231 results for Conference poster

  • A Computational Model For Cerebral Circulation And Its Application For Haemodynamic Modelling In Vascular Surgeries

    Ho, Harvey; Mithraratne, K; Hunter, Peter (2009)

    Conference poster
    The University of Auckland Library

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  • A Multiscale, Spatially-Distributed Model of Airway Hyper-Responsiveness

    Donovan, Graham; Politi, Antonio; Sneyd, A; Tawhai, Merryn (2009-05)

    Conference poster
    The University of Auckland Library

    Rationale: Airway hyper−responsiveness (AHR), along with airway hyper−sensitivity, is a defining feature of asthma, and greater understanding of this emergent phenomenon may lead to better insight into and treatment of the condition. We seek a multiscale, spatially−distributed, mathematical model of the lung to help us understand the role of airway smooth muscle and parenchymal material in AHR. Methods: Our model couples together the organ scale with the tissue scale in the lung in a multiscale approach to the problem. At the organ level, parenchymal tissue is modeled as a compressible Blatz−Ko material in three dimensions, with expansion and recoil of lung tissue due to tidal breathing. The governing equations of finite elasticity deformation are solved using a finite element method. An airway tree is embedded in this tissue, with airway smooth muscle behavior described by a modified Hai−Murphy cross−bridge model (Wang et al., Biophys. J. 94:2008). Each airway segment is initially assumed to be radially symmetric and longitudinally stiff, and thus the embedded airway tree is essentially 1D. Results: Our spatially−distributed, multiscale model yields organ−level observations while incorporating tissue−level modeling detail. Preliminary results from the integrated model indicate potential use in the study of many phenomena associated with asthmatic AHR, including spatial distribution of ventilation defects, patchiness, and effects of deep inspirations.

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  • Bronchoconstriction and the MBNW: Insights from anatomical lung modelling.

    Mitchell, Jennine; Tawahi MH (2010-11-30)

    Conference poster
    The University of Auckland Library

    Bronchoconstriction and the MBNW: Insights from anatomical lung modelling. Jennine Mitchell and Dr Merryn Tawhai Auckland Bioengineering institute The multiple breath nitrogen washout (MBNW) is a global test of lung function that produces two indices Sacin and Scond that are reflective of ventilation heterogeneity arising at the level of acinus and between more spatially disparate regions of the lung respectively. An important application of the MBNW is in the study of asthma. Ventilation defects have been noted to occur in imaging studies of asthma. These regional ventilation defects have not previously been considered in relation to the MBNW indices. Scond is purported to be related to the state of conducting airways however no modelling studies exist which directly link the airway state to Scond. In this work regional ventilation defects have been simulated in an anatomically based human lung model and theoretically linked to the MBNW indices Sacin and Scond. Ventilation is simualted to the level of the acinus in a model in which acinar ventilation is considered independent of ventialtion in other acini. As previously indicated in modelling studies a high degree of constriction is required to produce a ventilation defect. The relationship between the degree of constriction in airways leading to the defect and the Scond index is however highly non-linear and shows a sharp decrease at very high levels of constriction. Ventilation defects potentially cause non-communication of gas trapped in the ventilation defects with the mouth. This may alter the calculation of FRC if nitrogen dilution is used to calculate FRC. As the indices are dependent on the phase III slope for each breath being normalised by FRC this alters MBNW results. The index Scond is not be able to be explained simply in terms of increased time constants due to increased resistance in the main conducting airway tree. The model indicates that the Scond index is more complex than current MBNW theory indicates and cannot be simply explained in terms of a longer time constant due to constriction in the conducting airway tree resulting in increased late emptying of poorly ventilated regions.

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  • Doped Diamond-Like Carbon (DLC) coated surfaces to reduce fouling from milk

    Patel, Jaiminkumar; Bansal, B; Jones, MI; Hyland, M (2010-11-09)

    Conference poster
    The University of Auckland Library

    In the dairy industry, fouling of processing surfaces is a common and unresolved problem. Surface modification, for example through the application of a surface coating, can alter the surface properties of a material, and may be a potential way to reduce fouling. Typical dairy plant stainless steel surfaces were modified by the deposition of doped Diamond-Like Carbon (DLC) films with varying concentration of doped elements. These modified surfaces were studied for their fouling behavior with milk at both laboratory and pilot scale. None of the doped DLC modified surfaces investigated in the study presented benefits in fouling reduction as compared to unmodified surface.

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  • Three-Dimensional Structural Characterization of Tissue Engineered and Native Ovine Pulmonary Valves

    Eckert, Chad; Gerneke, Dane; LeGrice, IJ; Gottlieb, David; Mayer, JE; Sacks, MS (2009-04)

    Conference poster
    The University of Auckland Library

    OBJECTIVES: Efforts in tissue-engineered heart valves (TEHV) have shown increasingly equivalent mechanical/structural properties compared to native valves, though a literature gap exists regarding detailed structural information. This work was performed to provide such data of implanted TEHV, the native pulmonary valve (PV), and pre-implant scaffold to better understand developing TEHV. METHODS: Dynamically-cultured in vivo samples (“pre-implant”) and ovine TEHV PV in vitro samples (“explant”) were produced based on previous techniques; ovine PVs were excised. Samples were stained with picrosirius red and resinmounted. Using extended-volume scanning laser confocal microscopy (EV-SLCM), 1.5 x 1.5 x 0.4 mm full-thickness samples were imaged at 1 pixel/μm in 1 μm Z-direction steps. Custom software was used to process and visualize samples. Collagen, cell nuclei, and scaffold volume fractions were quantified; scaffold fiber trajectory and length were tracked using custom software. RESULTS: In a scaffold representative volume (90 μm thick), 104 fibers were tracked with a mean fiber length of 137.94 μm 55.4 μm (Fig.1). A comparison between pre-implant and explant samples showed collagen volume fraction increasing from 76.6% to 85.9%, with nuclei and scaffold decreasing from 2.8% to 0.5% and from 5.9% to 0.8%, respectively. With the native collagen volume fraction measured at 70%, pre-implant and explant samples showed an increase in collagen. CONCLUSIONS: This work captured important differences between in vivo/in vitro TEHV constituents; it is the first known work to utilize EV-SLCM on TEHV. A comparison to the native valve showed structural differences that could impact longterm functionality and improve design.

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  • The use of whole community bacterial indicators to monitor ecological health, function and variability within stream biofilms

    Lear, Gavin; Boothroyd, IK; Lewis, Gillian (2009-08-30)

    Conference poster
    The University of Auckland Library

    This study describes the extent of variability in biofilm bacterial community structure across a broad range of spatial and temporal scales and assesses whether this may be used as an indicator of stream ecological health and function. A community DNA fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis - ARISA) was used to examine the structure of bacterial communities within freshwater stream biofilms. When compared with macrobenthic invertebrate community assemblages using multi-dimensional scaling techniques, similar broad-scale trends in population structure were revealed between organisms at these different trophic levels. For both communities, spatial variability in community structure was greater between streams than within each site, or compared to temporal variability measured over 1 year. Distance-based redundancy analysis of both bacterial ARISA and macroinvertebrate data estimated that the largest cause of variation in community structure was due to differences in catchment land-use, rather than any single water quality parameter (e.g. ph or ammoniacal nitrogen). Multidimensional scaling of ARISA data also revealed significant differences in community structure between urban, and less impacted stream sites, providing evidence that whole-bacterial communities could be used as an indicator of freshwater ecological health, analogous to the way that macroinvertebrate communities have been used for many years. In conclusion, we propose the analysis of whole bacterial communities as a cost-effective, high throughput alternative indicator of freshwater ecological health.

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  • Ciliate Diversity in Stream Biofilms revealed by group-specific PCR primers.

    Dopheide, Andrew; Lear, Gavin; Stott, R; Lewis, Gillian (2008-08-17)

    Conference poster
    The University of Auckland Library

    The ciliates are a diverse protozoan phylum, thought to be of considerable ecological importance in stream ecosystems, including organisms which are abundant and important consumers of bacteria, algae and other protozoa. Understanding of ciliate diversity and ecology is limited, however, particularly in benthic habitats such as stream biofilms. In this study, phylum-specific PCR primers were used in combination with cloning, sequencing and terminal restriction fragment length polymorphism (T-RFLP) analysis to investigate ciliate communities in stream biofilms.

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  • Human Adenovirus ecology in environmental waters in New Zealand

    Dong, Yimin; Lewis, Gillian (2008-08-17)

    Conference poster
    The University of Auckland Library

    A major New Zealand study of pathogen occurrence in surface freshwaters identified occurrence of human adenovirus in 30% of sites and samples by qualitative PCR based methods. The source or nature of these viruses was not clear from the study and raises important questions in both viral ecology and human health protection. The aim of this study was to begin to unravel these questions by (i) development of specific quantitative analysis methods for adenoviruses in water and (ii) to target identifiable groups of adenovirus associated with human respiratory or gastrointestinal infections. These quantitative group specific real time PCR methods were tested in drinking water, recreational water, river water and wastewater. Adenovirus was detected in all primary wastewater samples tested (n=10) at high genome copy number (1.87 x104 to 4.6 x106 per litre) and in 33% (n=15) of the river water and 11% (n=27) of the treated drinking water samples. In addition, adenovirus was detected in 5 of the 6 estuarine recreational water samples (17 to 1190 virus genome copies per litre). DNA sequence analysis suggested that human adenovirus group C (respiratory infection associated) were most commonly associated with river, recreational and drinking water. Group F adenovirus (gastroenteritis associated viruses) were found to dominate in most wastewater (5 - 100 % total adenovirus) but were not detected in surface waters. This study suggests that the ecology of specific groups or types of adenovirus is sufficiently different, external to the host, to have important implications for human health risk assessment.

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  • Effect of light regimes on the utilisation of an exogenous carbon source by freshwater biofilm communities

    Lear, Gavin; Lewis, Gillian (2007-06-23)

    Conference poster
    The University of Auckland Library

    Biofilms are a major source of ‘in stream’ primary production, exhibiting high population density, and being an important source of carbon for microbial heterotrophs. Changing patterns of land-use within freshwater catchment areas may greatly impact on stream biofilm microbial community structure, which in turn may influence the speed and extent with which full ecosystem recovery may occur. This study reports how freshwater biofilm communities respond to additions of acetate, used as a proxy for organic matter, the primary source of carbon within shaded forests and headwater streams. The use of [ 13C] acetate and subsequent isolation of 13C-labelled nucleic acids from the metabolically active fraction of the bacterial community enabled substrate assimilating organisms to be identified. In addition, biofilms were exposed to varied levels of incident light to assess the relative contribution of phototrophic and heterotrophic nutrition.

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  • Ecosystem responses to multiple-stressor gradients: Nutrient and sediment addition to experimental stream channels

    Wagenhoff, A; Matthaei, CD; Lear, Gavin; Lewis, Gillian; Townsend, CR (2009-05-16)

    Conference poster
    The University of Auckland Library

    Agricultural land use can strongly affect stream ecosystems by increasing levels of nutrients and fine sediment cover on the streambed. Knowledge of patterns in ecological responses along gradients of these two stressors will help define thresholds of harm. Leaf breakdown rates, algal and bacterial communities are directly and/or indirectly influenced by nutrient supply and fine sediment cover. To investigate the effects of stressor gradients and their interactions on these biological response parameters, we designed a full-factorial experiment in circular stream-side channels with eight levels each of nutrients (36 to 6900 μg·l-1 DIN, 1.4 to 450 μg·l-1 DRP) and fine sediment (0 to 100 % cover). Algal biomass, bacterial diversity and leaf pack decomposition were determined after three weeks of exposure to both stressors. Algal biomass was significantly higher in channels with lower levels of fine sediment. Bacterial diversity generally increased with increasing nutrient concentrations up to an intermediate nutrient level but then decreased again with the exception of reaching the highest diversity overall at the top nutrient level. Thus, increased levels of nutrients and fine sediment caused major changes to the algal and bacterial communities. In turn, these changes affect other food-web components as well as ecosystem functioning, including decomposition.

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  • Molecular mechanisms of human T cell differentiation - a role for DNA methylation

    Sheppard, Hilary; Brooks, Anna; Dunbar, PR (2009-09-01)

    Conference poster
    The University of Auckland Library

    The differentiation state of CD8+ T cells is an important determinant of their ability to eradicate tumours and infection; progressive differentiation appears to lead to a decreased upregulated suggesting an indirect mechanism underlie T cell differentiation. Several key cell surface markers are down regulated as differentiation progresses see Fig. 1). We have found that promoter DNA methylation is one mechanism involved in the down regulation of these genes This suggests that manipulation of DNA methylation of key genes could be used to improve the survival and function of CD8+ T cells.

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  • Identifying and Visualizing Surface Detail on Michelangelo's David

    Rugis, John (2007)

    Conference poster
    The University of Auckland Library

    We present the results of new experiments in which we have identified, characterized, and produced visualizations of selected fine surface detail on Michelangelo’s David statue. Starting with available raw scan data [Levoy et al. 2000], we have applied a number of techniques, both developed and refined by us, including the calculation of curvature maps, 2.5D spatial noise filtering, texture projection merging [Rugis 2006], and image processing assisted physical measurement. ....

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  • Examination of miRNAs involved in programming human T cells

    Sheppard, Hilary; Feisst, Vaughan; Brooks, Anna; Dunbar, R (2011-09)

    Conference poster
    The University of Auckland Library

    The differentiation state of CD8+ T cells is an important determinant of their ability to eradicate tumours and infection; progressive differentiation appears to lead to a decreased effectiveness. Therefore the development of effective immunotherapies depends on a better understanding of the molecular mechanisms that underlie T cell differentiation. Several key cell surface markers are down regulated as differentiation progresses so we can define CD8+ T cells into 4 main subsets (see Fig. 1). Each subset is generated by a specific transcriptional programme. Our hypothesis is that miRNAs are important in this process of T cell differentation. If you take a cancer patient’s cells, expand in vitro, and re-infuse to the patient, the phenotype of the T cell will determine its efficacy in vivo. We have found that we can pre-condition T cells using the cytokine IL21 to have a more favourable phenotype than using the traditionally used cytokine IL2 (data not shown). We aim to explore this cytokine driven differentiation process by examining the miRNAs involved.

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  • Islet human amylin oligomer formation is differentially correlated with β-cell death and diabetes onset between homozygous and hemizygous human amylin transgenic mice

    Zhang, S; Liu, H; Li, XL; Au, M; Chuang, CL; Cooper, GJS (2010)

    Conference poster
    The University of Auckland Library

    One of the pathological features of type-2 diabetes mellitus (T2DM) is the presence of islet amyloid deposits comprising mainly human amylin (hA)/hIAPP. Recent studies suggested that soluble oligomers of human amylin may be the primary cause of β-cell damage and thus contribute to the onset/development of T2DM. However, the molecular basis of this process remains to be fully elucidated. We aimed to investigate the connection between soluble oligomers and hA cytotoxicity, and their correlation with diabetes development using a rodent model of diabetes.

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  • Fostering the exchange of geoscience resources for knowledge exploration and discovery

    Whitehead, Brandon; Gahegan, Mark; Everett, M; Hills, S; Brodaric, B (2010-11-11)

    Conference poster
    The University of Auckland Library

    Geoscience data capture is expensive. In order to extract maximum value, the data need to be consistently described, easily found, and then shared among those who need it. There has been recent momentum in the geoscience community to develop a common descriptive framework which facilitates data sharing. While storage and transfer standards are vital, they lack a descriptive element which standarizes the meaning of their contents. Metadata capture is appropriate for data stores, but often the terminology carries different meanings as domains become more specialised. For example, the term “migration” to a petroleum geochemist refers to the movement of hydrocarbons in geologic time, yet to a seismologist describes an imaging process. Furthermore, concepts associated with a term may change through time or as contextual factors in a discussion are modified. How, therefore, can the concepts evoked from geoscience resource terminology be defined and aligned to represent this multi-scaled orthogonal variability? Here we show how a community knowledge acquisition exercise was orchestrated to discuss fundamental concepts and their meanings as interpreted by leaders in basin characterization. The result of this exercise is a formal description of many of the features and processes associated with sedimentary basins, i.e. a basin ontology. This ontology allows the use of semantic connections between concepts as a backbone for search and discovery of research artifacts in large data stores.

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  • At your service: An interactive, flexible web-service for translating classification systems and taxonomies

    Whitehead, Brandon; Banchuen, Tawan; Gahegan, Mark; Smart, William; Masoud-Ansari, S (2010-11-11)

    Conference poster
    The University of Auckland Library

    Geoscientists have developed and applied classification systems and taxonomies in an effort to enhance and share their understanding of complex geoscience information. However, the classification systems and taxonomies used throughout the geosciences for land cover and land use, soils, geology are neither static nor universal; the classes that we use to represent the Earth vary considerably with time and from place to place. As a general example, think of a geologic map. There are instances when mapped data contains desirable categories, but the granularity of those categories is not suitable. There are also instances where two or more maps (or data sets) lack the desired categories, or the categories across maps are semantically incompatible. This is to be expected, given that: (i) new science, social and economic agendas change what we may wish to differentiate when we look at a map and (ii) new technologies make differentiation of previously inseperable classes more reliable, thus viable. This paper describes ongoing work to create a web-based semantic translation service that allows users to: (i) experiment with mappings between classification systems and taxonomies; (ii) visualize translation maps using a given mapping; and (iii) persist their translation maps, and share them with others. Semantic equivalence and similarity are supported via underlying ontologies, which also facilitate the merging and re-grouping of classes.

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  • Human Activities Modify Bacterial Diversity in Stream Benthic Biofilm Communities

    Lewis, Gillian; Roberts, Kelly; Turner, Susan; Lear, Gavin (2008-06-01)

    Conference poster
    The University of Auckland Library

    This study tests the hypothesis that human impact is an important driver of stream biofilm bacterial population diversity. The seasonal bacterial composition of biofilm in 4 streams with different levels of human impact was determined over 2 years. Bacterial diversity derived from 16S rDNA clone libraries, shows both between stream differences and seasonal transitions in bacterial occurrence and population dominance at a class and genus level. Diversity analysis calculated on pooled seasonal data (class level identification) shows that while composition of the populations are different there is a similar level of both bacterial richness and bacterial diversity in each stream. Trends in bacterial occurrence suggest that the most degraded stream were dominated by cyanobacteria, the mid range impact streams by aeromonads and gamma proteobacteria, while the unimpacted stream showed both high diversity and no dominance by any particular class.

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  • Using stream biofilm microbial communities as indicators of freshwater ecosystem health

    Lewis, Gillian; Ancion, PY; Lear, G; Roberts, K; Washington, V (2010-08-23)

    Conference poster
    The University of Auckland Library

    Stream biofilms are a complex aggregation of microorganisms embedded in a polymer matrix and cover almost every surface in freshwater environments. Because of their sedentary way of life, microorganisms associated with biofilms are affected by past and present environmental conditions and therefore constitute a potential integrative indicator of stream health. A wide range of experiments was conducted in both flow chamber microcosms and natural stream environments to investigate the main drivers of microbial community structure and composition and evaluate the potential use of biofilms as a bio-indicator of freshwater ecosystem health. Using community fingerprinting techniques such as terminal-Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis as well as 16S rRNA gene clone libraries we investigated variations occurring in biofilm bacterial and ciliate protozoan communities. Initial experiments conducted in flow chamber microcosms showed that significant differences in microbial community structure could be detected within only a few days of exposure to common water contaminants and remained detectable weeks after transfer to uncontaminated water. Further research investigating biofilm of more than 60 stream sites variously impacted by urbanization revealed a strong separation between rural and urban streams and confirmed the potential use of stream biofilm as a bio-indicator of stream health. Environmental monitoring techniques developed in this project were then successfully tested to investigate the efficacy of an enclosed stormwater treatment system, where traditional biological indicators such as macro-benthic invertebrates were not available. We are now extending our research to 300 different streams in order to define a general Bacterial Community Index characterising stream ecosystem health based on the structure of biofilm bacterial communities.

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  • An Approach for Evaluating Robustness of Edge Operators using Real-World Driving Scenes

    Al-Sarraf, Ali; Vaudrey, Tobi; Klette, Reinhard; Woo, Young Woon (2008)

    Conference poster
    The University of Auckland Library

    Conference Details: 2008 23rd International Conference Image and Vision Computing New Zealand Lincoln University, Christchurch, 26-28 November 2008. http://www.lvl.co.nz/ivcnz2008/ Over the past 20 years there have been many papers that compare and evaluate di erent edge operators. Most of them focus on accuracy and also do comparisons against synthetic data. This paper focuses on real-world driver assistance scenes and does a comparison based on robustness. The three edge operators compared are Sobel, Canny and the under-publicized phase-based Kovesi-Owens operator. The Kovesi- Owens operator has the distinct advantage that it uses one pre-selected set of parameters and can work across almost any type of scene, where as other operators require parameter tuning. The results from our comparison show that the Kovesi-Owens operator is the most robust of the three, and can get decent results, even under weak illumination and varying gradients in the images. Keywords: edge operators, edge robustness evaluation, Kovesi-Owens, phase operators

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  • A Variant of Adaptive Mean Shift-Based Clustering

    Li, Fajie; Klette, Reinhard (2008)

    Conference poster
    The University of Auckland Library

    Conference Details: ICONIP 2008 - 15th International Conference on Neural Information. Processing of the Asia-Pacific Neural Network Assembly November 25-28, 2008, Auckland, New Zealand We are interested in clustering sets of highly overlapping clusters. For example, given is an observed set of stars (considered to be a set of points); how to find (recover) clusters which are the contributing galaxies of the observed union of those clusters? Below we propose a modification of an adaptive mean shift-based clustering algorithm (called Algorithm 1) proposed in 2003 by B. Geogescu, I. Shimsoni and P. Meer

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