1,991 results for ResearchSpace@Auckland, 2015

  • Tissue Oxygenation and Wound Healing in Vascular Surgery

    Chiang, Nathaniel (2015)

    Doctoral thesis
    The University of Auckland Library

    Are there simple adjuncts that can be applied in patients with peripheral vascular disease that could enhance wound healing and tissue oxygenation? Two large-scale clinical studies were conducted with the aims of targeting two stages of care, namely (i) perioperative treatments to enhance peripheral oxygenation by influencing oxygen delivery via chemical and thermal vasodilation (high-dose oxygen, a prostacyclin analogue, and extended active warming) during bypass surgery to the lower limbs, and (ii) topical negative therapy (TNP) dressings for high-risk foot wounds, such as following debridement or minor amputations in the diabetic foot. These therapies have been shown to be of benefit in other clinical settings, such as abdominal surgery and to treat abdominal wounds. How these adjuncts would help in patients with vascular disease is unknown. Mechanisms underlying the potential effects of these treatments on wound healing were assessed biochemically by quantifying hydroxyproline (a surrogate marker of collagen), growth factors, cytokines, and their respective mRNAs. Healing rates were determined by changes in wound volume over time using an innovative stereophotographic device (FastScan???). Tissue oxygenation was measured using hyperspectral technology (OxyVu???). The reliability and feasibility of using these devices was tested in clinical studies. Measurements obtained using these innovative instruments yielded excellent inter-operator and intra-operator reliability and correlated well with other methods of measurement, thus showing promise for assessment of tissue oxygenation and wound healing in clinical settings. No benefits were demonstrated in 71 patients with regard to surgical wound healing or tissue oxygenation in bypass surgery by perioperative adjunctive treatment. OxyVu identified increased tissue oxygenation in the foot in the acute phase following bypass surgery, validating its clinical use. In acute foot wounds treated with TNP, there was no significant difference in wound volume reduction at 2 weeks when compared with traditional dressings (44.2% for TNP versus 20.9% for the control; p=0.15). However, there was a trend towards an enhanced healing rate, and maximum wound depth was significantly less than that achieved using traditional dressings (36.0% for TNP versus 17.6% for the control; p=0.03). Given that no differences were found in hydroxyproline levels, growth factors, or tissue oxygenation, the benefits of TNP might involve more than merely enhanced production of granulation tissue, possibly involving mechanical (macrostrain) effects.

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  • A Novel Biodegradable Fe-35wt.%Mn Alloy Produced via Powder Metallurgy

    Zhang, Qian (2015)

    Doctoral thesis
    The University of Auckland Library

    This doctoral project permitted to design, develop and study a degradable metallic biomaterial. Between 2011 and 2015, magnesium alloys and commercially pure iron were evaluated for their possibility for the use in biomedical areas. Their mechanical properties and degradation behaviors were not clinically well suited. Hermawan et al. investigated a series of Fe-Mn alloys via a powder metallurgical (PM) route followed by cold rolling and re-sintering cycles and found that manganese content of 35 wt% alloy was nonmagnetic and cell compatible. However, as a fully dense alloy, the degradation rate was still not satisfactory. In this doctoral project, the Fe-35wt.%Mn alloys were produced via several PM routes. This research employed three different starting powders, which were blended elemental (BE), mechanically milled (MMed) and BE powder with porogen. We aimed to develop a less dense alloy that has a higher degradation rate, suitable mechanical properties and good cell compatibility. The Fe-35Mn alloys were firstly fabricated by a simple blend-press-sinter method. Sintering temperatures and holding times were varied to investigate their influences on the microstructure evolution, densification, corrosion behavior as well as mechanical properties. The increase of sintering temperature and holding time led to the decrease of porosity level of the sintered compacts. Among these parameters, a sintering temperature of 1200??? and a holding time of 4 hours proved to be able to produce samples with a good densification level. The change of sintering temperature and time did not affect the final phase where non-ferromagnetic austenitic ?? and martensitic ?? were the main phase. A satisfactory degradation rate of 1.5 to 4 mmpy was obtained; but the mechanical strength was low. In order to enhance the mechanical properties, a mechanical milling (MMing) process was employed to obtain finer starting powder particles. The MMing parameters were investigated and ball-to-powder (B-P) ratio of 5:1 and milling time of 6 hours were identified to be able to produce the required powder. After milling, various pressing pressures using a steel die press were employed, followed by cold isostatic pressing (CIPing) at 200 MPa. Higher compaction pressure resulted in lower porosity level and CIPing further enhanced the densification. When compared with the BE powder, reducing the powder particle size via MMing had led to a decrease in porosity to 7 ~ 12%. Hence, a significant improvement of mechanical properties was then achieved. Porogen ammonium bicarbonate (NH4HCO3) particles were added to fabricate porous Fe-35Mn alloy foam which had varying degrees of porosity level. By the addition of 10 and 20 volumetric percent of NH4HCO3, the degradation rates of the Fe-35Mn samples with the introduction of the NH4HCO3 porogen were significantly accelerated when compared with the samples without NH4HCO3 addition. The electrochemical corrosion rates were ranging from ca. 2 to 8 mmpy in both 5% NaCl and SBF solutions. The proposed degradation mechanisms were uniform corrosion in addition to crevice corrosion. Iron ion release during a one-month???s dynamic corrosion was slightly higher than that of manganese. However the mechanical properties of these Fe-35Mn foams posed a limitation for the development of Fe-35Mn foams in the load-bearing applications. The stress corrosion cracking (SCC) investigation in a physiological environment followed. A slow strain rate test (SSRT) method was used in order to achieve a better understanding with regard to the stress corrosion behavior. The SCC susceptibility was sensitive to the strain rate and the testing environment. A slower strain rate and a more aggressive environment resulted in a higher SCC susceptibility. The higher density level of the sintered samples led to a reduction of SCC susceptibility. Intergranular fracture was observed on the sample surface of all tested specimens. SCC cracking was initiated from crevices and pores in both BE and MMed Fe-35Mn alloy samples. The cytocompatibility of Fe-35Mn alloys were then investigated using an indirect cell-material interaction by culturing L929 cell line in Fe and Mn ion-rich elution containing up to 1.29 and 1.12 ppm of released Fe and Mn ions. Results showed L929 mammalian cells proliferated and grew healthily in all testing extractions. It was suggested that Fe-35Mn alloys were biocompatible since no significant difference was found in the cell viability response to the material elutes. It has to be pointed out that the simple blend-press-sinter method was able to produce a Fe-35Mn alloy that met degradation requirement. MMing could increase the samples??? mechanical strength. However the strength level is still insufficient for load-bearing applications. A further investigation of optimizing the PM parameters is needed to increase mechanical strength while maintaining sufficiently fast degradation.

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  • Haemodynamic Assessment of Coronary Flow with CFD and Phase-Contrast MRI

    Beier, Susann (2015)

    Doctoral thesis
    The University of Auckland Library

    Coronary artery atherosclerosis is a major cause of morbidity and mortality worldwide. Some anatomical characteristics of coronaries may increase the likelihood of disease development, and stenting, a common treatment, has a high probability of restenosis and in-stent thrombosis. Coronary flow patterns, determined by vessel geometry and stent design and deployment, are thought to be related to adverse clinical outcomes. This thesis represents a comprehensive assessment of the relationships between flow and major coronary artery shape, and stent design and deployment. It further demonstrates the feasibility of assessing dynamically scaled coronary phantom flow with phase-contrast magnetic resonance imaging (PC-MRI). A range of idealised and patient-specific coronary artery geometries, with and without stents, were generated based on a statistical shape database from computed tomography (CT) angiograms, and micro-CT scanned benchtop deployed stents, using a computer aided drawing program. Transient flow was simulated using computational fluid dynamics (CFD). The geometries were also up-scaled, 3D printed, and incorporated into a dynamically scaled blood-analogue flow circuit for velocity acquisition with PC-MRI. The CFD results revealed little flow effect for bifurcation angle when varied in non-stented and stented idealised and patient-specific bifurcations. Flow was also computed in four patient geometries with wide shape variation, where a statistical shear stress analysis suggested that the vessel tortuosity may influence the effect of bifurcation angle. Similarly complex flow alterations were observed when systematically analysing the flow effects of major stent design features. The haemodynamic interrelations provided insights for the development of design guidelines for stent manufacture. Computational findings were validated by means of a new approach using dynamically scaled phantom flow and PC-MRI acquisition for non-invasive imaging with higher effective resolution (7-fold up-scaled geometries). The co-registered flow fields yielded good agreement (R2>0.8, magnitude error <8%) after using the PC-MRI measured inlet flow to inform the computational boundary conditions. A complementary approach of CFD and dynamically scaled PC-MRI can deliver further insights into the important haemodynamic effects of vessel shape and stent design and deployment. The results represent a potential clinical assessment tool, new considerations for stent design guidelines and deployment strategies, and a novel approach for coronary flow assessment for patient-profiling and pre-surgical planning.

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  • Academic repatriates: adjustment, work engagement, and intention to leave

    James, Robinson (2015)

    Doctoral thesis
    The University of Auckland Library

    This thesis examines the impact of academic repatriates??? proactive behaviours (job change negotiation, positive framing, and networking), perceived organizational support, and perceived co-worker support on repatriation adjustment, and the impact of adjustment on academic repatriates??? intention to leave and work engagement. This study also examines the impact of academic repatriates??? organizational commitment and perceived external employment opportunities on their intention to leave. Three theories: uncertainty reduction theory; socialization resource theory; and organizational socialization theory were combined to explain the hypothesized relationships. The study was conducted with a group of 172 Sri Lankan academic repatriates who had been attached to a foreign academic institution for two or more years and had been involved in academic activities (teaching/research/higher studies). Results indicated that repatriates??? proactive behaviors (except networking), perceived organizational support and perceived co-worker support each had an important role to play in the prediction of repatriation adjustment. In turn, academics who adjusted to their repatriation better were highly likely to stay at their home university and engage in their work. Repatriates??? perceived organizational support decreased their intention to leave through adjustment and commitment. In addition, when repatriates had trouble in adjustment and perceived high external employment opportunities, they reported higher intentions to leave the university than those who perceived fewer external employment opportunities. The overall findings underline the essential role of individuals, groups, and the organization in the adjustment process of academic repatriates. Thus, rather than passively adapt to their environment, this research shows how repatriates can actively shape their own repatriation experience. An in-depth discussion of findings, contributions, limitations, and implications for further research and practice are presented.

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  • High functioning autism and common coexisting conditions: An EEG investigation

    Bullot, AK (2015)

    Doctoral thesis
    The University of Auckland Library

    Autism spectrum disorder is a lifelong neurodevelopmental condition for which there is no known cure. The rate of psychiatric comorbidity (and comorbidity with other neurodevelopmental disorders) in autism is extremely high, which raises questions about the nature of the co-occurring symptoms. It is unclear whether these additional conditions are true comorbid conditions, or simply behaviour that is better conceptualised through the ASD diagnosis. The overall aim of the current thesis is to investigate the shared behavioural and neural basis of coexisting ADHD and anxiety in ASD. The studies in the current thesis consisted of an investigation of behavioural characteristics using profiling techniques (Total n = 83 (ADHD = 23; anxiety = 12; ASD = 25; controls = 23)), in addition to four experimental studies conducted during concurrent EEG recording. These tasks were: emotion processing (Total n = 74 (ADHD = 22; anxiety = 12; ASD = 20; control = 20)); lexical decision (Total n = 83 (ADHD = 21; anxiety = 12; ASD = 20; control = 20)); inhibitory control (Total n = 57 (ADHD = 16; anxiety = 9; ASD = 15; control = 17)) and a resting state recording (Total n = 46 (ADHD = 11; anxiety = 10; ASD = 13; control = 12)). The diagnostic categories listed above include those with a comorbid condition, the groups are split further with respect to comorbid condition (e.g., ASD pure, ASD and comorbid ADHD) in each study. Together, these experiments covered a spectrum of core difficulties evident in ASD: difficulties with social interactions; language; repetitive behaviour (inhibitory control) and aberrant brain growth. By examining difficulties with they occur alone in ASD versus together with ADHD or anxiety, we are able to build a profile of singular and co-occurring ASD. In the behavioural profiling study, using the wider diagnostic categories (e.g., ASD, ADHD and anxiety), results demonstrate that each group was able to be distinguished from one another, and from neurotypical controls, using the profiling measures. In individuals who present with both ASD and anxiety together, the symptoms of ASD are not significantly higher, but symptoms of anxiety do increase compared to those with ASD alone. This suggests that anxiety is a separate condition when it occurs together with ASD. When ASD and ADHD occur together, there were significantly higher ASD symptoms than in the ASD only group and significantly lower ADHD symptoms than the ADHD alone group (but not the ASD only group). This suggests that there might be some degree of symptom overlap when ASD and ADHD present as a comorbid condition. In the emotion processing task, there were no group differences in the latency or amplitude of the N170. There were, however, differences in the amplitude of the P250. Those with ASD and ADHD showed a differential profile in response to sad and neutral stimuli on the P250 from one another. Those with ASD had larger amplitudes toward mouth stimuli than eye stimuli, and those with ADHD had larger amplitudes toward eye stimuli than toward mouth stimuli. In addition, there was larger N170 amplitudes in the ASD pure group versus those with ASD and anxiety or ADHD. This suggests an additive effect. In the lexical decision task, overall, the results indicated larger P100 amplitudes in the right versus the left hemisphere (most strongly shown in control participants). When the ASD and ADHD present as a comorbid condition, the mean P100 latency for the comorbid group lay between the two means for the ASD and ADHD pure groups. This suggests an additive effect. In the inhibitory control study, the group level analysis did not show any differences between the experimental groups on the latency or amplitude of the N2 or P3 components. Upon closer inspection using regression analyses, smaller N2 and P3 amplitudes were associated with more severe symptoms of ADHD. Therefore, it is possible that inhibitory control deficits are associated with ADHD but not ASD or anxiety. In the resting state study, the results demonstrate patterns of decreased coherence in those with ASD, and patterns of increased coherence in ADHD and anxiety compared to neurotypical controls. The patterns of coherence established in the ASD pure group are no longer evident when comorbid conditions are included in the analyses. Thus, this suggests that the conditions are additive. Taken together, the studies in this thesis demonstrate that when ASD presents as a comorbid condition, ERPs adopt unique characteristics of each condition in its pure form. We argue that this is evidence for an additive effect which suggests that the conditions are indeed separate, rather than a misinterpretation (or increased severity) of ASD symptoms. This information is important to researchers when screening for comorbid conditions in ASD research, as underlying brain activity appears to be altered in each condition. This may significantly influence research findings. In addition, the results of the current study will also help to inform medical practitioners when administering a diagnosis and deciding on a plan to treat specific difficulties associated with comorbid ASD.

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  • Construing consumer resistance: comparing Tongan and European female non-smokers in New Zealand

    Fifita, Ilaisaane (2015)

    Doctoral thesis
    The University of Auckland Library

    Smoking remains the largest cause of preventable morbidity and mortality worldwide and in 2011 New Zealand committed to the goal of being smoke-free by 2025. Despite decades of comprehensive tobacco control efforts and an overall reduction in tobacco use, M??ori and Pacific peoples have substantially higher smoking prevalences than the general New Zealand population. There is also an increased risk of lung and breast cancer incidence in M??ori and Pacific women. Prior research suggests that females and people from more collectivist cultures are more susceptible to interpersonal influence and are therefore more vulnerable to peer pressure to try smoking. Once smoking is started, its addictive nature makes it extremely difficult to give up. The more people in a group who smoke, the more likely it is that others in their group will take up smoking, creating a vicious cycle. To move the field forward and achieve the smoke-free goal by 2025, it is important to understand how people can resist smoking even in the face of interpersonal influence. Responses to peer pressure may be influenced by a person???s cultural values and norms. Selfconstrual, the way one construes self in relation to others, is a useful lens for understanding cultural differences in smoking resistance. However, much of the relevant prior empirical research on smoking prevention/cessation and self-construal is based on people from Western cultures, potentially limiting the applicability of these findings to people from non-Western cultures. Consequently, the study reported in this thesis sought to shed light on how selfconstrual influences smoking resistance among New Zealand Tongan (Tongan) females, using New Zealand European (NZE) females as a comparison group. In-depth interviews conducted with 29 (14 Tongan and 15 NZE) females who self-identified as non-smokers were open, axial and selectively coded before being interpreted against the context provided by the relevant literature. The findings revealed that non-smokers were initially motivated to resist smoking initiation because they wished to avoid the negative consequences of smoking and/or to gain the positive consequences of not smoking. The findings further revealed that creating and maintaining a smoking-resistant identity was central to successful, long-term smoking resistance in both cultural groups interviewed. Specific values, traits and coping strategies were found to help sustain smoking-resistant identities. Finally, the findings revealed the importance of self-construal in unpacking how both Tongan and NZE women resist smoking. Although independent self-construals were central to NZE women???s resistance to smoking, both independent and interdependent self-construals were important in Tongan women???s smoking resistance. The thesis concludes with a discussion of the theoretical, methodological and substantive contributions.

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  • Skin Disease and Vitamin D

    Jarrett, Paul (2015)

    Doctoral thesis
    The University of Auckland Library

    Background There is a growing interest in the role of vitamin D beyond its effect on bone health. The vitamin D receptor is widely expressed in many different tissues, including the skin. Aim The aim was to investigate the association between 25-hydroxyvitamin D and cutaneous lupus erythematosus, and the effect of vitamin D on psoriasis. Two additional studies about the population prevalence of cutaneous lupus and the cardiovascular risk of psoriasis were undertaken. Methods Patients with cutaneous lupus were identified from multiple sources from both the hospital and the community. The database compiled was then used to clinically assess both the scarring and the activity of cutaneous lupus in association with 25-hydroxyvitamin D status. A randomised, placebo-controlled study of the effect of oral 100,000 IU monthly Vitamin D3 (cholecalciferol) was undertaken with participants who had psoriasis and had been recruited to a larger study called the Vitamin D assessment study. Results One hundred and forty-five patients with cutaneous lupus were identified. Ma??ori and Pacific people were found to have a higher prevalence of all types of cutaneous lupus compared with the European population [relative risk 2.47 (95% CI: 1.67???3.67)] and especially discoid lupus [relative risk 5.96 (95% CI: 3.06???11.6)]. No relationship was found between cutaneous lupus (either active disease or scarring) and 25-hydroxyvitamin D levels. Sixty-five patients with mild psoriasis were recruited. The mean Psoriasis Area Severity Index was 3.0 and 3.3 in the placebo and active group respectively. No improvement in psoriasis was recorded by the addition of vitamin D3 when assessed by the Psoriasis Area Severity Index, Global Physician???s Assessment, Dermatology Life Quality Index or the Psoriasis Disability Index (p > 0.05). There was no increase in cardiovascular risk in the psoriasis participants (p > 0.05). Conclusions 25-hydroxyvitamin D status is not a significant factor for cutaneous lupus. Further research is needed to examine why Ma??ori and Pacific peoples have high rates of cutaneous lupus. Oral vitamin D3 is not a therapeutic option for patients with mild psoriasis, and the low cardiovascular risk of a New Zealand patient cohort with mild psoriasis is confirmed.

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  • An Improved Clinical and Pathophysiologic Characterisation of Post-Operative Ileus

    Vather, Ryash (2015)

    Doctoral thesis
    The University of Auckland Library

    INTRODUCTION Post-operative ileus is a major cause of morbidity globally. The objectives of this body of work are to classify and define ileus, evaluate the efficacy of Gastrografin in shortening its duration, predict the occurrence of prolonged ileus, and describe changes in peri-operative and post-surgical intestinal motility. METHODS A systematic literature review and online global survey were conducted to clarify terminology and provide concise, clinically quantifiable definitions for ileus. A retrospective cohort study, narrative review, and laboratory analysis were used to inform design and execution of a double-blinded, placebo-controlled, randomised trial investigating the therapeutic value of Gastrografin in shortening duration of prolonged ileus following elective colorectal surgery. Risk factors predictive of prolonged ileus following colorectal surgery were identified by a prospective cohort study. In vivo high resolution manometry was utilised to assess changes in intestinal motility peri-operatively and post-surgically. RESULTS Three classes of ileus can be identified and defined ??? post-operative ileus, prolonged post-operative ileus, and recurrent post-operative ileus. In an episode of prolonged ileus, orally-administered Gastrografin accelerates resolution of lower gastrointestinal symptoms (abdominal distension; absence of flatus and stool) but does not affect upper gastrointestinal symptoms (nausea and vomiting; intolerance of an oral diet). Independent predictors for prolonged ileus include male gender, decreasing pre-operative albumin, open/converted technique, increasing wound size, operative difficulty and bowel handling, total intravenous crystalloid, red cell transfusion, and day of first mobilisation. Ileus is underpinned by cyclic motor activity which occupies the majority of the immediate postoperative period; by contrast, short and long single motor patterns appear infrequently and sporadically. Those who have previously undergone segmental colorectal resection (and preserved normal bowel function) exhibit a normal colonic meal response with evidence of coordinated trans-anastomotic motor activity. CONCLUSIONS Three classes of ileus can be broadly identified and defined; Gastrografin is not clinically useful in shortening an episode of prolonged ileus; predictive scoring systems may identify individuals at risk of developing prolonged ileus; ileus is characterised by ubiquitous cyclic motor activity of likely myogenic origin; and normal motility is eventually restored in patients who have undergone segmental colorectal resection.

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  • The Tracking & Analysis of Cell Movement with Cell-Derived Active Contours & Generative Graphical Models

    Nejati Javaremi, Alireza (2015)

    Doctoral thesis
    The University of Auckland Library

    There has been a continuous effort (Li et al., 2009; Al-Kofahi and Lassoued, 2010; Al-Kofahi et al., 2011; Amb??hl et al., 2012; Meijering, 2012; Ma??ka et al., 2014) to provide tools for large-scale automated analysis of live cell morphology in vitro, as this very important for studying biological development and disease. In this thesis, we outline a set of theoretical and practical tools that we have developed for this purpose. In chapters 1-5 we present a new cell-derived active contour (CDAC) method for cell tracking that achieves higher tracking accuracy using knowledge about cell movements. This knowledge consists of the way cells move by adhering to the substrate and propelling their cell membranes in the direction normal to the edge. This allows use of fast optimal search methods. Our method is designed for phase contrast microscopy, which allows access to a wider variety of experimental data. It can operate under conditions of low illumination. This is important for live-cell imaging as high illumination can damage cells. Additionally, our method demonstrates a higher robustness to noise than many previous methods. We then develop a statistical framework for cell shape analysis. Due to the large dimensionality of the space of cell shapes, we first use a neural network model to extract a small set of relevant features. This allows efficient learning and this makes our method distinct from previous methods (such as kernel density estimation). We then develop a rotation-invariant framework - a property that has not been incorporated in previous cell shape model studies and is a limitation of other models - to construct a hierarchical Bayesian generative model to learn the distribution of cell shapes. We show that this new property allows, for the first time, deriving features such as elongation or cell asymmetry directly from the data without any prior assumptions. In this work we maintain a close relationship between experiment and theory. The problem of calculation of cell movement indices from experiment is studied and related to theoretical models. We also use theoretical models to validate our morphology analysis framework, showing good statistical agreement with natural cells.

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  • Structural and functional studies on pantetheinylation: An essential post-translational modification in two pathogenic bacteria

    Jung, J (2015)

    Doctoral thesis
    The University of Auckland Library

    Pantetheinylation is a form of post-translational modification that is essential across all three domains of life and is responsible for activating a wide range of primary and secondary metabolic pathways. Such pathways include the biogenesis of essential fatty acids, polyketides and non-ribosomal peptides that serve as virulence factors in pathogenic bacteria. Phosphopantetheinyl transferases (PPTases) covalently attach the pantetheine (4'-PP) cofactor group to their recipient carrier proteins (CPs). CPs then carry the metabolic intermediates, covalently tethered to the long and flexible 4'-PP arm, from one reaction centre to the next. Pantetheine attachment by PPTases is thus essential for the activity of key biosynthetic pathways and ultimately for the viability of the organisms. This research focused on PPTases from two pathogenic bacteria, AcpS and PptT from Mycobacterium tuberculosis (Mtb) and PcpS from Pseudomonas aeruginosa (Pa), and on selected CPs (MbtL, PpsC and AcpM) from Mtb. Structural and functional studies have been carried out to aid in developing selective inhibitors of these bacterial PPTases.

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  • Weighted likelihood and calibration for countermatched designs

    Rivera Rodriguez, Claudia (2015)

    Doctoral thesis
    The University of Auckland Library

    The use of all information available on an entire cohort when fitting Cox models can be limited due to exposures of interest available only in a sample. If a case- cohort design is used, the standard estimation method (pseudolikelihood) allows for methods from survey sampling, such as calibration, to be used in order to take advantage of auxiliary information. However, under countermatching designs, the standard estimation method (partial likelihood) utilizes only one variable on the entire cohort and it does not admit the use of calibration. In this dissertation, calibrated weights are applied to countermatched designs. The calibration variables are an approximation of the influence functions of the estimator. The methods are evaluated through simulations for models with time- fixed and time varying covariates. Situations in which countermatching can be preferred over case -cohort or matching are considered. These situations include the case when a rare exposure is available for the sample, but there is a surrogate of this on the cohort. Countermatching on the surrogate leads to more efficient estimates. The new method is compared to partial likelihood and pseudolikelihood with standard weights under different designs (matching and case -cohort). Pseudolikelihood with calibrated weights returns more efficient estimators than the other methods in most situations, particularly for coeffi cients whose variables are available on the entire cohort. Partial likelihood can be more efficient than pseudolikelihood in the presence of confounding variables in the model or for variables that are unrelated to the countermatching variables. However, calibrated weights can recover the efficiency lost if suitable auxiliary information is available. The efficiency of the methods under misspecified models is also discussed. Pseudolikelihood is a more suitable method if the interest is to estimate the cohort coefficients. Furthermore, asymptotic normality of pseudolikelihood estimators with both standard and calibrated weights is discussed using an empirical processes approach. The result is attained for time -fixed Cox models. A potential information bound for under the missing at random assumption in two -phase sampling designs is studied and compared to the proposed methods .

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  • The Case for Subsidiarity as a Constitutional Principle in New Zealand

    Gussen, Benjamen (2015)

    Doctoral thesis
    The University of Auckland Library

    This doctoral thesis uses historical analysis, constitutional economics, and complexity theory to furnish positive and normative arguments for subsidiarity as a constitutional principle in New Zealand. The principle of subsidiarity is the hypostasis of the Treaty of Waitangi, both in its English and M??ori texts. It is also evident in the thinking behind the New Zealand Constitution Acts of 1846 and 1852. This constitutional tradition has been occulted since the abolition of the New Zealand provincial system in 1876. Constitutional economics suggests an optimal limit to jurisdictional footprints (territories). This entails preference for political orders where sovereignty is shared between different cities rather states where capital cities dominate. The resuscitation of subsidiarity as a foundational element of our constitution holds the key to economic prosperity in a globalising world. Moreover, insights from complexity theory suggest that sustainability is a response to the ???problem of scale???. It is a fitness trait that prevents highly complex systems from collapsing. The nation state is a highly complex system within which cities function as ???attractors???. The collapse of such systems would ensue if there were strong coupling between attractors. Such coupling obtains under legal monism. Only subsidiarity can make this eventuality improbable. Understanding the ???emergent properties??? of sustainability and the ???selforganizing??? properties of subsidiarity entails a shift in policy emphasis towards the latter. The thesis recommends changes to the Constitution Act 1986 to reinstitute subsidiarity as a constitutional principle. New Zealand cities, in particular the Auckland supercity, would benefit from wider local autonomy under this vision. Nevertheless, constitutional change will have to start with public opinion, especially in relation to subsidiarity and its role in shaping the relationship between cities and the central government.

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  • Zinc-Magnesium and Zinc-Aluminium- Magnesium Coatings Produced by Magnetron Sputtering and Melt Dipping

    Yao, Caizhen (2015)

    Doctoral thesis
    The University of Auckland Library

    Zn coating is the most economic and widely used sacrificial coating to protect steels against corrosion. Since the corrosion resistance of pure Zn coating is not satisfactory under alkaline or high humidity environments, over the past few decades, demands for better corrosion resistance and mechanical properties arising from various industries and sectors have driven the research and study on alternative coatings of pure zinc coating. The most successful substitutions are Zn-Al alloy coatings, e.g. zincalume (55% Al-44% Zn-1% Si) and galfan (5% Al) coatings. These coatings combine the sacrificial protection of zinc and a long lasting physical barrier of alumina together, thus corrode 5-10 times slower than pure Zn coating. Recently, Zn-Mg and Zn-Al-Mg coatings have been developed from the traditional Zn and Zn-Al coatings by the addition of small amount of Mg. A great attention has been attracted due to their excellent properties. Evidence suggests that up to a 10-fold drop in weight loss has been found in Zn-Mg coating in comparison with pure Zn coating. The performance of Zn-Al-Mg coating in salt spray test is better than that of Zn coating by 10-20 times and Zn- Al coating by 2-5 times. Furthermore, Zn-Al-Mg coating is found to have self-healing capability. Various coating methods, including hot dipping and physical vapour deposition (PVD), have been employed in past studies, and each method results in its unique microstructure and properties in the coating. Those coatings can be used in perforated plates in civil construction, automobile bodies and parts, green house structures in agriculture and switch cabinets in electric power and telecommunication applications. The improvements of corrosion resistance properties from addition of Mg in Zn-(Al)-Mg coatings have been evidenced by researchers. However, detailed information on the corrosion mechanism of Zn-(Al)-Mg coatings is still lack in open literatures, and a number of unclear factors need to be investigated. For example, the effect of Mg content on the microstructure of Zn-(Al)-Mg coating; how does the microstructure interrupt the corrosion process of Zn-(Al)-Mg coating; is there an economic way for the mass production of Zn-(Al)- Mg coating to substitute the traditional Zn coating, and the environment that Zn-(Al)-Mg coating can be used. What???s more, as a novel technology, electrochemical method is seldom used in the study on corrosion properties of Zn-(Al)-Mg coating. This research aims to study the processing methods, microstructure and properties of Zn- (Al)-Mg alloys and coatings with varying Mg contents, to investigate the mechanisms of microstructure formation and corrosion behaviour. The ultimate aim is to apply this new type of coating into industrial practice. The processing methods adopted in this research are hot dipping, electroplating and magnetron sputtering. Alloys and coatings are characterized and tested by optical microscopy (OM), environmental scanning electron microscopy (ESEM), energy dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), microhardness test and electrochemical tests e.g. Open circuit potential (OCP)-time curve, potentio-dynamic polarization curve, electrochemical impedance spectroscopy (EIS) have been used to investigate the morphologies, chemical compositions, mechanical and corrosion properties of coatings. Salt water immersion test (SWI) and neutral salt spray test (NSS) was performed to further investigate the corrosion properties and mechanisms of coating specimens. The main findings from this study include: (1) The microhardness of Zn-(Al)-Mg alloys increased with increasing Mg content, probably due to the grain refinement strengthening effect and the formation of more intermetallic phase at grain boundary areas. Potentio???dynamic polarization curves indicated that the Ecorr of Zn???3 wt.% Mg alloy is more positive than that of Zn, with a low icorr of ~34% of Zn, probably due to its nanostructure. The nano???structure of Zn + Mg2Zn11 eutectic in Zn???3 wt.% Mg alloy may contribute to a general precipitation of Mg???modified simonkolleite and retard localized corrosion, contributing to the excellent corrosion resistance of Zn???3 wt.% Mg alloy. Zn-5 wt.% Al-2 wt.% Mg alloy contains a large amount of Mg2Zn11, and it has the highest impedance 5.11??103 ohm according to EIS results and the lowest icorr 1.03??10???3 A/cm2 according to the polarization curves among tested Zn-Al-Mg alloys. We assume that the improved corrosion property may relate to the formation of Mg2Zn11 intermetallic. (2) The Polarization curves showed that corrosion resistance of Zn coating was enhanced significantly by the magnetron sputtered Zn-Mg layer. Salt water immersion test in 3.5 wt.% NaCl solution also showed corrosion property improvement. The corrosion products on magnetron sputtered Zn-Mg coating mainly contain Mg modified simonkolleite and magnesium hydroxyl carbonate. The much improved corrosion resistance of Zn-Mg coating can be attributed to the formation of the uniform layer of Mg modified Zn5(OH)8Cl2H2O compound. During the corrosion process, less noble Mg reacts preferentially and a layer of magnesium hydroxyl carbonate forms on the coating surface, which is electrochemically inert. The magnesium hydroxyl carbonate has the effect to neutralize the OH- associated with Zn5(OH)8Cl2H2O formation, resulting in the precipitation of Zn5(OH)8Cl2H2O. This uniform Zn5(OH)8Cl2H2O layer formed on coating surface further reduces the corrosion rate of Zn-Mg coating. (3) For hot dipped Zn-Mg coating, with the increasing of Mg content, a significant improvement in the microhardness was observed as a result of grain refinement strengthening effect and the formation of intermetallic. Based on the results of XRD and EDS analyses, it was concluded that laminar eutectic MgZn2 and Zn formed at Zn grain boundary areas during the solidification of the coating. Electrochemical test indicated that the current density of Zn???3 wt.% Mg coating was appreciably lower than that of Zn coating, suggesting that Zn???3 wt.% Mg coating possessed improved corrosion resistance. This result was further proved in salt water immersion test. The formation of flocculent type of simonkolleite may be a reason for its improved corrosion resistance. (4) For hot dipped Zn-Al-Mg coating, optical microscope images showed that with the increasing Mg content, Zn grain size decreased and eutectic areas at Zn grain boundaries increased. Zn-5 wt.% Al-1.5 wt.% Mg coating has two continuous layers. Mg is prone to exist in the surface layer while Al is prone to exist in the inner layer. The inner layer is composed of Al5Fe2Zn0.4 intermetallic and the outer layer is composed of Zn grains surrounded by Zn and Mg2Zn11 eutectic. This is a well combination of Zn, Al and Mg structure: the inner intermetallic layer containing Al increased the microhardness and adhesive properties of the coating and the outer layer containing Mg contributed to the corrosion resistance of the coating. Zn-5 wt.% Al-1.5 wt.% Mg coating showd the best corrosion resistance among tested Zn-Al-Mg coatings. The outstanding corrosion resistance property of Zn-5 wt.% Al-1.5 wt.% Mg coating is due to the formation of flocculent type of simonkolleite. The structure of simonkolleite prolongs the micro-path and impedes the movement of O2 and H2O, ultimately retards the overall corrosion process of Zn-5 wt.% Al- 1.5 wt.% Mg coating. (5) For Zn-Al-Mg-Cu coating, three different compositions (in wt.%) of dipping bath were prepared: Zn???0.1Cu (G), Zn???5Al???0.1Cu (ZA) and Zn???5Al???1Mg???0.1Cu (ZAM). Results showed that ZAM coating consists of five different phases: hcp Zn phase, base centered Al5Fe2Zn0.4 phase, laves phase MgZn2, cubic lattice Mg2Zn11 and Zn-Fe intermetallic compound. The microhardness of ZAM coating was improved to 178 HV comparing with 43 HV of G coating and 89 HV of ZA coating. The improved microhardness of ZAM coating is due to the strengthening effect of grain boundary at which intermetallic compounds of Al5Fe2Zn0.4, MgZn2 and Mg2Zn11 precipitated. ZAM coating has the best corrosion resistance among three types of coatings as evidenced by electrochemical test and salt spry test. The protective nature of ZAM coating may be attributed to the initial corrosion of Mg-rich phases. The corrosion products of Zn, Al and Mg agglomerate on the cathodic area, which act as inhibitors, blocking the corrosion paths (the micro paths for the diffusion of O2 and H2O) along the grain boundaries of Zn crystals, and increasing the impedance of coating surface, Thus, the overall corrosion process of ZAM coating is retarded. Future works for this research are also suggested in the end of thesis.

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  • Characterisation of a protease-dependent gene regulation system for gene therapy applications

    Naidoo, Jerusha (2015)

    Doctoral thesis
    The University of Auckland Library

    Gene therapy is a promising approach for the treatment of a wide range of chronic diseases. These therapies typically utilise strong, constitutively active promoters to drive high levels of recombinant protein expression. Unregulated gene expression is a key issue limiting clinical translation of promising gene therapies due to the potential for side-effects from excessive levels of protein that indiscriminately affect both diseased and non-diseased cells. Ideally gene expression would be regulated such that it would be quiescent under basal conditions and induced to a therapeutic level in at-risk cells only. This thesis describes the characterisation of a novel bicistronic autoregulatory gene expression system that relies on cell stress-induced activation of specific proteases to drive transgene expression. The functionality of this system was assessed in vitro in a model of cellular stress and in vivo in a neurotoxin model of Parkinson???s disease, a neurodegenerative disorder associated with aberrant activation of the specific proteases caspase-3 and calpain. The results showed that transgene expression under control of the gene regulation system was low under basal conditions and inducible in a concentration-dependent and temporal manner in response to cellular stress induced by the cytotoxin okadaic acid in vitro. Following adeno-associated viral vector (AAV)-mediated delivery of a green fluorescent protein (GFP) reporter gene under control of the regulatory system to the rat substantia nigra pars compacta, expression of GFP was induced in response to cellular stress initiated in the striatum. In the final study the protective efficacy of the anti-apoptotic gene X-linked Inhibitor of Apoptosis Protein (XIAP) under the control of this system was examined in comparison to constitutive XIAP expression in the 6-OHDA model. The results showed that regulating XIAP expression with this system afforded greater protection of dopamine neurons in comparison to control animals that express GFP under control of the regulatory system. In contrast, the extent of dopamine cell loss in animals injected AAV vectors expression XIAP under control of a constitutively active promoter was not different to the corresponding control GFP vector-injected rats. Together these results provided proof-of-principle evidence of the utility of this system for the treatment of brain disorders associated with increased activation of proteases.

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  • Toward understanding the structure and plasticity of the human olfactory bulb in the normal and Parkinson's disease brain

    Tan, Shu-Li (2015)

    Doctoral thesis
    The University of Auckland Library

    Hyposmia, or the diminished capacity to smell, is a robust precursor to the motor symptoms of Parkinson???s disease (bradykinesia, rigidity, a resting tremor, and a shuffling gait), preceding these by 4-10 years. In pursuit of what causes hyposmia in the virtually unstudied human olfactory bulb, a computerised 3D model of the olfactory bulb was created using a combination of automated, fluorescent immunohistochemistry and 3D reconstruction methods that provided quantitative parameters and a unique method for visualisation of the constituents of the olfactory bulb and its functional units (olfactory glomeruli). Antibodies to V-GLUT2 (vesicular glutamate transporter type 2) and NCAM (neural cell adhesion molecule) enabled the identification of olfactory glomeruli. The number of glomeruli, as counted from the 3D model, was highly variable amongst four normal cases (2, 436 ??? 9, 999 glomeruli) and not significantly different from three Parkinson???s disease bulbs (1, 840 ??? 8, 341 glomeruli). Total glomerular and bulb volume was also measured but no significant differences were observed. Nonetheless, the experimental and analytical approach employed in these studies represents a unique and powerful method for visualisation and objective quantification. The second major aspect to this thesis was an experimental approach to understanding the control mechanism of polysialic acidneural cell adhesion molecule (PSA-NCAM), a post-translational modification that aids cellular migration and dendritic foraging. The putative role of sialidase IV (NEU4) in the downregulation of PSA-NCAM was examined; the removal of polysialic acid being a critical step for correct positioning of neuroblasts upon migrating into the olfactory bulb. To do this, NEU4 was expressed in the TE671 rhabdomyosarcoma cell line, and its effects on PSA-NCAM expression were measured. No significant changes in overall PSA-NCAM levels were seen in cells expressing either the short or long isoform of NEU4. This was seen under conventional culture conditions and also when cells were cultured in an extracellular matrix. In order to detect more subtle changes that may be occurring at the cell surface, the same experiments were performed and analysed using immunocytochemistry and high content analysis. Depending on the mode of analysis small changes were detected suggesting that NEU4 may be involved in reducing the amount of PSA-NCAM present at the cell surface. However, owing to the experimental design, I was not able to definitively implicate or exclude NEU4 from involvement in the down-regulation of PSA-NCAM. Collectively, the findings of this thesis are of relevance when elucidating the mechanisms of olfactory bulb wiring and organisation, and how neural progenitors serve to maintain this brain region over a lifetime.

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  • Scour at submerged weirs

    Guan, Dawei (2015)

    Doctoral thesis
    The University of Auckland Library

    Weirs or bed sills are river training structures that are used for raising upstream water level, bed stabilization and reducing flow velocity. During high flow events, the weir is fully submerged in the river and scouring occurs both upstream and downstream of the weir. Many empirical scour equations have been proposed for prediction of scour depth downstream of unsubmerged weirs. Research on scour at submerged weirs is very limited. For a fully submerged weir, the scour mechanism around the weir is dependent on approach flow intensity (clear-water scour conditions or live-bed scour conditions) and flow regimes (surface flow regime or impinging jet regime) over the weir. Under livebed scour conditions, the rapid evolution of underwater mobile topographies and propagating bedforms increases the complexities of the scour process and the difficulties for scour measurement at the submerged weir. The aim of this study is to experimentally investigate flow structures and scour process at submerged weirs in sand channels. The experimental programmes were conducted in a tilting recirculating flume. Both clear-water scour and live-bed scour conditions were applied. The experimental results of an investigation of flow structures at the weir show that a large recirculation zone and a flow reattachment region are formed downstream of the submerged weir. Strongly paired cellular secondary flows were observed in the scour hole. The turbulence structures ahead of the recirculation zone govern the dimensions of the scour hole downstream of the weir. In the coarse sand tests, bed elevation changes were measured in the approach flow reach and in the scour zones both upstream and downstream of the weir using a Seatek multiple transducer array. The highly contaminated raw bed-elevation data were filtered using a data processing technique. In the fine sand tests, the scour process was monitored using Logitech HD webcams on both sides of the flume. Image analysis was implemented to obtain bed profiles and scour depths over time. Under clear water scour conditions, the temporal development of maximum scour depth downstream of the weir has three stages: 1) initial fast stage, 2) progressing stage, 3) equilibrium stage. Under live bed scour conditions, the scour occurs both upstream and downstream of the weir, and sediment transport processes are highly influenced by strong turbulence in the vicinity of the submerged weir. A scour-and-fill process occurs immediately upstream from the weir in response to periodic approaching bed-forms. The dimensions of the scour hole downstream of the weir fluctuate due to the unsteady upstream sediment input and the development of secondary flows. The flow regimes over the submerged weir are found to be independent of the sediment size, and the transition flow regime boundary can be expressed as a function of upstream Froude number and the ratio of weir height to tailwater depth. On the basis of the experimental data, equations for prediction of equilibrium scour depths both upstream and downstream of the submerged weir are proposed. A design method is given in this study for estimating the maximum scour depths at the submerged weir.

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  • Disgust in colorectal cancer contexts: Does it cause avoidance and could mindfulness help?

    Reynolds, Lisa (2015)

    Doctoral thesis
    The University of Auckland Library

    Disgust???s evolved function is to minimise health threats through a process of rejection, avoidance, and withdrawal. Despite its seemingly obvious relevance, however, research investigating disgust in physical health settings remains scant. By exploring the emotion of disgust in the context of colorectal cancer, the current work sought to address this research deficit, and in doing so, add to the emerging literature examining the emotional bases of avoidance in health. The colorectal cancer trajectory presents numerous established disgust elicitors (faeces, surgical wounds, anal investigations, etc.), and avoidance can have serious physical and psychological consequences. Thus, the aims of this work were to establish: (1) whether disgust predicts and/or causes avoidance in colorectal cancer contexts, and if so, (2) consider whether mindfulness may help to ameliorate this effect? Following a systematic review of literature pertaining to colorectal cancer and disgust, a series of correlational and experimental studies in clinical and non-clinical populations were conducted. The first of these empirical works???Study 1, a prospective, correlational design with anal incontinence patients???found that greater disgust sensitivity predicted poorer psychological and environmental well-being, and moderated the link between symptom severity and outcome. In Study 2a, trait disgust predicted, and experimentally-induced disgust caused, greater immediate avoidance behaviours related to colorectal cancer. In addition, trait disgust increased the influence of state disgust on decisions regarding anticipated future avoidance. With the relationship between disgust and avoidance established, the focus of this work then turns to consider whether mindfulness might ameliorate disgust???s effects. Data from the prior study was revisited in Study 2b, and contrary to expectations, analyses showed that greater trait mindfulness exaggerated avoidance behaviours rather than diminishing them. Similarly, Study 3???an experimental study in which both disgust and mindfulness were experimentally induced???found that state disgust caused social avoidance in relation to bowel health scenarios and, again, state mindfulness exaggerated the effect. Finally, Study 4, a randomised controlled trial with first time chemotherapy patients, found that a brief mindfulness intervention led to detrimental effects???greater distress and increased social avoidance???in comparison to relaxation training. Taken together, these studies are the first to clearly demonstrate that (a) disgust both predicts and causes avoidance in contexts related to colorectal cancer, and (b) that mindfulness does not ameliorate disgust???s effects, at least in these contexts. This thesis thus highlights the importance of considering the emotion of disgust in both colorectal cancer and in physical health settings more broadly, and has important clinical implications. Through better understanding of a key affective mechanism of avoidance (i.e., the disgust response), these findings have potential to inform interventions designed to reduce deleterious avoidance. This work ends on a note of caution, suggesting that mindfulness-based interventions may not be optimally suited to some physical health populations, and suggests alternative potential avenues for future research and clinical intervention.

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  • Molten territories: 21st century articulations of Auckland???s volcanoes

    Mathews, N (2015)

    Doctoral thesis
    The University of Auckland Library

    Auckland city is built upon over 50 volcanoes. This research explores key selected meanings of these, with an eye to the role of physicality in meaning creation. The methodology includes landscape phenomenology and autoethnography placed in conversation with textual analysis of the New Zealand Herald newspaper. Representational and nonrepresentational accounts are addressed, including ???nonhuman charisma???. I develop a perspective that combines materialist insight with discourse theory to situate the meanings of the volcanoes in a more-than-human context. The thesis is structured around different methodological moments and actors. Analysis is backgrounded by a history of the reciprocal relationship between volcanoes and Auckland city. This suggests an augmentation of nonhuman charisma over time, as smaller and more distant volcanoes were quarried away and already-prominent cones gained physical, and later visual, protection. My own experiences are used to engage with the contemporary form of one volcano, Maungawhau/Mount Eden. This highlights the centrality of afforded vision and demonstrates intersections with concepts of ???nature???. These themes are echoed in the visual presence of volcanic cones when moving through the city. Charismatic volcanoes are also prominent semiotically and tied to local and city identity. This uneven familiarity and affective identification is shown to have formed an integral part of a recent media campaign to ???save??? certain volcanoes from damage. Other conservation tactics included selective mobilisation of ???heritage??? discourse, and obscure legislation that was itself granted efficacy through repeated media coverage. The physical and semiotic prominence of Maungakiekie/One Tree Hill can be similarly seen to underlie its persistent and emotive use as symbolic focus for race relation discussion. I note a shift in the presentation of the volcanoes following plans to return many volcanic cones to the iwi collective, Ng?? Mana Whenua o T??maki Makaurau, embodied in local media by use of ???maunga???, articulating volcanic cones as a group with contemporary Maori interests. The importance of a re-articulation with Maori is underscored by the volcanoes??? persistent and affective association with ???nature??? through geology and imagined disaster. This analysis draws on a bodily ???sublime??? aesthetic, the celebration of which paradoxically haunts even recent drives towards risk mitigation.

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  • An Ethnography of Everyday Practices: Young IT Professionals??? Engagement with Technologies

    Chughtai, Hameed (2015)

    Doctoral thesis
    The University of Auckland Library

    Information Systems (IS) research deals with the nature of information technology (IT) in our practices. The problem is that we, including IS researchers and practitioners, find ourselves deeply absorbed in our everyday practices. The fact that we tend to take our practices for granted makes discovering the logic of these practices an elusive enterprise. How, then, can we study these practices? In an attempt to furnish critical interpretations of the nature of our interaction with IT in our everyday practices, I used ethnographic research to study the practices of young tech savvy people (sometimes called ???digital natives???) because in their everyday lives they are always absorbed in ubiquitous IT phenomena. The ethnographic fieldwork began with a simple overarching question: how do young IT professionals interact with technologies in their everyday practices? It was envisioned that the ethnographic fieldwork would disclose deeper layers of meaning underlying practices of epistemic and ontological significance in terms of engagement with technology. Indeed, following the entwinement perspective of Martin Heidegger, I found that people are increasingly getting entwined with IT in their everyday practices; but further, entwinement can be seen as a ludic phenomenon, that is to say a play-like engaged absorption in one???s everyday being in the world. Technology is thus disclosed as an ordinary plaything in their practice worlds. Further, I found that when engaged absorption is seen as play, practices are bounded by everyday spaces where many playing fields are constantly being created by the players. In the final phases of ethnography, spatiality was discovered as a significant aspect of the field enquiry: how can an ethnographer make sense of a play-like engaged practice in which, and precisely where he or she is already absorbed in the field? The latter half of the fieldwork was thus focused on the examination of the spatial field that envelops the phenomenon where a technological practice is grounded. This thesis adopts a ???thesis with publications??? model and includes six original articles. The thesis also suggests some strategies to make sense of everyday practices, design practices, and the management of the younger workforce. Finally, the study aims to contribute to the ethnographic toolkit by suggesting the use of novel methodological tools such as ???thrownness???, play or ???ludic practices???, ???entwinement??? and ???spatial volatility??? of the fieldwork.

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  • Human Adenoviruses As Indicators Of Faecal Contamination And Pathogen Indices In The Environment And Shellfish

    Hewitt, Joanne (2015)

    Doctoral thesis
    The University of Auckland Library

    The main aim of this study was to assess the use of human adenoviruses (HAdVs) as occurrence indicators of human enteric viruses in the environment and shellfish. The second aim was to consider human polyomaviruses (HPyVs) for the same roles. To gain a better understanding of the ecology of HAdV, their diversity in the environment was also investigated. Method development included validation of an ultrafilter for virus concentration from water samples; real-time quantitative PCR (qPCR) assay development; evaluation of culture-qPCR using different cell lines; and assessment of guanidine hydrochloride to inhibit enterovirus growth in virus quantification assays. The presence, quantity, and where possible, infectivity (using HEK-293 cells in a culture-qPCR assay with guanidine hydrochloride) of HAdVs were determined in a range of environmental samples and shellfish. The presence and quantity of HPyVs, noroviruses and enteroviruses were also determined where appropriate. HAdVs, predominantly species F and other HAdV species at lower concentrations, were frequently present in high concentrations in wastewater influent, independently of wastewater treatment plant size. They were also present in non-disinfected effluent irrespective of treatment type. HPyVs were prevalent at concentrations at least as high as HAdVs in wastewaters. In biosolids, the occurrence of HAdVs and HPyVs were comparable to enteroviruses and like wastewater, were detected more frequently than noroviruses. In urban streams, rivers and estuaries, neither HAdVs nor HPyVs were dominant in terms of their occurrence and so should be used as part of a multi-tool source tracking system. Shellfish studies showed a low occurrence of HAdVs and HPyVs, probably due to poor virus recovery. Further studies are required to investigate this. The results of this study strongly supported the hypothesis that HAdVs and HPyVs are suitable indices for viral contamination from faecal sources. Furthermore, due to their continued occurrence in the environment and their host specificity, these viruses also have potential for microbial source tracking applications. However, one caveat identified was the difficulty in recovering HAdVs, and presumably HPyVs, from shellfish. In conclusion, although it is unlikely that the detection of a single indicator by one method will be sufficient to identify health risks and faecal contamination sources, HAdVs and HPyVs together are a good option for viral indicators of faecal contamination and as pathogen indices in the environment.

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