89,483 results

  • A computationally efficient optimization kernel for material parameter estimation procedures

    Schmid, H; Nash, Martyn; Young, Alistair; R??hrle, O; Hunter, Peter (2007)

    Journal article
    The University of Auckland Library

    Estimating material parameters is an important part in the study of soft tissue mechanics. Computational time can easily run to days, especially when all available experimental data are taken into account. The material parameter estimation procedure is examplified on a set of homogeneous simple shear experiments to estimate the orthotropic constitutive parameters of myocardium. The modification consists of changing the traditional least-squares approach to a weighted least-squares. This objective function resembles a L2-norm type integral which is approximated using Gaussian quadrature. This reduces the computational time of the material parameter estimation by two orders of magnitude.

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  • A vision and strategy for the virtual physiological human in 2010 and beyond.

    Hunter, Peter; Coveney, PV; De Bono, Bernard; Diaz, V; Fenner, J; Frangi, AF; Harris, P; Hose, R; Kohl, P; Lawford, P; McCormack, K; Mendes, M; Omholt, S; Quarteroni, A; Sk??r, J; Tegner, J; Randall Thomas, S; Tollis, I; Tsamardinos, I; van Beek, JH; Viceconti, M (2010-06-13)

    Journal article
    The University of Auckland Library

    European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for nearly 2 years. The VPH network of excellence (NoE) is helping in the development of common standards, open-source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also helping to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by framework 6 strategy for a European physiome (STEP) project in 2006. It is now time to assess the accomplishments of the last 2 years and update the STEP vision for the VPH. We consider the biomedical science, healthcare and information and communications technology challenges facing the project and we propose the VPH Institute as a means of sustaining the vision of VPH beyond the time frame of the NoE.

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  • Modeling Cardiac Electrical Activity at the Cell and Tissue Levels

    Austin, Travis; Hooks, Darren; Hunter, Peter; Nickerson, David; Pullan, Andrew; Sands, Gregory; Smaill, Bruce; Trew, Mark (2006-10)

    Journal article
    The University of Auckland Library

    Significant tissue structures exist in cardiac ventricular tissue, which are of supracellular dimension. It is hypothesized that these tissue structures contribute to the discontinuous spread of electrical activation, may contribute to arrhythmogenesis, and also provide a substrate for effective cardioversion. However, the influences of these mesoscale tissue structures in intact ventricular tissue are difficult to understand solely on the basis of experimental measurement. Current measurement technology is able to record at both the macroscale tissue level and the microscale cellular or subcellular level, but to date it has not been possible to obtain large volume, direct measurements at the mesoscales. To bridge this scale gap in experimental measurements,we use tissue-specific structure and mathematical modeling. Our models,which can incorporate ion channel models at the cell level into the reaction???diffusion equations at the tissue level, have enabled us to consider key hypotheses regarding discontinuous activation.

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  • Uraba lugens (Lepidoptera: Nolidae) in New Zealand: Pheromone trapping for delimitation and phenology

    Suckling, David; Gibb, AR; Dentener, PR; Seldon, David; Clare, GK; Jamieson, L; Baird, D; Kriticos, DJ; El-Sayed, AM (2005-08)

    Journal article
    The University of Auckland Library

    This article is the copyright property of the Entomological Society of America and may not be used for any commercial or other private purpose without specific written permission of the Entomological Society of America A synthetic sex pheromone trapping survey of the leaf skeletonizer Uraba lugens Walker (Lepidoptera: Nolidae) demonstrated the unexpectedly widespread distribution of the insect across <1% of damaged trees with traps failed to catch adult moths. Damage by larval feeding was correlated with male trap catch in the previous generation, offering good prospects for a pest management decision support system, provided that an economic threshold is developed. Catches increased by 3.4-fold in the same georeferenced trapping grid between November and December 2003 and between March and April 2004 across two generations, over the summer. A vertical transect showed that catches increased with height up to the top trap at 13 m (60% of mean tree height). Options for managing the insect will need to overcome the high rate of increase, the rate of spread, and the vertical distribution of the insect on tall eucalyptus trees.

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  • Steady streaming: A key mixing mechanism in low-Reynolds-number acinar flows

    Kumar, Haribalan; Tawhai, Merryn; Hoffman, EA; Lin, C-L (2011)

    Journal article
    The University of Auckland Library

    Copyright 2011 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in Physics of Fluids 23(4):21 pages Article number 041902 2011 and may be found at http://dx.doi.org/10.1063/1.3567066. Study of mixing is important in understanding transport of submicron sized particles in the acinar region of the lung. In this article, we investigate transport in view of advective mixing utilizing Lagrangian particle tracking techniques: tracer advection, stretch rate and dispersion analysis. The phenomenon of steady streaming in an oscillatory flow is found to hold the key to the origin of kinematic mixing in the alveolus, the alveolar mouth and the alveolated duct. This mechanism provides the common route to folding of material lines and surfaces in any region of the acinar flow, and has no bearing on whether the geometry is expanding or if flow separates within the cavity or not. All analyses consistently indicate a significant decrease in mixing with decreasing Reynolds number (Re). For a given Re, dispersion is found to increase with degree of alveolation, indicating that geometry effects are important. These effects of Re and geometry can also be explained by the streaming mechanism. Based on flow conditions and resultant convective mixing measures, we conclude that significant convective mixing in the duct and within an alveolus could originate only in the first few generations of the acinar tree as a result of nonzero inertia, flow asymmetry, and large Keulegan???Carpenter (KC) number.

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  • EFFECT OF FUNGAL METABOLITE PERAMINE AND ANALOGS ON FEEDING AND DEVELOPMENT OF ARGENTINE STEM WEEVIL (LISTRONOTUS-BONARIENSIS)

    ROWAN, DD; DYMOCK, JJ; Brimble, Margaret (1990-05-01)

    Journal article
    The University of Auckland Library

    Peramine, a pyrrolopyrazine alkaloid produced by the fungal endophyte of perennial ryegrassAcremonium lolii, deterred the feeding of both adults and larvae of the graminacious herbivore, the Argentine stem weevil (Listronotus bonariensis), at 0.1 g/g and 10 g/g, respectively. In a no-choice test fewer stem weevil larvae fed and developed on diet containing as little as 2 g/g peramine. The proportion of larvae which did not develop beyond the first instar was higher on diet containing peramine and appeared to be due to a higher proportion of larvae which did not feed. For larvae which fed on the peramine-containing diet, feeding scores and times to pupation were not significantly different from those of controls. A number of simple peramine analogues showed feeding-deterrent activity against adult weevils, indicating the importance of the pyrrolopyrazine ring system of peramine in determining feeding-deterrent activity.

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  • The first enantioselective total synthesis of the anti-Helicobacter pylori agent (+)-spirolaxine methyl ether

    Robinson, James; Brimble, MA (2005)

    Journal article
    The University of Auckland Library

    The first enantioselective synthesis of the anti-Helicobacter pylori agent (+)-spirolaxine methyl ether has been carried out in a convergent The first enantioselective synthesis of the anti-Helicobacter pylori agent (+)-spirolaxine methyl ether has been carried out in a convergent fashion by heterocycle-activated Julia olefination of a spiroacetal-containing sulfone fragment with a phthalide-containing aldehyde fragment. The total synthesis of (+)-spirolaxine methyl ether establishes the absolute stereochemistry of the natural product to be (3R,2???R,5???R,7???R).

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  • Automatic prediction of myocardial contractility improvement in stress MRI using shape morphometrics with independent component analysis.

    Suinesiaputra, Avan; Frangi, AF; Lamb, HJ; Reiber, JH; Lelieveldt, BP (2005)

    Journal article
    The University of Auckland Library

    An important assessment in patients with ischemic heart disease is whether myocardial contractility may improve after treatment. The prediction of myocardial contractility improvement is generally performed under physical or pharmalogical stress conditions. In this paper, we present a technique to build a statistical model of healthy myocardial contraction using independent component analysis. The model is used to detect regions with abnormal contraction in patients both during rest and stress.

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  • Uptake and distribution of gadolinium in the ocular lens

    Vaghefi Rezaei, Seyed; Jacobs, MD (2008)

    Journal article
    The University of Auckland Library

    The lens of the eye has no blood vessels. Although necessary for transparency, this feature of the ocular lens implies that any circulation in the lens tissue must be avascular. A range of previous studies attests to the metabolic activity of the fiber cells that make up the body of the lens. It is also established that the continuing transparency of the lens depends upon this metabolic activity. When metabolism is disturbed, cataracts (lens opacities) result. It has been proposed that metabolism occurs throughout the lens, enabled by an intercellular micro-circulation system driven by ion pumps and cell volume-regulation mechanisms. The present study attempted directly to trace micro-circulation in the ocular lens on a spatially coarse scale. High field strength magnetic resonance imaging was used to record the movement of gadolinium into the lens and the global distribution patterns that result. Our data lend new support to previous attempts at documenting, by other techniques, differential micro-circulation mechanisms in the ocular lens.

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  • Fast left ventricular mass and volume assessment in mice with three-dimensional guide-point modeling

    Young, Alistair; Barnes, H; Davidson, D; Neubauer, S; Schneider, JE (2009)

    Journal article
    The University of Auckland Library

    Purpose To investigate the accuracy (vs. standard manual analysis) and precision (scan???rescan reproducibility) of three-dimensional guide-point modeling (GPM) for the assessment of left ventricular (LV) function in mice. Methods Six male wildtype C57/Bl6 mice (weight 26.2 ?? 1.1 g) were scanned twice, 3 days apart. Each scan was performed twice, at 0.2 mm/pixel with one average and at 0.1 mm/pixel with two averages. The 24 studies were anonymized and analyzed in blinded fashion using GPM and standard manual slice summation. Results The average error between GPM and standard analysis was 2.3 ?? 5.8 mg in mass, 1.7 ?? 3.2 ??L in end-diastolic volume, 2.3 ?? 3.1 ??L in end-systolic volume, ???2.7 ?? 4.3% in ejection fraction, ???0.6 ?? 3.3 ??L in stroke volume, and ???0.31 ?? 1.56 ml ?? min???1 in cardiac output (mean difference ?? SD of differences, n = 24). The average time taken was 8.0 ?? 2.5 minutes for 3D GPM and 48.5 ?? 8.9 minutes for standard analysis (n = 24). Scan???rescan reproducibility results were similar to the standard analysis. No significant differences were found using linear mixed effects modeling in either accuracy or precision between scan resolutions or analysis method. Conclusion 3D GPM enables fast analysis of mouse LV function, with similar accuracy and reproducibility to standard analysis. An image resolution of 0.2 mm/pixel with one average is adequate for LV function studies. J. Magn. Reson. Imaging 2009.

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  • Reduction of a chelating bis(NHC) palladium(II) complex to [{??bis( NHC)}2Pd2H]+: A terminal hydride in a binuclear palladium(I) species formed under catalytically relevant conditions

    Boyd, Peter; Edwards, AJ; Gardiner, MG; Ho, CC; Lem??e-Cailleau, MH; McGuinness, DS; Riapanitra, A; Steed, JW; Stringer, DN; Yates, BF (2010)

    Journal article
    The University of Auckland Library

    Keywords: coupling reactions;homogeneous catalysis;N-heterocyclic carbenes;palladium;reduction Half-way house: The first palladium(I) N-heterocyclic carbene complex has been isolated in high yield by the base-assisted reduction of a palladium(II) precursor. The location of the unique terminal hydride (see picture; PdI???cyan, H???white, N???blue) was established by neutron crystal structure determination, and the solution fluxional behavior of the complex was explored.

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  • In-line automated tracking for ventricular function with magnetic resonance imaging

    Li, Bo; Liu, Y; Occleshaw, CJ; Cowan, Brett; Young, Alistair (2010-08)

    Journal article
    The University of Auckland Library

    An efficient nonrigid registration algorithm was implemented on the image reconstruction computer to enable in-line automatic tracking of features in steady-state free precession cine images. Four-dimensional left ventricle function analysis was performed with and without use of the in-line automatic tracking result. The method was tested in 30 patients referred for cardiac magnetic resonance imaging for a variety of clinical assessments. The time required for in-line tracking was 10 +/- 2 s per slice using an image reconstructor with dual Advanced Micro Devices single-core Opteron 248 CPUs (2.2 GHz) and 8GB random access memory. The precision of clinical estimates of left ventricular volumes was significantly improved relative to the ground truth research estimates with automatic tracking versus without (6 ml vs. 9 ml in end-diastolic volume; 5 ml vs. 10 ml in end-systolic volume; both p < 0.05). In-line automatic tracking of image features shows promise for facilitating clinical analysis of ventricular function.

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  • Ethyl 4-hydroxymethyl-2-methylpyridine-5-carboxylate

    Boyd, Peter; Lena, G; Spicer, Julie (2008-05)

    Journal article
    The University of Auckland Library

    The title compound, C10H13NO3, was obtained as a by-product of the aldolization reaction of furo[3,4-c]pyridin-3(1H)-one with thiophene-2-carboxaldehyde. The substituents on the pyridine ring are nearly coplanar, with an 8.1 (2)degrees rotation of the hydroxmethyl group from this plane. The molecules assemble in the crystal structure as chains via O-H center dot center dot center dot N hydrogen bonding between the pyridine N atom and a neighbouring hydroxymethyl OH group.

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  • A unique micromechanocalorimeter for simultaneous measurement of heat rate and force production of cardiac trabeculae carneae

    Han, June; Taberner, Andrew; Kirton, Robert; Nielsen, Poul; Smith, Nicolas; Loiselle, Denis (2009)

    Journal article
    The University of Auckland Library

    To study cardiac muscle energetics quantitatively, it is of paramount importance to measure, simultaneously, mechanical and thermal performance. Ideally, this should be achieved under conditions that minimize the risk of tissue anoxia, especially under high rates of energy expenditure. In vitro, this consideration necessitates the use of preparations of small radial dimensions. To that end, we have constructed a unique micromechanocalorimeter, consisting of an open-ended flow-through microcalorimeter, a force transducer, and a pair of muscle-length actuators. The device enables the metabolic and mechanical performance of cardiac trabeculae carneae to be investigated for prolonged periods in a continuously replenished oxygen- and nutrient-rich environment.

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  • Can activation account for 80% of skeletal muscle energy use during isometric contraction?

    Barclay, CJ; Loiselle, Denis (2007)

    Journal article
    The University of Auckland Library

    TO THE EDITOR: We are struck by the remarkable results contained in the article by Zhang et al. (5). Put bluntly, if these results are independently verified, then a fundamental reappraisal of over four decades of muscle energetics will be required. This is because Zhang et al. (5) infer from their data that, under conditions of submaximal stimulation (at 30??C), ???80% of the metabolic cost of contraction of isolated, fast-twitch, skeletal muscle [mouse extensor digitorum longus (EDL)] is attributable to Ca2+ pumping by the sarcoplasmic reticulum (SR), leaving only 20% to cross-bridge cycling. These values are roughly the converse of what is conventionally considered to be the economics of energy expenditure by active striated muscle. We are rather skeptical, for the following reasons.

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  • Free radical scavenging and cytoprotective activities of phenolic antioxidants

    Zhang, J; Stanley, RA; Adaim, A; Melton, Laurence; Skinner, Margot (2006)

    Journal article
    The University of Auckland Library

    The free radical scavenging activities of three flavonoids (quercetin, rutin and catechin) and four hydroxycinnamic acids (caffeic, ferulic, sinapic, and chlorogenic acids) were evaluated using both oxygen radical absorbance capacity (ORAC) and lipid peroxidation inhibition capacity (LPIC) assays. The cytoprotective effects of these compounds were also measured by the degree of protection against H2O2-induced damage of human Jurkat cells. All compounds exhibited protection against H2O2- mediated cytotoxicity in a dose-dependent manner. The concentrations required to result in a 50% reduction in cell death (EC50 value) were calculated from their dose-response curves. These ranged from 0.15???2.65 lM. Overall, the four hydroxycinnamic acids tested were less effective than the three flavonoids, and of all compounds tested, quercetin offered the strongest protection against H2O2-induced cell death. A comparison of the results showed that the ability to inhibit peroxidation of lipids in a liposomal system (LPIC) correlated well with the cytoprotective activities (EC50), but not with the ability to protect an aqueous fluorescent substrate in the ORAC assays. The results suggest that the behavior of antioxidants in a liposomal membrane is to some extent similar to the mechanism involved in the protection of living cells from oxidative damage.

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  • A systematic review of skills transfer after surgical simulation training

    Sturn, LP; Windsor, John; Gosman, PH; Cregan, P; Hewett, PJ; Maddern, GJ (2008)

    Journal article
    The University of Auckland Library

    Objective: To determine whether skills acquired by simulationbased training transfer to the operative setting. Summary Background Data: The fundamental assumption of simulation- based training is that skills acquired in simulated settings are directly transferable to the operating room, yet little evidence has focused on correlating simulated performance with actual surgical performance. Methods: A systematic search strategy was used to retrieve relevant studies. Inclusion of articles was determined using a predetermined protocol, independent assessment by 2 reviewers, and a final consensus decision. Only studies that reported on the use of simulationbased training for surgical skills training, and the transferability of these skills to the operative setting, were included. Results: Ten randomized controlled trials and 1 nonrandomized comparative study were included in this review. In most cases, simulation-based training was in addition to normal training programs. Only 1 study compared simulation-based training with patient- based training. For laparoscopic cholecystectomy and colonoscopy/ sigmoidoscopy, participants who received simulation-based training before undergoing patient-based assessment performed better than their counterparts who did not receive previous simulation training, but improvement was not demonstrated for all measured parameters.

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  • Ethnic variance in iron status: is it related to dietary intake?

    Wall, Clare; Brunt, D; Grant, Cameron (2009)

    Journal article
    The University of Auckland Library

    Objective: In New Zealand (NZ), Fe deficiency (ID) is present in 14% of children aged ,2 years. Prevalence varies with ethnicity (NZ European 7%, Pacific 17 %, Maori 20 %). We describe dietary Fe intake, how this varies with ethnicity and whether intake predicts Fe status. Design: A random sample of children aged 6???23 months. Usual Fe intake and dietary sources were estimated from 2 d weighed food records. Associations were determined between adequacy of Fe intake, as measured by the Estimated Average Requirement (EAR), and ID. Subjects: Sampling was stratified by ethnicity. Dietary and blood analysis data were available for 247 children. Results: The median daily Fe intake was 8?3mg (age 6???11 months) and 6?3mg (age 12???23 months). Breast milk and milk formulas (median 58 %; age 6???11 months), and cereals (41 %) and fruit and vegetables (17 %; age 12???23 months), were the predominant dietary sources of Fe. Fe intake was below the EAR for 25% of the children. Not meeting the EAR increased the risk of ID for children aged 6???11 months (relative risk518?45, 95% CI 3?24, 100?00) and 12???23 months (relative risk54?95, 95% CI 1?59, 15?41). In comparison with NZ European, Pacific children had a greater daily Fe intake (P50?04) and obtained a larger proportion of Fe from meat and meat dishes (P50?02). Conclusions: A significant proportion of young NZ children have inadequate dietary Fe intake. This inadequate intake increases the risk of ID. Ethnic differences in Fe intake do not explain the increased risk of ID for Pacific children.

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  • Why do children hospitalised with pneumonia not receive antibiotics in primary care?

    Grant, Cameron; Harnden, A; Mant, D; Emery, D; Coster, G (2012-01)

    Journal article
    The University of Auckland Library

    Background: Although antibiotics are recommended for the primary care management of community-acquired pneumonia, a recent UK study reported that most children admitted to hospital had not received antibiotics. Objective: To describe primary care antibiotic use for children subsequently hospitalised with community-acquired pneumonia. Design/methods: A case series of 280 children 15??109/l (RR=2.29; 95% CI 1.61 to 2.98) and bacteraemia (RR=6.68, 95% CI 1.08 to 58.44). Conclusions: Young children with community-acquired pneumonia may not receive an antibiotic before hospital admission because the illness evolves rapidly or the prescribed medicine is not given by parents. However, missed opportunities for appropriate antibiotic prescribing by health professionals in primary care appear to be common.

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  • Factors associated with depression in patients referred to headache specialists.

    Jelinski, SE; Magnusson, Jane; Becker, WJ (2007)

    Journal article
    The University of Auckland Library

    Objective: To evaluate the relationship between selected demographic characteristics and clinical features in patients with headache and depression. Methods: We studied demographic and clinical data collected at the time of consultation for 712 new patients with headache referred to five headache specialty clinics in Canada. Data were analyzed as part of the Canadian Headache Outpatient Registry and Database (CHORD) Project. The Beck Depression Inventory (BDI-II) was used to identify the presence of depression. Multivariable logistic regression analysis was employed to evaluate associations between age, gender, employment status, marital status, diagnosis, headache days per month, medication overuse, headache impact (HIT-6), and headache disability (MIDAS) and the presence of depression as measured by the BDI-II. Results: Among the sample of patients with headache, 27% (n = 189) had moderate to severe depression. Factors independently associated with depression included age less than 50 years, being unemployed, being on disability pension or welfare, being widowed, separated, or divorced, a diagnosis of transformed migraine or headache associated with head trauma or cervical spine disorder, and showing severe headache impact as measured by the HIT-6, or severe disability as measured by the MIDAS. Conclusions: In patients with headache referred for specialist consultation, depression is strongly associated with being on disability or welfare, unemployment, age under 50 years, showing severe headache impact on the Headache Impact Test???6, and receiving a diagnosis of transformed migraine. The possibility of a concomitant depression should be strongly considered in patients with headache with any of these characteristics.

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