrative approach to examine the key influences shaping these dyads. Firstly, this study identifies key influences and then explains how these have contributed to shaping these family business women, their families and their approaches to their business undertakings. Within-dyad and across-dyad findings across four overarching themes: the influence of family of origin, the influence of created family and motherhood, the influence of mother-daughter relationship and career, business and opportunity journey contribute to shared narratives for both generations. A ???baseline understanding??? (Gross, 1998; Shenton, 2004) informing a baseline typology was derived for the four mother-daughter family business dyads in this study. This was garnered from the shared narratives using axes of business approach: entrepreneurial or small business, income and time. The categorizations that emerged were ???The Lifestylers???, ???The Artisans,??? ???The Growth-Opportunists??? and ???The Dependents.??? This baseline typology or characterization of these four dyads provides a starting point towards further understanding of the mother-daughter phenomenon in future studies. The dearth of studies on mother-child firms indicate that a potentially rich contribution in family business discourse is being largely overlooked. Nelton (1998), Vera and Dean (2005) and Higginson (2010) have called for more research on mother-daughter family business successions. This study, examining two generations of family business women leading their own family firms, contributes to further gendered discourse on the influences shaping mother-daughter family business dyads and goes some way towards answering their call.

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  • The intercultural dimension in language classrooms in Aotearoa New Zealand: A comparative study across languages and teachers??? levels of proficiency

    Suarez Ramirez, EM (2018)

    Doctoral thesis
    The University of Auckland Library

    In the last two decades, language teaching around the world have shifted the place of culture from the periphery to the core, acknowledging that cultures shape language and how it is used. This has led to the development of intercultural language teaching. The benefits of this approach and how teachers understand and implement it are part of a growing field. However, few studies have addressed the issue of the influence of language teachers??? level of proficiency in this context. Language teachers in Aotearoa New Zealand schools are encouraged to follow an intercultural approach in their classrooms. In 2010, a report was published to provide language teachers with an intercultural communicative language teaching (iCLT) framework of principles to integrate culture into the teaching of languages (Newton, Yates, Shearn, & Nowitzki, 2010). The report focuses on the development of intercultural capacities to communicate empathetically and respectfully with people of different languages and cultures, rather than simply concentrating on language skills. This study investigated the relationships between language teachers??? conceptualisations of iCLT and their practices. Furthermore, it investigated whether teachers??? level of proficiency in the target language was related to their conceptualisations and practices. Subsequently, potential points of departure (i.e., opportunities) for language teachers??? development of interculturality in their classrooms are illustrated. These examples may also be useful beyond the context of Aotearoa New Zealand. Given that the iCLT framework (Newton et al., 2010) was influenced by intercultural theory from various contexts, this study is part of a global conversation around the implementation and development of the intercultural dimension in the language classroom. Qualitative data were gathered from semi-structured interviews, teachers??? reflections, and classroom observations of 16 language teachers of Chinese, Japanese, French, and Spanish (four of each) in Aotearoa New Zealand. Data were analysed using Newton et al.???s (2010) framework of principles as a lens for interpretation. The findings demonstrated an inconsistent relationship between conceptualisations and practices. Evidence of a principle in teachers??? conceptualisations was not a reliable indication of the principle in their practices, or vice versa. The data were also quantified to provide a visual depiction of teachers??? conceptualisations and practices, and the relative difficulty participants experienced with implementing aspects of the principles in their classrooms. As a contribution to the field of iCLT, the findings suggest that neither being a first language (L1) speaker, nor proficiency in the target language, ensured teachers??? implementation of iCLT. Across all languages and teachers??? levels of proficiency, participants generally demonstrated an implicit potential for intercultural teaching. Implicit potential is understood as unconscious, unplanned, and automatic abilities, conceptualisations and practices, attributes that were investigated to indicate teachers??? intercultural communicative competence (ICC) and iCLT. Furthermore, the target language did not appear to play a role in the development of the intercultural dimension in teachers??? classes. There was some evidence of the efficacy of teacher professional development on intercultural communicative language teaching, highlighting that professional development appeared to be most effective when interculturally targeted. Finally, another contribution of this thesis is an illustrative narrative for language teachers, constructed to summarise the complexity inherent in the iCLT principles; to demonstrate each principle???s inextricability from the others; and to facilitate their implementation.

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  • Poly-phase Inductive Power Transfer Systems for Electric Vehicles

    Kim, Seho (2017)

    Doctoral thesis
    The University of Auckland Library

    Inductive power transfer (IPT) was ???rst discovered over a century ago as a method of electromagnetically transferring power. The absence of physical contact enables IPT systems to achieve advantages over conventional conductive methods, allowing greater freedom of movement in the secondary, electrical isolation and resistance to abrasion, corrosion and environmental factors. Due to these advantages, IPT systems have become increasingly ubiquitous during the past two decades in a wide spectrum of applications ranging from materials handling to biomedical devices and battery charging. One application of IPT systems that has shown promise recently is wireless charging of electric vehicles (EVs). As the number of EVs on the road continues to increase in the future due to lower life-time costs of EVs and environmental concerns, wireless charging of EVs is a convenient alternative that could complement the relatively short range of EVs. As IPT systems for EV charging is an active topic of research, numerous systems have been suggested to date. However, a disjoint is present between many of the proposed systems since each system is designed for a speci???c range of power levels for either smaller passenger vehicles or larger vehicles for materials and public transportation. The interoperability problem is further exacerbated by the systems using di???erent magnetic structures topologies with sizes and tolerances to misalignments that are speci???c to their application. Additionally, these IPT systems need to minimise the generation of leakage magnetic ???ux, which is the unwanted stray magnetic ???ux that may be harmful to people. Constraining the leakage magnetic ???ux below the regulatory guidelines potentially impedes IPT systems from transferring high levels of power. This thesis investigates the use of multiple independent coils in IPT systems to solve the challenges in power transfer capability and leakage magnetic ???ux. A collation of mathematical models are derived in order to understand the functionality of systems with a single coil or multiple independent coils. A controller is designed based on the mathematical models to optimise the energisation of the systems with multi-ple independent coils to generate magnetic ???eld shapes that minimise e???ort exerted from the primary electronics to transfer power. The controller is implemented on a new magnetic structure proposed in this thesis called the Tripolar pad (TPP), which consists of three independent coils that can be energised individually, to evaluate the performance of the proposed pad. A TPP under optimal control conditions for maximising coupling to the secondary is shown to be interoperable with existing magnetic structure topologies and highly tolerant to misalignments of the secondary by generating magnetic ???eld shapes that best suit power transfer. IPT systems using such a TPP to transfer power at 3.3 kW and 20 kW are examined in the thesis to show that the TPP is suitable for transferring both lower and higher power. The TPP can also be built using a similar volume of material to conventional pads and driven with power electronics with lower VA ratings, which substantially o???sets some of the cost from the additional switches, diodes and tuning networks. The TPP is also found to generate less leakage magnetic ???ux than other magnetic structure topologies in most cases, especially when the secondary is misaligned. The ???ndings in the thesis indicate that IPT systems using multiple independent coils, such as the TPP, are a viable alternative to other conventional IPT systems for EV charging.

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  • Studies Towards the Design, Synthesis and Analysis of Antifreeze Peptides and their Potential Applications

    Kong, Ho (2017)

    Doctoral thesis
    The University of Auckland Library

    Polar organisms produce antifreeze proteins (AFPs) that bind ice, modifying and inhibiting the growth of large ice crystals, and thereby protecting the host from freeze damage. This phenomenon has huge potential and AFPs are ideal candidates for cryopreservation applications ranging from biomedical to food technologies. In this thesis, a biomimetic approach to control ice crystal growth is proposed, based on AFPs from polar fish and insects. In the first part of this thesis, a range of AFP analogues based on those produced by polar fish and insects were synthesized and systematically studied for their effects on ice crystal shape with and without a small-molecule enhancer. The results highlighted some important structure-activity relationships of the AFPs and illustrated the effect of length, amino acids, and intra-coil bridging mechanisms on the ice-shaping behaviour of the peptides. The effects ranged from no shape modification and no thermal hysteresis to a strong shape modification and a significant thermal hysteresis. The results were then related to a general AFP ice binding model. CD spectroscopy was undertaken to determine the conformation of the peptides in solution. In the second part of this thesis, the general principles of crystal growth modification using peptides as additives (described in Part I) were used to explore the potential application of AFPs in frozen food. AFPs were used as an antifreeze treatment for frozen food that successfully modified the growth of ice crystals within the food structure. The effects of these AFPs on the ice crystal size, drip loss, texture, volatile compounds, total phenol content, total anthocyanins content, and total antioxidant properties of frozen fruits and vegetables were investigated. The results showed a significant positive effect of AFPs in frozen food applications. Based on the results, future work to develop efficient peptides for cryopreservation applications is suggested.

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  • Whatuora: Whatu k??kahu and living as M??ori women

    Smith, HL (2017)

    Doctoral thesis
    The University of Auckland Library

    M??ori women play a vital role in enabling our children and grandchildren to live secure, positive cultural identities ???as M??ori???. In utero we surround our children in a protective kahu (meaning cloak and also amniotic sac) and after they enter the world we continue to ???cloak??? them in tangible and abstract ways with our values, beliefs and aspirations. Of the multiple aspirations that M??ori women hold for ourselves and our wh??nau to be healthy, happy and ???whole???, this research concerns itself with M??ori women???s aspirations to ???live as M??ori??? ??? understood as living a full and holistically well life, connected to people and places, and able to participate confidently in both te ao M??ori and the global world. A qualitative project grounded in Kaupapa M??ori and Mana W??hine theory, this study explores the stories of eight M??ori women ??? including myself as researcher. As I taught the women to weave traditionally-made M??ori cloaks, they told stories of reclaiming, restoring and revisioning ???living as M??ori??? for themselves and their wh??nau. A ???new??? Kaupapa M??ori methodology emerged from the ???old??? practice of whatu as a theorised decolonising methodology for this project ??? a research approach I name Whatuora. The methods and methodology developed here offer a way to think about the transforming changes M??ori women create through our deliberate and conscious actions to live ???as M??ori???. Collectively our stories give voice to M??ori women???s work to reclaim and revision M??ori ways of being, while Whatuora methodology forwards a unique approach to research that intertwines Mana W??hine theory, M??ori creative practice and M??ori and Indigenous methodologies into an interwoven set of ideas and theory.

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  • Investigation into the assembly of adiponectin as a target for countering obesity related diseases

    Hampe, Lutz (2016)

    Doctoral thesis
    The University of Auckland Library

    Adiponectin, a collagenous hormone secreted abundantly from adipocytes, possesses potent anti-diabetic and anti-inflammatory properties. Mediated by the conserved Cys39 located in the variable region of the N-terminus, the trimeric (low molecular weight (LMW)) adiponectin subunit assembles into different higher order complexes, e.g. hexamers (middle molecular weight (MMW)) and 12-18-mers (high molecular weight (HMW)), the latter being mostly responsible for the insulin-sensitizing activity of adiponectin. The endoplasmic reticulum (ER) chaperone ERp44 retains adiponectin in the early secretory compartment and tightly controls the oxidative state of Cys39 and the oligomerization of adiponectin. Biologically active, recombinant and pure adiponectin oligomers are difficult to produce hampering the analyses of the oligomerisation process. To mitigate this production problem, we engineered and synthesized a model peptide of the N-terminal domain of adiponectin. We demonstrated that the peptide could be used for probing the influence of the variable domain on the multimerization of this important circulating hormone as well as the interaction between the adiponectin and ERp44. Using cellular and in vitro assays, we showed that ERp44 specifically recognizes the LMW and MMW forms but not the HMW form. Binding assays with short peptide mimetics and the aforementioned peptide model of the N-terminal domain of adiponectin suggest that ERp44 intercepts and converts the pool of fully oxidized LMW and MMW adiponectin, but not the HMW form, into reduced trimeric precursors. In vivo, these ERp44-bound precursors in the cis-Golgi may be transported back to the ER and released to enhance the population of adiponectin intermediates with appropriate oxidative state for HMW assembly, thereby underpinning the process of ERp44 quality control. Obesity-induced ER stress causes dysregulation of ER chaperone activity in vivo including ERp44 action, resulting in a decreased level of secreted HMW, which is associated with insulin resistance and type 2 diabetes. Using adipocyte cells and genetically obese mice we demonstrated that designed peptide mimetics derived from ERp44 clients can restore dysregulated ERp44 activity and in turn facilitated adiponectin assembly into HMW form and promote adiponectin release from the ER. Therefore, these peptides can act as reagents to counteract impaired adiponectin multimerization caused by dysregulation in ER chaperone activity.

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  • Early Cartilage Degeneration: Correlation of Micro-Structural and Proteomic Analysis

    Jacob, Bincy (2017)

    Doctoral thesis
    The University of Auckland Library

    Pre-osteoarthritis in the joint remains elusive to the cartilage researcher. To address this, a bovine model of early cartilage degeneration has been used in recent years. In this study the state of early tissue degeneration in bovine cartilage was investigated, correlating subtle microstructural changes in the tissue with its protein profiles. A total of 44 bovine patellae showing a range of tissue states from completely intact (healthy) to those with localised mild-to-moderate degeneration of the cartilage surface (non-healthy) were used. The degeneration was highly localised to the distal-lateral quarter of the patella and this tissue state has been validated in previous studies to be an early state of degeneration in osteoarthritis. From each patella showing mild-to-moderate tissue degeneration, two samples were used for the analyses, one from the localised site of degeneration and the other from an adjacent intact region. The healthy patellae provided control samples, where two intact cartilage samples were obtained from the distal lateral quarter, and a region adjacent to it. In the first part of this study, the cartilage samples were systematically characterised based on their microstructural changes using Differential Interference Contrast optical microscopy and Mankin histological scoring. The main changes in the microstructure in early cartilage degeneration were found to be as follows: (1) cartilage surface irregularity with a progressive diminishing of the tangential zone, where in severe degeneration there were clefts and fissures, (2) chondrocyte clustering, (3) fibrillar matrix ???destructuring??? and re-aggregation, (4) thickening of the zone of calcified cartilage and (5) presence of bone spicules and signs of an advancing cement line. These microstructural changes are consistent to being analogous to a pre-osteoarthritic state in human joints. Based on the above microstructural variations from early degeneration, the second part of the study reports on the associated protein profile variation. Comprehensive iTRAQ (Isobaric tags for relative and absolute quantitation) labelled LC-MS/MS were performed on whole cartilage tissue samples. A total of 191 proteins were identified. Correlating microstructural variations to known protein functions, 15 proteins, further validated using MRM assays, were identified as potential markers for the early degenerative process. These proteins, including a novel protein WFDC18-like protein, and their specific role in the subtle structural changes in cartilage are discussed in this work. Of interest also is that in the range of tissues with early degeneration, the differences in protein profiles were more pronounced in those from the mildly degenerated tissue group. The third part of this study involved analysing secretome profiles (unstimulated) of the cartilage explants from the different examined groups. The explants from cartilage with moderate levels of degeneration were found to have enhanced secretory action than samples from mildly degenerated tissues, contrasting to the abundance levels noted in the earlier part of the study (see above). An explanation for this reduction in protein abundance levels in the cartilage tissue with moderate level of degeneration, in which the secretome levels were higher than cartilage with mild degeneration, may be due to the increasingly destructured fibrillar matrix that facilitates protein loss. Also seen in the secretome profile was the novel protein WFDC18-like, with potential anti-protease activity, which was found to be significantly upregulated in the intact cartilage regions of the non-healthy patellae. Finally, in the last part of the study, a relatively new technique for studying cartilage protein profiles, MALDI-IMS, was explored. This technique allowed for easy quantification of region-to-region peptide variation of localised degenerated sites and adjacent intact tissue.

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  • Urban ecology of an endemic pigeon, the kerer??

    Baranyovits, Alice (2017)

    Doctoral thesis
    The University of Auckland Library

    Urban areas are continuing to grow and intensify to accommodate an increasing urban human population. While urban areas can be challenging places for wildlife, some species have adapted to these novel environments. However, as urban areas continue to develop, there is a danger that without careful planning, those characteristics of urban areas that support urban wildlife could disappear. The presence of urban wildlife in cities can benefit urban residents through the provision of ecosystem services and can help residents form connections with nature, and, in the case of indigenous species, can help to create a unique sense of place. Kerer?? (New Zealand pigeon; Hemiphaga novaeseelandiae), a large frugivorous pigeon, are one of the few endemic bird species to regularly occur in urban areas in New Zealand, although at relatively low densities. Kerer?? are important seed dispersers for many plant taxa, and as an easily identifiable and charismatic species, they are an ideal species to promote urban conservation. This thesis investigates the urban ecology of kerer?? in Auckland, New Zealand???s largest city, by investigating kerer?? distribution across the city, urban kerer?? diet and the space???use and movement of kerer?? in urban and peri???urban areas. Human modification of the landscape can lead to changes in a species space???use and movement behaviours. ARGOS satellite telemetry was used to track the annual space???use and movements of 13 kerer?? in urban and peri???urban areas of the Auckland region. The majority of the tracked individuals remained localised throughout the year in a single home???range area (mean ?? one standard error = 326 ?? 45 ha), suggesting that sufficient resources are available throughout the year. However, one individual was more transient and was recorded in three discrete areas separated by 35 km and 45 km. This individual is estimated to have travelled at least 270 km during a 40 day period. Much of the previous work on kerer?? space???use and movement has used radio???telemetry, which can miss longdistance movements if the individual flies out of range. The use of satellite telemetry, as in this study, increases the likelihood of detecting the infrequent long???distance movements as observed for this one transient individual. Monitoring urban wildlife can help inform conservation and urban planning decisions but it can be logistically difficult due to the large amount of privately owned land. Involving members of the public through citizen science projects is one solution, although there are many potential sources of error and bias that must be addressed. The ???Auckland Kerer?? Project??? was a local web???based project created to collect data on kerer?? occurrence in the city and on the resources available to kerer?? in residential gardens. A total of 311 people participated in the project during the two years (April 2014???2016) that it was running, with most people only contributing to the project once. Large increases in participation occurred immediately following high profile media releases, but did not continue. Participation was also spatially uneven and associated with socio???economic status; most participants resided in more affluent suburbs. Despite the potential biases, citizen science remains a useful tool particularly for collecting data on low???density species in urban areas as there are high numbers of potential observers. Understanding a species current distribution in urban areas and the environmental variables that are most important in predicting it, can help inform conservation policies and identify areas of importance to ensure a species continued persistence in urban areas. In this study, a maximum entropy species distribution modelling approach was used to characterise kerer?? distribution across urban Auckland, using kerer?? occurrence data collected by members of the public. The estimated relative probability of kerer?? occurrence was unevenly distributed across the city, with areas of higher probability occurring in the north and central city. The two main predictors of kerer?? distribution were distance to indigenous forest and amount of vegetation cover (5 ???15 m in height) per hectare. South Auckland had, on average, less vegetation cover and fewer patches of indigenous forest and as such had lower estimated relative probability of kerer?? occurrence. These variables may be correlated with socio???economic deprivation in some parts of the city. One impact of urbanisation is that it can alter the availability of resources for urban wildlife, through the reduction and fragmentation of indigenous vegetation, combined with the addition of many exotic plant taxa and other novel anthropogenic resources. A flexible diet is a useful strategy for species adapting to urban environments. I used feeding observations collected through the ???Auckland Kerer?? Project??? as well as my own observations, combined with analysis of stomach contents to assess kerer?? diet. In addition, a garden plant survey and a focal plant phenology study were used to investigate resource availability. Kerer?? were recorded consuming 28 indigenous plant taxa and 23 exotic plant taxa, but 69% of feeding observations were on just six taxa; p??riri (Vitex lucens) 24%; k??whai (Sophora spp.) 14%, plum (Prunus spp.) 8%, n??kau (Rhopalostylis sapida) 7%, loquat (Eriobotrya japonica) 7%, and guava (Psidium spp.) 6%. P??riri was also the most common plant taxa recorded in residential gardens and as it produces fruit throughout the year, it is an important component of urban kerer?? diets in Auckland. Loquat and guava, two introduced, potentially invasive taxa, appeared to be highly attractive to kerer??, which may be of concern due to the seed dispersal capabilities of kerer??. Despite the year round availability of fruit, vegetation was also consumed throughout the year, but the proportion of vegetation in the diet was highest in winter and spring. There were very few observations of kerer?? consuming tawa (Beilschmiedia tawa), taraire (B. tarairi) or miro (Prumnopitys ferruginea), all of which are plant taxa with highly nutritious fruits that are important components of kerer?? diets elsewhere. Currently, urban areas appear to be satisfactory substitute habitat for kerer?? in Auckland, but more could be done to ensure the availability of food resources throughout the year. Additionally, it would be constructive to address the socially unequitable distribution of trees in Auckland as this would increase habitat for kerer?? (and other species) across the city as well as ensuring residents across the city gain the benefits of urban wildlife and trees. Kerer?? are a well???liked part of the urban biota and an ideal species to promote urban conservation.

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  • Intertemporal preferences of individual and collective decision-makers

    Anchugina, Nina (2017)

    Doctoral thesis
    The University of Auckland Library

    This thesis contributes to theoretical modelling of time preferences of individual and collective decision-makers. In the context of an individual decision-maker we study two problems: axiomatization of time preferences and the effect of delay on the ranking of sequences of dated outcomes. In the context of a group of decision-makers we investigate the problem of aggregation of time preferences. First, we provide a new axiomatic foundation for exponential, quasi-hyperbolic and semi-hyperbolic discounting when preferences are expressed over streams of consumption lotteries. The key advantage of our axiomatic system is its simplicity and its use of a common framework for finite and infinite time horizons. Second, we analyse preferences with the property that the ranking of two sequences of dated outcomes can switch from one strict ranking to the opposite at most once as a function of some common delay -- the "one-switch" property of Bell [12]. We demonstrate that time preferences satisfy the one-switch property if and only if the discount function is either the sum of exponentials or linear times exponential. This is a revision of Bell's result [12], who claimed that the only discount functions compatible with the one-switch property are sums of exponentials. We also show that linear times exponential discount functions exhibit increasing impatience in the sense of Takeuchi [77]. To the best of our knowledge, linear times exponential discount functions have not been used in the context of time preference before. Finally, we study the problem of aggregating time preferences when individual time preferences exhibit decreasing impatience. If decision-makers have the same level of decreasing impatience, our result proves that the aggregate discount function is strictly more decreasingly impatient than each of individual discount functions. This is a generalization of Prelec's and Jackson and Yariv's results on the aggregation of discount functions [46, 63]. We also analyse the situation in which the aggregation problem arises because of some uncertainty about the discount function. In this context we prove the analogue of Weitzman's influential result [81], showing that if a decision-maker is uncertain about her hyperbolic discount rate, then long-term costs and benefits will be discounted at a hyperbolic discount rate which is the probability-weighted harmonic mean of the possible hyperbolic discount rates.

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  • New Zealand port characterisation and wharf seismic response

    Ragued, Bilel (2017)

    Doctoral thesis
    The University of Auckland Library

    New Zealand Ports perform the vital role of facilitating the transfer of goods to and from the world markets. This critical infrastructure has been identified as a lifeline that needs to remain operational immediately after a natural hazard. For this reason the aim of this research presented was to investigate the vulnerability of New Zealand ports to seismic hazards. The research was specifically focused on understanding the seismic response of wharves. Data regarding all of New Zealand???s 14 ports was collected from port companies and was used to characterise New Zealand wharves and determine the most common structural configurations. The Cashin Quay 3 wharf at Lyttelton Port was chosen as a case study because it experienced significant damage as a result of the Canterbury Sequence of Earthquakes. For the purpose of quantifying the impact of earthquakes on wharves, a numerical model of the Cashin Quay 3 wharf was developed using OpenSees. The model was validated against measured deck displacements after the September 4th and February 22nd Canterbury earthquakes. Time-history, sensitivity and fragility analyses were conducted on the model to quantify its seismic response. In the time-history analysis the model was subjected to the entire earthquake sequence and the resulting deck displacement and pile moment history was presented. The results confirmed the presence of ongoing displacements as a result of small aftershocks experienced at Lyttelton Port and showed the significance of modelling both the wharf and soil embankment in an integrated model that captured the interaction between both components. The sensitivity analysis confirmed the influence of geotechnical parameters on overall wharf response. Fragility analysis of the CQ3 model consisted of subjecting the model to a series of scaled ground motions and fitting the response data to lognormal probability distributions. The CQ3 fragility curves accurately captured the damage state reached by the wharf after the September 4th and February 22nd earthquakes. Five variations were made to the CQ3 model based on the wharf characterisation study. These variations represent typical combinations of lateral load resisting mechanisms. Fragility analysis of the variations indicated the superior performance of the combination of tie-back and moment resisting pile-deck connections over the use of a raked pile.

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  • Product- and Factor Market Contact and Competitive Aggressiveness: The Moderating Effect of Competitive Intensity

    Ljubownikow, Grigorij (2015)

    Doctoral thesis
    The University of Auckland Library

    In the quest to understand the antecedents and outcomes of firms??? competitive behaviours, theories about the consequences of interdependencies have received increasing attention. While the literature on multimarket contact has contributed valuable insights, there is still limited understanding of how different types of interdependencies influence competitive behaviour. In particular, limited research has analysed the effects of factor market interdependencies. Drawing on multimarket contact and factor market competition literature, the study argues that firms refrain from competitive behaviour when they experience multimarket contact in both product and factor markets, but that this effect is stronger in the case of product multimarket contact. Identifying boundary conditions has also become an integral part of multimarket contact literature. In this vein, competition has received particular attention, with a focus on industry and market level competition. Complementing these approaches, the study builds on ecological models of competition to analyse how idiosyncratic competitive circumstances influence the multimarket contact-competitive aggressiveness relationship. The study argues that competitive intensity limits aggressive behaviour. Furthermore, it argues that competitive intensity positively moderates the relationship between product multimarket contact and competitive aggressiveness and negatively moderates the relationship between factor multimarket contact and competitive aggressiveness. The study tests these predictions on 1,276 (8,065 firm-year observations) large bank holding companies operating from 2001-2011 in the US. The empirical results suggest that different types of interdependencies have distinct implications for competitive behaviour and that idiosyncratic competitive circumstances may contribute towards understanding the boundary conditions of the mutual forbearance hypothesis. These findings contribute to the literature on multimarket contact, competitive dynamics, factor market competition and ecological models of competition. In particular, current multimarket contact literature largely focuses on the same types of contact to analyse the effect on competitive behaviour, yet the results of this study show that different types of contact may have distinct effects. In addition, the effect of industry or market level competition has received some attention, but this study emphasises idiosyncratic competitive circumstances. Specifically, the results reported here suggest that idiosyncratic competitive circumstances play a significant role in delineating the boundaries of the mutual forbearance hypothesis.

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  • Structure-function analysis of calcitonin and amylin receptors

    Gingell, Joseph (2015)

    Doctoral thesis
    The University of Auckland Library

    The calcitonin receptor (CTR) is a peptide binding family B G protein-coupled receptor (GPCR). CTR alone has high affinity for calcitonin (CT) but when expressed with receptor activitymodifying proteins 1, 2 and 3 (RAMPs) it forms the AMY1, AMY2 and AMY3 receptors, which have increased affinity for amylin and CT gene-related peptide (CGRP). Family B GPCRs have a long N-terminal extracellular domain (ECD) that forms an important part of the peptide binding site. While peptide bound ECD structures are available for several family B GPCRs, there is no structural information available on the CTR. The precise binding sites of the peptides CT, amylin and CGRP within the ECD are unknown and it is also unclear if or how the presence of the RAMP changes the peptide binding site to allow high affinity amylin and CGRP binding. In this thesis, site-directed mutagenesis and functional assays were performed on the CTR ECD with the aim of identifying residues involved in peptide interactions. CTR ECD mutants were characterised with CT, CGRP and amylin in the presence and absence of RAMPs, to investigate how RAMPs influence peptide binding. In addition beta amyloid 1-42, was investigated as a potential novel agonist of AMY receptors. The isolated ECDs of the CTR and RAMP1 were also expressed with the aim of characterising them by X-ray crystallography. The mutagenesis data identified CTR ECD residues involved in CT, CGRP and amylin interactions. Interestingly there were differences in CT and amylin interactions with the CTR; alanine mutants W79A, F99A, D101A, F102A, W128A and Y131A, significantly reduced CT potency, however only W79A, F102A and Y131A reduced amylin potency. At the AMY receptors seven receptor mutants; W79A, F99A, D101A, F102A, R126A, W128A and Y131A resulted in a significant decrease in amylin potency, indicating that additional receptor residues become involved in amylin binding when RAMPs are present. This suggests that RAMPs may act indirectly to alter peptide binding at AMY receptors.

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  • Investigating the role of the NlpC/P60 cysteine peptidases in Trichomonas vaginalis

    Lopes Pinheiro, JC (2016)

    Doctoral thesis
    The University of Auckland Library

    Trichomonas vaginalis is a flagellated protozoan parasite that causes trichomoniasis, the world most common non-viral sexually transmitted infection. Although infections may be asymptomatic, trichomoniasis has been associated with an increased risk of cervical and prostate cancers, pre-term delivery and low birth weight infants and has been implicated as a risk factor for acquisition of the human immunodeficiency virus. As an obligate extracellular protozoan parasite, adherence to the vaginal epithelial cells is critical in order to establish and maintain infection. Nevertheless, the biochemical processes behind T. vaginalis infection and its interaction with the vaginal microbiota are still not well defined. The draft genome sequence of T. vaginalis strain G3 identified nine NlpC/P60-like members (Clan CA, family C40). The NlpC/P60 proteins define a superfamily with diverse enzymatic functions, where the majority of the members are cell-wall hydrolases. Since T. vaginalis does not have a cell wall, investigating origins and whether the NlpC/P60 genes are functional and aiding parasite infection became the main focus of this research. Bioinformatics analyses of the nine NlpC/P60 genes in T. vaginalis revealed that these genes were acquired via lateral gene transfer (LGT) from bacteria and belong to the P60-like family. To investigate the function of the NlpC/P60 family of proteins in T. vaginalis, two members were expressed, purified and crystallised with their threedimensional structure determined at resolutions of 1.2 ?? and 2.3 ??, by X-ray diffraction. The enzymatic activity of three NlpC/P60 enzymes in T. vaginalis was characterised in a peptidoglycan cleavage assay, revealing these members to be active D, L-endopeptidases. The gene expression analysis showed that all genes are up-regulated when in contact with host microbiota. Further analyses revealed the NlpC proteins to be located in different cellular compartments and parasite transfectants to possess a really strong phenotype with bacteriolytic activity. Overall these results suggest that T. vaginalis is using the LGT acquired genes against the vaginal microbiota. This work sheds light into the interaction of T. vaginalis and the host microbiota, highlighting the role of new molecules that are possibly involved in the parasite pathogenesis. Understanding how T. vaginalis interact in the vaginal ecosystem and the discovery of molecules involved in these interactions can be of potential use to develop vaccines and drugs in the future.

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  • Hidden Number Problems

    Shani, Barak (2017)

    Doctoral thesis
    The University of Auckland Library

    The hidden number problem is the problem of recovering an unknown group element (the "hidden number") given evaluations of some function on products of the hidden number with known elements in the group. This problem enjoys a vast variety of applications, and provides cross-fertilisation among different areas of mathematics. Bit security is a research field in mathematical cryptology that studies leakage of information in cryptographic systems. Of particular interest are public-key cryptosystems, where the study revolves around the information about the private keys that the public keys leak. Ideally no information is leaked, or more precisely extraction of partial information about the secret keys is (polynomially) equivalent to extraction of the entire keys. Accordingly, studies in this field focus on reducing the problem of recovering the private key to the problem of recovering some information about it. This is done by designing algorithms that use the partial information to extract the keys. The hidden number problem was originated to study reductions of this kind. This thesis studies the hidden number problem in different groups, where the functions are taken to output partial information on the binary representation of the input. A special focus is directed towards the bit security of Diffie-Hellman key exchange. The study presented here provides new results on the hardness of extracting partial information about Diffie-Hellman keys.

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  • Region-specific interneuronal degeneration in the human cerebral cortex in Huntington???s disease correlates with symptomatology

    Mehrabi, Fahimeh (2015)

    Doctoral thesis
    The University of Auckland Library

    Huntington???s disease (HD) is an autosomal dominant neurodegenerative disorder characterised by variable symptoms (choreiform movements, cognitive, mood and neuropsychological changes), with variable neuropathology of the basal ganglia and cerebral cortex. Recent studies from our laboratory have shown that the pattern of cortical pyramidal cell loss in 8 different cortical regions correlates with the phenotypic variability in HD; and that in 2 regions of the cerebral cortex (the primary motor cortex, and the anterior cingulate gyrus) the pattern of interneuronal degeneration correlates with pyramidal cell death and variable HD symptom profiles. The present study completes this overview of human cortical neuronal degeneration in the human brain in HD. This study of the HD human brain specifically examines the pattern of interneuronal degeneration in the primary sensory cortex, superior frontal cortex, and superior parietal cortex, and correlates these findings with the well characterised clinical and pathological history of the HD cases. To undertake this investigation, unbiased stereological counting methods were used to quantify the three major types of interneurons immunoreactive for calbindin-D28k, calretinin, and parvalbumin in the three cortical regions of 14 HD and 13 control cases of post-mortem human brain. Based on their predominant symptom, the HD cases were categorised into three groups (???motor???, ???mood???, ???mixed???). The results demonstrated a heterogeneous loss of interneurons across the three cortical regions, which paralleled the heterogeneous pattern of pyramidal cell loss in the same cortical areas. Most interestingly, the pattern of GABAergic interneuronal loss in these cortical regions correlated with the variable symptom profiles in different human HD cases. These findings extend our understanding about the role of the cerebral cortex in the HD pathogenesis and symptomatology by showing a precise correlation between the cortical interneuronal loss and heterogeneous symptomatology in HD.

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