91,631 results

  • Synthesis of Neoglycopeptides via Click Chemistry

    Miller, N; Williams, Geoffrey; Brimble, Margaret (2010)

    Journal article
    The University of Auckland Library

    Novel chemical methods to access homogeneous samples of glycopeptides and glycoproteins and their mimetics, so-called neoglycopeptides and neoglycoproteins, have developed rapidly in recent years owing to an increased need to investigate both their roles in molecular biology and their potential as therapeutic agents. This article summarizes the application of the copper-catalyzed azide-alkyne cycloaddition for the chemical synthesis of neoglycopeptides and neoglycoproteins.

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  • Allylic functionalization of the 1,7-dioxaspiro[5.5]-undec-4-ene and 1,6,8-trioxadispiro[4.1.5.3]-pentadec-13-ene ring systems

    Brimble, Margaret; Edmonds, MK; Williams, GM (1992)

    Journal article
    The University of Auckland Library

    Allylic bromination of the bicyclic spiroacetals 5, 6 and 7 gave predominantly the axial bromides 15, 21 and 23 which underwent SN2 displacement to the equatorial alcohols 17, 22 and 25 respectively, using potassium superoxide and 18-crown-6 in THF/DMSO (10:1). Allylic bromination of the cis-bis-spiroacetal 26 gave predominantly the rearranged allylic bromide 29 which afforded alcohols 30 and 31 resulting from both SN2??? and SN2 displacement upon treatment with potassium superoxide. Bromination of the trans-bis-spiroacetal 27 afforded a complex mixture from which only the non-rearranged bromide 34 could be isolated. This bromide 34 afforded the axial alcohol 37 upon treatment with potassium superoxide.

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  • A model for ex vivo spinal cord segment culture - a tool for analysis of injury repair strategies

    Zhang, Jie; OCarroll, Simon; Wu, A; Nicholson, Louise; Green, Colin (2010)

    Journal article
    The University of Auckland Library

    Most spinal cord injury research is undertaken using in vivo animal models but the extensive care associated with spinalised animals, inherent variability between animals, and complex surgeries makes alternative models especially valuable. Here we present a novel ex vivo model that enables culture of intact post-natal spinal cord segments for up to five days and the assessment of peripheral nerve grafting repair, enhanced with connexin43 antisense oligodeoxynucleotides (Cx43 AsODN), in this model. Down-regulating Cx43 expression with Cx43 AsODN in cultured spinal cord segments prevents cell death and inhibits inflammation spreading from the site of injury to neighbouring tissue, hence maintaining culture viability. Reduction in segment swelling and improvement in neuron survival were evident after Cx43 AsODN treatment. Furthermore, the combination of Cx43 AsODN with peripheral nerve graft implants into cultured spinal cords promoted axon sprouting from the spinal cord into the peripheral nerve graft. This ex vivo spinal cord segment culture model provides a valuable addition to tools currently available for spinal cord injury research.

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  • Synthesis and anti-inflammatory structure-activity relationships of thiazine-quinoline-quinones: inhibitors of the neutrophil respiratory burst in a model of acute gouty arthritis.

    Chia, EW; Pearce, Allison; Berridge, MV; Larsen, L; Perry, NB; Sansom, CE; Godfrey, CA; Hanton, LR; Lu, Guo-Liang; Walton, M; Denny, William; Webb, VL; Copp, Brent; Harper, Jacquie (2008)

    Journal article
    The University of Auckland Library

    Sixteen new thiazine???quinoline???quinones have been synthesised, plus one bicyclic analogue. These compounds inhibited neutrophil superoxide production in vitro with IC50s as low 60 nM. Compounds with high in vitro anti-inflammatory activity were also tested in a mouse model of acute inflammation. The most active compounds inhibited both neutrophil infiltration and superoxide production at doses 2.5 ??mol/kg, highlighting their potential for development as novel NSAIDs.

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  • Evaluation of 2D and 3D glove input applied to medical image analysis

    Zudilova-Seinstra, EV; de Koning, PJH; Suinesiaputra, Avan; van Schooten, BW; van der Geest, RJ; Reiber, JHC; Sloot, PMA (2010-06)

    Journal article
    The University of Auckland Library

    We describe a series of experiments that compared 2D/3D input methods for selection and positioning tasks related to medical image analysis. For our study, we chose a switchable P5 Glove Controller, which can be used to provide both 2DOF and 6DOF input control. Our results suggest that for both tasks the overall performance and accuracy can be improved when the input device with more degrees of freedom (DOF) is used for manipulation of the visualized medical data. 3D input turned out to be more beneficial for the positioning task than for the selection task. In order to determine a potential source of the difference in the task completion time between 2D and 3D input, we also investigated whether there was a significant difference between 2DOF and 6DOF input methods with regard to the time spent on task-specific basic manipulations.

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  • An overview of CellML 1.1, a biological model description language

    Cuellar, AA; Lloyd, CM; Nielsen, Poul; Bullivant, DP; Nickerson, David; Hunter, Peter (2003)

    Journal article
    The University of Auckland Library

    CellML is an XML-based exchange format developed by the University of Auckland in collaboration with Physiome Sciences, Inc. CellML 1.1 has a component-based architecture allowing a modeller to build complex systems of models that expand and reuse previously published models. CellML Metadata is a format for encoding contextual information for a model. CellML 1.1 can be used in conjunction with CellML Metadata to provide a complete description of the structure and underlying mathematics of biological models. A repository of over 200 electrophysiological, mechanical, signal transduction, and metabolic pathway models is available at www.cellml.org.

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  • GPU accelerated non-rigid registration for the evaluation of cardiac function

    Li, Bo; Young, Alistair; Cowan, Brett (2008)

    Journal article
    The University of Auckland Library

    We present a method for the fast and efficient tracking of motion in cardiac magnetic resonance (CMR) cines. A GPU accelerated Levenberg-Marquardt non-linear least squares optimization procedure for finite element non-rigid registration was implemented on an NVIDIA graphics card using the OpenGL environment. Points were tracked from frame to frame using forward and backward incremental registration. The inner (endocardial) and outer (epicardial) boarders of the heart were tracked in six short axis cines with ~25 frames through the cardiac cycle in 36 patients with vascular disease. Contours placed by two independent expert observers using a semi-automatic ventricular analysis program (CIM version 4.6) were used as the gold standard. The method took 0.5 seconds per frame, and the maximum Hausdorff errors were less than 2 mm on average which was of the same order as the expert inter-observer error. In conclusion, GPU accelerated Levenberg-Marquardt non-linear optimization enables fast and accurate tracking of cardiac motion in CMR images.

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  • Interactive cardiac image analysis for biventricular function of the human heart

    Lam, Hoi; Cowan, Brett; Nash, Martyn; Young, Alistair (2010)

    Journal article
    The University of Auckland Library

    We developed an interactive tool for biventricular function analysis from cardiac magnetic resonance (MR) images based on the guide point modelling (GPM) approach [1]. First we built a deformable model of both ventricles of the human heart which consisted of 138 nodes and 82 hexahedral elements, each with bicubic-B??zier-linear interpolation. The model was fitted to a digitized human data set for use as the prior shape in the GPM scheme, which we modified to have a 'predictor' step that used a host mesh fitting algorithm [2] to generate predicted points (PPs) based on the user-defined guide points (GPs). Then the model was fitted towards both GPs and PPs through linear least square minimization. The inclusion of the PPs significantly improved the numerical stability of the linear least square fit and significantly accelerated the solution time. This methodology requires further validation for future application in clinical biventricular analysis.

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  • Characterization of dicarboxylic salts of protonated triethylenetetramine useful for the treatment of copper-related Pathologies

    Soehnel, Kathrin; Boyd, Peter; Sohnel, T; Allen, GR; Phillips, Anthony; Cooper, Garth (2007-09)

    Journal article
    The University of Auckland Library

    X-ray crystal structures of three salts of protonated triethylenetetramine, (H(4)TETA)(4+), with succinate, maleate, and fumarate anions are reported. Structures of the complexes (H-4-triethylenetetramine)(hydrogenmaleate)(4)center dot 2H(2)O [(H(4)TETA)(Hmal)(4)center dot 2H(2)O] (1), (H4-triethylenetetramine)(hydrogenfumarate)(4)center dot 3.3H(2)O [(H(4)TETA)(HfuM)(4)center dot 3.3H(2)O] (2), and (H-4-triethylenetetramine)(succinate)(2) [(H(4)TETA)(suc)(2)] (3) all form assemblies of alternating two-dimensional layers of (H(4)TETA)(4+) and the anionic species via hydrogen-bond networks. Both classical and nonclassical hydrogen bonds between the protonated amine groups, anions, and water molecules were observed. X-ray powder diffraction measurements, differential thermal analysis/thermogravimetry, density vapor sorption, and Karl Fischer titration measurements were performed to obtain confirmatory information about the water content in the structures 1 and 2 and to examine polymorphism within the salts. The nonhydrated salt 3 was determined to be the most favorable salt formulation for use in medicinal applications.

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  • 2,8,12,18-Tetrabutyl-3,7,13,17-tetramethyl-5,15-bis(3-nitrophenyl)porphyrinogen methanol disolvate

    Boyd, Peter; Hosseini, A; Rickard, CEF (2006-07)

    Journal article
    The University of Auckland Library

    The title compound, C52H66N6O4??2CH3OH, is a 5,15-diaryloctaalkylporphyrinogen. The molecule is centrosymmetric, with the pyrrole rings adopting a 1,2-alternate arrangement. The methanol molecules are included in the tetrapyrrole cavity through hydrogen bonding and O-H interactions. The molecules form chains in the crystal structure via phenyl C-H-pyrrole stacking.

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  • [1,2-bis(diphenylphosphino)ethane]bis-(N,N-dimethyldithiocarbamato)iron(III) tetrafluoroborate

    Boyd, Peter; Rickard, CEF (2006-06)

    Journal article
    The University of Auckland Library

    The title compound, [Fe(C3H6NS2)2(C26H24P2)]BF4, contains a six-coordinate iron(III) cationic complex, with two bidentate dimethyldithiocarbamate and one 1,2-bis(diphenylphosphino)ethane ligands, and a disordered tetrafluoroborate anion. The cation possesses a crystallographic twofold rotation axis. The cations assemble in the crystal structure in two-dimensional layers via complementary C-H(phenyl) interactions with channels occupied by tetrafluorborate anions.

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  • (4-(Ferrocene-1-carboxamido)pyridine)(tetraphenylporphyrinato)zinc(II). Toluene sesquisolvate

    Boyd, Peter; Hosseini, A (2006)

    Journal article
    The University of Auckland Library

    The title compound is a five-coordinate square-pyramidal zinc-porphyrin complex, [(C44H28N4)Zn(C10H9N2O)Fe(C5H5)]??1.5C7H8, with a 4-(ferrocene-1-carboxamido)pyridine apical ligand. The complexes assemble in the crystal structure by head-to-tail stacking of the 4-(ferrocene-1-carboxamido)pyridine groups, which interact through - stacking of the pyridine and cyclopentadienyl rings.

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  • Bis(N,N-diethyl-dithio-carbamato)(1,10-phenanthroline)cobalt(III) tetra-fluorido-borate

    Boyd, Peter; Rickard, CEF (2008)

    Journal article
    The University of Auckland Library

    The cationic complex in the structure of the title compound, [Co(Et2NCS2)(2)(C12H8N2)] BF4, has a Co-III atom with a distorted octahedral coordination formed by four S atoms of two diethyldithiocarbamate and two N atoms of 1,10-phenanthroline ligands. The crystal structure features head-to-tail stacking of the phenanthroline ligands. The tetra-fluoridoborate anions are positioned in the channels between the cation stacks running along the a axis, and form weak C-H center dot center dot center dot F interactions.

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  • Tracking and finite element analysis of stripe deformation in magnetic resonance tagging.

    Young, Alistair; Kraitchman, DL; Dougherty, L; Axel, L (1995)

    Journal article
    The University of Auckland Library

    Magnetic resonance tissue tagging allows noninvasive in vivo measurement of soft tissue deformation. Planes of magnetic saturation are created, orthogonal to the imaging plane, which form dark lines (stripes) in the image. The authors describe a method for tracking stripe motion in the image plane, and show how this information can be incorporated into a finite element model of the underlying deformation. Human heart data were acquired from several imaging planes in different orientations and were combined using a deformable model of the left ventricle wall. Each tracked stripe point provided information on displacement orthogonal to the original tagging plane, i.e., a one-dimensional (1-D) constraint on the motion. Three-dimensional (3-D) motion and deformation was then reconstructed by fitting the model to the data constraints by linear least squares. The average root mean squared (rms) error between tracked stripe points and predicted model locations was 0.47 mm (n=3,100 points). In order to validate this method and quantify the errors involved, the authors applied it to images of a silicone gel phantom subjected to a known, well-controlled, 3-D deformation. The finite element strains obtained were compared to an analytic model of the deformation known to be accurate in the central axial plane of the phantom. The average rms errors were 6% in both the reconstructed shear strains and 16% in the reconstructed radial normal strain.

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  • Staphylococcal superantigen super-domains in immune evasion.

    Langley, Ries; Patel, D; Jackson, N; Clow, F; Fraser, John (2010)

    Journal article
    The University of Auckland Library

    Staphylococcus aureus is a robust pathogen that is capable of growing in virtually any part of the human body, and can also survive and grow in many other species. S. aureus remains the most frequent cause of hospital-acquired infection and, with the emergence and spread of drug-resistant, hypervirulent, community-acquired strains, the specter looms of the ultimate superbug. S. aureus produces an array of immune evasion factors that target various components of host immune defense. Among them are the powerful superantigen (SAg) and SAg-like (SSL) molecules, which are coded for by genes scattered across several genomic and pathogenicity islands. The SAgs universally bind MHC (major histocompatibility complex) class II and T-cell receptors to induce profound T-cell activation, while the SSLs target a range of molecules regulating opsonophagocytosis and neutrophil function. Despite functional differences, the SAgs and SSLs have clearly evolved from a single ancestral gene that now codes for a stable, two-domain protein, with each domain responsible for binding a different target molecule. This superstructure tolerates extensive surface variation, enabling a wide assortment of virulence factors targeting multiple steps in innate immunity. Notably, both the SAgs and the SSLs exhibit optimal activity for humans and non-human primates, clearly indicating that primates have been the preferred host for S. aureus evolution. This restricted function makes it difficult to assess their role in staphylococcal virulence using animal models of infection. This brief review focuses on the structural features of SAgs and SSLs and their individual functions as we currently understand them.

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  • A new distal myopathy with mutation in anoctamin 5

    Mahjneh, I; Jaiswal, J; Lamminen, A; Somer, M; Ferguson, Lynnette; Kiuru-Enari, S; Bashir, R (2010-12)

    Journal article
    The University of Auckland Library

    We have been following clinically and with muscle MRI for the past 3-decades a Finnish family with two patients with distal muscular dystrophy. Previously we demonstrated the cellular defect in these patients to be defective membrane repair and more recently have identified the causative gene to be anoctamin 5 (ANO5). The disorder seen in these patients is characterized by onset in the third decade. First symptoms were burning sensation on the calves and later on calf tightness during running. Muscle weakness and wasting were asymmetric and early involving the calf muscles, later spread to the thigh muscles. Biceps brachi was later manifestation. Clinical course was slow. CK levels were high. Muscle biopsy showed dystrophic pattern and multifocal disruption of the sarcolemmal membrane but no subsarcolemmal vesicle accumulation nor active inflammation. We conclude that the disease seen in our cases is a new separate clinical, genetic and histopathologic entity to include within the classification of autosomal recessive distal muscular dystrophies.

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  • Significantly enhanced DNA thermal stability resulting from porphyrin H-aggregate formation in the minor groove of the duplex

    Stephenson, AWI; Bomholt, N; Partridge, Ashton; Filichev, VV (2010)

    Journal article
    The University of Auckland Library

    Too groovy: The covalent attachment of up to four porphyrins to complementary strands led to the formation of DNA porphyrin zippers with significantly increased DNA duplex stability. This is a result of H-aggregate formation in the minor groove. To the best of our knowledge this is the first report showing such a significant thermal duplex stabilization.

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  • Damage classification and estimation in experimental structures using time series analysis and pattern recognition

    De Lautour, OR; Omenzetter, Piotr (2010)

    Journal article
    The University of Auckland Library

    Developed for studying long sequences of regularly sampled data, time series analysis methods are being increasingly investigated for the use of Structural Health Monitoring (SHM). In this research, Autoregressive (AR) models were used to fit the acceleration time histories obtained from two experimental structures: a 3-storey bookshelf structure and the ASCE Phase II Experimental SHM Benchmark Structure, in undamaged and limited number of damaged states. The coefficients of the AR models were considered to be damage-sensitive features and used as input into an Artificial Neural Network (ANN). The ANN was trained to classify damage cases or estimate remaining structural stiffness. The results showed that the combination of AR models and ANNs are efficient tools for damage classification and estimation, and perform well using small number of damage-sensitive features and limited sensors.

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  • Modeling degradation and metabolite formation kinetics of estrone-3-sulfate in agricultural soils

    Scherr, FF; Sarmah, Ajit; Di, HJ; Cameron, KC (2008)

    Journal article
    The University of Auckland Library

    Estrone-3-sulfate (E1-3S), formed in the kidneys of pregnant cattle, can act as a precursor to the free hormone estrone (E1) known for its endocrine disrupting potential in wildlife. Laboratory microcosm studies were conducted to investigate the aerobic degradation of E1-3S in three contrasting pasture soils at 7.5, 15, and 25 ??C. Deconjugation of E1-3S resulted in the formation of the metabolite E1. Two kinetic modelsa single first-order and a biexponential kinetic modelwere applied to fit the observed degradation dynamics and to derive degradation end-points (DT50 and DT90) for the parent compound and the metabolite for each condition. Model selection and evaluation of their performance were based on a suit of statistical measures (one-way ANOVA, AICc, R2adj, ??2 error-%, and SRMSE). The results showed rapid initial degradation of E1-3S, followed by a much slower decline with time, and rate of degradation was temperature dependent. The DT50 and DT90 values of E1-3S ranged from a few hours to several days, while the formation of the major metabolite (E1) was concomitant with E1-3S degradation in all nonsterile soils. The parent compound degradation and formation and subsequent dissipation of metabolite were successfully predicted by both models, however, the nonlinear biexponential model improved the goodness-of-fit parameters in most cases.

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  • A survey of endocrine disrupting chemicals (EDCs) in municipal sewage and animal waste effluents in the Waikato region of New Zealand

    Sarmah, Ajit; Northcott, GL; Leusch, FDL; Tremblay, Louis (2006)

    Journal article
    The University of Auckland Library

    We report the results of a recent survey of the concentration of natural estrogens (17??-estradiol, 17??-estradiol, estrone, estriol) and the synthetic estrogen, 17??-ethynylestradiol in representative animal wastes and sewage treatment plant (STP) effluents in the Waikato region of New Zealand. Dairy farm effluent samples showed high levels of estradiol (19???1360 ng/L) and its breakdown product estrone (41???3123 ng/L) compared with piggery or goat farm effluents. The combined load for these estrogens (excluding ?? epimer) varied from 60 to > 4000 ng/L. The piggery effluent provided the lowest total estrogen load (46 ng/L), with estrone accounting for nearly 60% of the measured estrogens in this sample. The synthetic analogue, 17??-ethynylestradiol was detected only in one wastewater treatment plant sample, albeit at trace level. An estrogen receptor competitive binding assay was used to test the biological activity of the samples and confirmed that most agricultural waste samples contain high levels of estrogenic compounds. The potential of these wastes to cause endocrine disruption in the receiving ecosystem is unknown at present.

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