2,837 results for ResearchSpace@Auckland, 2011

  • Chemical and biological explorations of the electrophilic reactivity of the bioactive marine natural product halenaquinone with biomimetic nucleophiles

    Wang, J; Bourguet-Kondracki, M-L; Longeon, A; Dubois, J; Valentin, A; Copp, Brent (2011-02-15)

    Journal article
    The University of Auckland Library

    The electrophilic reactivity of the bioactive marine sponge natural product halenaquinone has been investigated by reaction with the biomimetic nucleophiles N-acetyl-L-cysteine and N(??)-acetyl-L-lysine. While cysteine reacted at the vacant quinone positions C-14 and C-15, lysine was found to react preferentially at the keto-furan position C-1. A small library of analogues was prepared by reaction of halenaquinone with primary amines, and evaluated against a range of biological targets including phospholipase A(2), farnesyltransferases (FTases) and Plasmodium falciparum. Geranylamine analogue 11 exhibited the most potent activity towards FTases (IC(50) 0.017-0.031 ??M) and malaria (IC(50) 0.53-0.62 ??M).

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  • Grounded Theory for geeks

    Hoda, Rashina; Noble, J; Marshall, S (2011)

    Conference item
    The University of Auckland Library

    Grounded Theory (GT) is gaining popularity as research method in Software Engineering; however, it is still not widely understood. We present some patterns based on the use of GT to study Software Engineering contexts including our own experiences of applying classic GT in an attempt to make it more accessible for Software Engineering researchers (aka 'geeks').

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  • Behavioral Studies of Project Dispute Negotiation in Engineering and Construction: Visit to Bandura's Self-Efficacy Theory

    Yiu, Tak Wing; Cheung, SO (2011)

    Journal article
    The University of Auckland Library

    This essay explains project dispute negotiation as it widely applies to the engineering management and provides a short review of the behavioral studies of project dispute negotiation. Furthermore, a popular psychological theory, Bandura???s self-efficacy theory, is introduced. The potential research opportunities of researching and applying this theory are also discussed in the last section of this forum.

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  • Marine natural products

    Blunt, JW; Copp, Brent; Munro, MHG; Northcote, PT; Prinsep, MR (2011-02)

    Journal article
    The University of Auckland Library

    Covering: 2009.

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  • Economic growth, agriculture and poverty reduction in Cambodia

    Ngin, C (2011-03-06)

    Conference item
    The University of Auckland Library

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  • Bioactive Indole Derivatives from the South Pacific Marine Sponges Rhopaloeides odorabile and Hyrtios sp.

    Longeon, A; Copp, Brent; Quevrain, E; Roue, M; Kientz, B; Cresteil, T; Petek, S; Debitus, C; Bourguet-Kondracki, M-L (2011-05-24)

    Journal article
    The University of Auckland Library

    Indole derivatives including bromoindoles have been isolated from the South Pacific marine sponges Rhopaloeides odorabile and Hyrtios sp. Their structures were established through analysis of mass spectra and 1D and 2D NMR spectroscopic data. Their potential inhibitory phospholipase A2 (PLA2), antioxidant and cytotoxic activities were evaluated. The new derivative 5,6-dibromo-l-hypaphorine (9) isolated from Hyrtios sp. revealed a weak bee venom PLA2 inhibition (IC50 0.2 mM) and a significant antioxidant activity with an Oxygen Radical Absorbance Capacity (ORAC) value of 0.22. The sesquiterpene aureol (4), also isolated from Hyrtios sp., showed the most potent antioxidant activity with an ORAC value of 0.29.

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  • Establishment of the absolute configuration of the bioactive marine alkaloid eudistomin X by stereospecific synthesis

    Finlayson, R; Brackovic, A; Simon-Levert, A; Banaigs, B; O'Toole, RF; Miller, CH; Copp, Brent (2011-02-16)

    Journal article
    The University of Auckland Library

    A stereospecific synthesis of both enantiomers of the marine alkaloid eudistomin X using the amino acid chiral pool is achieved. Comparison of 1H and 13C NMR chemical shifts of the synthetic product as either the free base, mono-salt or disalt with those reported for the natural product established that the ascidian metabolite was originally characterised as a mono-salt and that the absolute configuration was (10R).

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  • Didemnidines A and B, indole spermidine alkaloids from the New Zealand ascidian Didemnum sp.

    Finlayson, R; Pearce, Allison; Page, MJ; Kaiser, M; Bourguet-Kondracki, M-L; Harper, JL; Webb, VL; Copp, Brent (2011-02-24)

    Journal article
    The University of Auckland Library

    Two new indole spermidine alkaloids, didemnidines A (1) and B (2), have been isolated from the New Zealand ascidian Didemnum sp. The structures of the metabolites, determined by analysis of 2D NMR spectra and confirmed via synthesis, embody an indole-3-glyoxylamide moiety linked to the N(1) position of spermidine, the latter motif being particularly rare among marine natural products. Didemnidine B and a synthetic precursor exhibited mild in vitro growth inhibition of Plasmodium falciparum with IC(50)'s of 15 and 8.4 ??M, respectively.

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  • Antimalarial ??-Carbolines from the New Zealand Ascidian Pseudodistoma opacum

    Chan, STS; Pearce, Allison; Page, MJ; Kaiser, M; Copp, Brent (2011-09-23)

    Journal article
    The University of Auckland Library

    One tetrahydro-??-carboline, (-)-7-bromohomotrypargine (1), and three alkylguanidine-substituted ??-carbolines, opacalines A, B, and C (2-4), have been isolated from the New Zealand ascidian Pseudodistoma opacum. The structures of the metabolites were determined by analysis of mass spectrometric and 2D NMR spectroscopic data. Natural products 2 and 3, synthetic debromo analogues 8 and 9, and intermediate 16 exhibited moderate antimalarial activity toward a chloroquine-resistant strain of Plasmodium falciparum, with an IC50 range of 2.5-14 ??M. The biosynthesis of 1-4 is proposed to proceed via a Pictet-Spengler condensation of 6-bromotryptamine and the ??-keto acid transamination product of either arginine or homoarginine. Cell separation and 1H NMR analysis of P. opacum identified tetrahydro-??-carboline 1 to be principally located in the zooids, while fully aromatized analogues 2-4 were localized to the test.

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  • Benchmarking and modeling disk-based storage tiers for practical storage design

    Lee, Dong Jin; O'Sullivan, Michael; Walker, Cameron (2011)

    Conference item
    The University of Auckland Library

    This paper presents benchmark experiments for designing an optimal archival storage system. The benchmark utilizes archival workloads developed from an analysis of historical file size distributions. The workloads provide more appropriate measurements of system performance as an archive than traditional approaches. We use these benchmarks to measure disk-based archival systems. We then consider designing an archival system based on our benchmark measurements and produce a low cost design for a commodity disk-based archival storage system. Combining results of predictions along with our optimization-driven design, we discover an ideal building block for an archival storage system.

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  • Relationship between walk tests and parental reports of walking abilities in children With cerebral palsy

    Chong, J; Mackey, Anna; Broadbent, Elizabeth; Stott, Ngaire (2011-02)

    Journal article
    The University of Auckland Library

    Objectives To test the strength of association between 2 clinic-based measures of walking ability, the 1-minute walk test (1MWT) and the six-minute walk test (6MWT), and the parental report of usual walking performance, measured by the ABILOCO-Kids logit score, in children with cerebral palsy (CP). Design Observational study. Setting Tertiary level outpatient clinics. Participants Children and youth with CP (N=60; 32 boys, 28 girls; mean age, 11.2y [range, 5???18y]), Gross Motor Function Classification System (GMFCS) level I to IV. Interventions Not applicable. Main Outcome Measures The 10-item ABILOCO-Kids questionnaire, the 1MWT, and the 6MWT. Results ABILOCO-Kids logit scores were significantly correlated with the 1MWT (??=.70, Ps walking ability in the community correlate with clinic-based walking tests in ambulatory children with CP, providing evidence of convergent validity for the 1MWT and 6MWT. However, parents report a much wider range of walking abilities in children who function at a high level (GMFCS I) than is reflected by their walk test results.

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  • Evaluating the use of stereo-photogrammetry for gravel-bed roughness analysis

    Bertin, Stephane; Friedrich, Heide; Heays, K (2011)

    Conference item
    The University of Auckland Library

    In this work, three different measurement technologies are employed to study the hydraulic roughness in a laboratory flume with a gravel-bed. The gravel-bed topography is measured with (i) an acoustic bed-profiler; (ii) a hand-held laser-scanner; and (iii) stereo-photogrammetry. Digital Elevation Models (DEMs) are obtained with each technique. Statistical roughness analyses of the DEMs are undertaken by estimating the vertical roughness length, represented by the standard deviation of bed elevations. In addition, Probability Distribution Functions (PDFs) and two-dimensional second-order structure functions of bed elevations are used for the analyses. All three measurement techniques were found precise enough to reach the grain-scale of laboratory gravel-beds. However, important disparities were found between the DEMs, which were not always visible statistically. The acoustic bed-profiler and the laser-scanner were found suitable for gravel-bed roughness characterisation. With stereo-photogrammetry, the complex operational processes must be improved to obtain realistic high-resolution DEMs and to derive faithful statistics.

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  • Do New Zealand children with non-cystic fibrosis bronchiectasis show disease progression?

    Munro, KA; Reed, PW; Joyce, H; Perry, D; Twiss, J; Byrnes, Catherine; Edwards, EA (2011-02)

    Journal article
    The University of Auckland Library

    Background There is minimal literature available on the long-term outcome of pediatric non-cystic fibrosis (CF) bronchiectasis. Aim To document 5-year outcomes of children with chest computerized tomography (CT) scan diagnosed bronchiectasis from a tertiary New Zealand (NZ) respiratory clinic. Methods Review of a clinical database identified 91 children. Demographics, clinical data, lung function, chest X-ray (CXR), sputum, presumed etiology, admission data, and the NZ deprivation index (NZDep) were collected. Univariate and multivariate regression were used to correlate clinical findings with lung function data and CXR scores using the Brasfield Scoring System.

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  • Modelling collagen fibre orientation in porcine skin based upon confocal laser scanning microscopy

    Jor, Jessica; Nielsen, Poul; Nash, Martyn; Hunter, Peter (2011)

    Journal article
    The University of Auckland Library

    Background: The mechanical properties of skin, and its ability to resist a wide range of deformations, are mainly determined by the collagen network within the dermis. Aims: In order to quantify the structure???function relationship of skin, quantitative data on collagen orientation are acquired in this study. Materials & Methods: Saggital cryosections from the abdominal region of young pigs were stained with picrosirus red for collagen detection and images were acquired by confocal laser scanning microscopy (CLSM). Spatial distributions of collagen orientation were determined using a structure???tensor approach. Orientation data were fitted to a mixture of two von Mises distributions. Results: It was observed that collagen is organised into large bundles in the reticular dermis that run obliquely between the epidermis to hypodermis along two predominant orientations. Discussion: This distinct lattice structure was apparent in all sections, regardless of the sectioning orientation. Based on our observations from CLSM images,we propose a conceptual model expressed in terms of a density distribution function to describe collagen orientation. Conclusion: We demonstrate that two parameters of this distribution (the mean and spread parameter) may be directly determined using CLSM image analysis. An important advantage of this approach is that model parameters can be estimated directly from observable microstructural features.

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  • A discrete model to study reaction-diffusion-mechanics systems

    Weise, LD; Nash, Martyn; Panfilov, AV (2011-07-11)

    Journal article
    The University of Auckland Library

    This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

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  • Lymphatic drainage and tumour prevalence in the breast: a statistical analysis of symmetry, gender and node field independence

    Blumgart, Evan; Uren, RF; Nielsen, Poul; Nash, Martyn; Reynolds, Hayley (2011-06)

    Journal article
    The University of Auckland Library

    Current understanding of the lymphatics draining the breast is controversial, despite its known importance in the spread of breast cancer. Similarly, knowledge regarding the spatial distribution of primary tumours in the breast is limited. This study sought to test commonly held assumptions in this field, including: (i) that breast lymphatic drainage and tumour prevalence are symmetric between the left and right sides of the body, (ii) that males and females have the same drainage patterns and tumour prevalences, and (iii) that lymphatic drainage in the breast occurs independently to different node fields. This study has used lymphoscintigraphy data from 2304 breast cancer patients treated at the RPAH Medical Centre, Sydney, Australia. Symmetry of lymphatic drainage and tumour distribution as well as gender differences were tested using Fisher's exact test. Drainage independence was assessed using Fisher's exact test, and a multivariate probit model was used to test for drainage correlations. Results showed that the breasts are likely to have symmetric lymphatic drainage and tumour prevalence, and that there is no significant difference between males and females. Furthermore, results showed that direct lymphatic drainage of the breasts is likely to be independent between node fields. Collectively, these results serve to further our understanding of lymphatic anatomy and the distribution of tumours in the breast.

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  • Predicting lymphatic drainage patterns and primary tumour location in patients with breast cancer

    Blumgart, Evan; Uren, RF; Nielsen, Poul; Nash, Martyn; Reynolds, HM (2011-11)

    Journal article
    The University of Auckland Library

    Detailed knowledge of the lymphatic drainage of the breast is limited. Lymphoscintigraphy is a technique used during breast cancer treatment to accurately map patterns of lymphatic drainage from the primary tumour to the draining lymph nodes. This study aimed to create a statistical model to analyse the spread of breast cancer and primary tumour location using a large lymphoscintigraphy database, and visualise the results with a novel computational model. This study was based on lymphoscintigraphy data from 2,304 breast cancer patients treated at the Royal Prince Alfred Hospital Medical Centre in Sydney, Australia. Bayesian inferential techniques were implemented to estimate the probabilities of lymphatic drainage from each region of the breast to each draining node field, to multiple node fields, and to determine probabilities of tumour prevalence in each breast region. A finite element model of the torso and discrete model of the draining node fields were created to visualise these data and a software tool was developed to display the results (www.abi.auckland.ac.nz/breast-cancer). Results confirmed that lymphatic drainage is most likely to occur to the axillary node field, and that there is significant likelihood of drainage to the internal mammary node field. The likeli- hood of lymphatic drainage from the whole breast to the axillary, internal mammary, infraclavicular, supraclavicular and interpectoral node fields were 98.2, 35.3, 1.7, 3.1, and 0.7%, respectively; whilst the probability of lymphatic drainage to multiple node fields was estimated to be 36.4%. Additionally, primary tumours are most likely to develop in the upper regions of the breast. The models developed pro- vide quantitative estimates of lymphatic drainage of the breast, giving important insights into understanding breast cancer metastasis and have the potential to benefit both cli- nicians and patients during breast cancer diagnosis and treatment.

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  • Optimising echocardiographic screening for rheumatic heart disease in New Zealand: Not all valve disease is rheumatic

    Webb, Rachel; Wilson, NJ; Lennon, Diana; Wilson, EM; Nicholson, RW; Gentles, TL; O'Donnell, CP; Stirling, JW; Zeng, Sui; Trenholme, AA (2011-07)

    Journal article
    The University of Auckland Library

    Echocardiography detects a greater prevalence of rheumatic heart disease than heart auscultation. Echocardiographic screening for rheumatic heart disease combined with secondary prophylaxis may potentially prevent severe rheumatic heart disease in high-risk populations. We aimed to determine the prevalence of rheumatic heart disease in children from an urban New Zealand population at high risk for acute rheumatic fever. To optimise accurate diagnosis of rheumatic heart disease, we utilised a two-step model. Portable echocardiography was conducted on 1142 predominantly M??ori and Pacific children aged 10???13 years. Children with an abnormal screening echocardiogram underwent clinical assessment by a paediatric cardiologist together with hospital-based echocardiography. Rheumatic heart disease was then classified as definite, probable, or possible. Portable echocardiography identified changes suggestive of rheumatic heart disease in 95 (8.3%) of 1142 children, which reduced to 59 (5.2%) after cardiology assessment. The prevalence of definite and probable rheumatic heart disease was 26.0 of 1000, with 95% confidence intervals ranging from 12.6 to 39.4. Portable echocardiography overdiagnosed rheumatic heart disease with physiological valve regurgitation diagnosed in 28 children. A total of 30 children (2.6%) had non-rheumatic cardiac abnormalities, 11 of whom had minor congenital mitral valve anomalies. We found high rates of undetected rheumatic heart disease in this high-risk population. Rheumatic heart disease screening has resource implications with cardiology evaluation required for accurate diagnosis. Echocardiographic screening for rheumatic heart disease may overdiagnose rheumatic heart disease unless congenital mitral valve anomalies and physiological regurgitation are excluded.

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  • Human ventricular fibrillation during global ischemia and reperfusion: Paradoxical changes in activation rate and wavefront complexity

    Bradley, Christopher; Clayton, RH; Nash, Martyn; Mourad, A; Hayward, M; Paterson, David; Taggart, P (2011)

    Journal article
    The University of Auckland Library

    Background- Ischemic ventricular fibrillation in experimental models has been shown to progress through a series of stages. Progression of ischemic VF in the in vivo human heart has not been determined. Methods and Results- We studied 10 patients undergoing cardiac surgery. Ventricular fibrillation was induced by burst pacing. After 30 seconds, global myocardial ischemia was induced by aortic cross-clamp and maintained for 2.5 minutes, followed by coronary reflow. Epicardial activity was sampled (1 kHz) with a sock that contained 256 unipolar contact electrodes. Dominant frequencies were calculated with a fast Fourier transform with a moving window. The locations of phase singularities and activation wavefronts were identified at 10-ms intervals. Preischemic (perfused) ventricular fibrillation was maintained by a disorganized mix of large and small wavefronts. During global myocardial ischemia, mean dominant frequencies decreased from 6.4 to 4.7 Hz at a rate of -0.011??0.002 Hz s(-1) (P<0.01) and remained unchanged during reflow, at 10.3. The number of wavefronts showed a similar time course to the number of phase singularities. Conclusions- In human ventricular fibrillation, we found an increase in complexity of electric activation patterns during global myocardial ischemia, and this was not reversed during reflow despite an increase in activation rate.

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  • Quantitative characterisation of seafloor substrate and bedforms using advanced processing of multibeam backscatter???Application to Cook Strait, New Zealand

    Lamarche, Geoffroy; Lurton, X; Verdier, A-L; Augustin, J-M (2011-02)

    Journal article
    The University of Auckland Library

    A comprehensive EM300 multibeam echo-sounder dataset acquired from Cook Strait, New Zealand, is used to develop a regional-scale objective characterisation of the seafloor. Sediment samples and high-resolution seismic data are used for ground-truthing. SonarScope?? software is used to process the data, including signal corrections from sensor bias, specular reflection compensation and speckle noise filtering aiming at attenuating the effects of recording equipment, seafloor topography, and water column. The processing is completed by correlating a quantitative description (the Generic Seafloor Acoustic Backscatter???GSAB model) with the backscatter data. The calibrated Backscattering Strength (BS) is used to provide information on the physical characteristics of the seafloor. The imagery obtained from the BS statistical compensation is used for qualitative interpretation only; it helps characterizing sediment facies variations as well as geological and topographic features such as sediment waves and erosional bedforms, otherwise not recognised with the same level of detail using conventional surveying. The physical BS angular response is a good indicator of the sediment grain size and provides a first-order interpretation of the substrate composition. BS angular response for eight reference areas in the Narrows Basin are selected and parameterised using the GSAB model, and BS angular profiles for gravelly, sandy, and muddy seafloors are used as references for inferring the grain size in the reference areas. We propose to use the calibrated BS at 45?? incidence angle (BS45) and the Specular-To-Oblique Contrast (STOC) as main global descriptors of the seafloor type. These two parameters enable global backscatter studies by opposition to compensated imagery whose intensity is not comparable from one zone to the other. The results obtained highlight the interest of BS measurements for seafloor remote sensing in a context of habitat-mapping applications.

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