87,482 results

  • The Cardiac Physiome: perspectives for the future

    Bassingthwaighte, J; Hunter, Peter; Noble, D (2009-05-01)

    Journal article
    The University of Auckland Library

    The Physiome Project, exemplified by the Cardiac Physiome, is now 10 years old. In this article, we review past progress and future challenges in developing a quantitative framework for understanding human physiology that incorporates both genetic inheritance and environmental influence. Despite the enormity of the challenge, which is certainly greater than that facing the pioneers of the human genome project 20 years ago, there is reason for optimism that real and accelerating progress is being made.

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  • Visualization of transverse diffusion paths across fiber cells of the ocular lens by small animal MRI

    Vaghefi Rezaei, Seyed; Pontre, Beau; Donaldson, Paul; Hunter, Peter; Jacobs, Marc (2009)

    Journal article
    The University of Auckland Library

    The sense of vision requires that light penetrate through the ocular lens. Experiments, performed and published by many research groups, have suggested that the lens, which has no blood vessels, relies on internally directed ion and water fluxes for its circulation, survival and transparency. We investigated the internal diffusive pathways of the lens in order to better understand the constraints that may be operating on directional lens fluxes. Small animal magnetic resonance imaging, including T2-weighted and diffusion tensor imaging, was used to measure tissue properties and diffusivity throughout cultured bovine lenses. A range of concentric regions of signal intensity was distinguished inside the lens, by both T2-weighted signal and mean diffusivity. Diffusivity mapping of the lens revealed novel anisotropic polar and equatorial zones of pronounced diffusivity directed transverse to the fiber cells. In contrast, an inner zone including the lens nucleus showed isotropic and weak diffusivity. Our results lend support to models of internally directed lens micro-circulation, by placing non-structural diffusive constraints on global patterns of fluid circulation.

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  • Myocardial material parameter estimation - a non-homogeneous finite element study from simple shear tests

    Schmid, Holger; O'Callaghan, P; Nash, Martyn; Lin, WL; Le Grice, Ian; Smaill, Bruce; Young, Alistair; Hunter, Peter (2008)

    Journal article
    The University of Auckland Library

    The passive material properties of myocardium play amajor role in diastolic performance of the heart. In particular, the shear behaviour is thought to play an important mechanical role due to the laminar architecture of myocardium. We have previously compared a number of myocardial constitutive relations with the aim to extract their suitability for inverse material parameter estimation. The previous study assumed a homogeneous deformation. In the present study we relaxed the homogeneous assumption by implementing these laws into a finite element environment in order to obtain more realistic measures for the suitability of these laws in both their ability to fit a given set of experimental data, as well as their stability in the finite element environment. In particular, we examined five constitutive laws and compare them on the basis of (i) ???goodness of fit???: how well they fit a set of six shear deformation tests, (ii) ???determinability???: how well determined the objective function is at the optimal parameter fit, and (iii) ???variability???: how well determined the material parameters are over the range of experiments. Furthermore, we compared the FE results with those from the previous study. It was found that the same material law as in the previous study, the orthotropic Fung-type ???Costa-Law???, was the most suitable for inverse material parameter estimation for myocardium in simple shear.

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

    Jor, JWY; Nielsen, PMF; Nash, MP; Hunter, PJ (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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  • The Cardiac Physiome: at the heart of coupling models to measurement

    Smith, Nicolas; Hunter, Peter; Paterson, DJ (2009-05)

    Journal article
    The University of Auckland Library

    Over the last two decades, technical breakthroughs in experimental physiology have paved the way for an explosion in the quality and quantity of data available for analysis. These developments have underpinned many of the postgenomic era???s advances, through the collection of individual data sets frommany species, including humans. In parallelwith these experimental developments, advances in computing and numerical techniques have accelerated our capacity to handle large volumes of data, making possible the integration of these data sets through the application of biophysically based, computational models.

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  • The Virtual Kidney: an eScience interface and Grid portal

    Harris, PJ; Buyya, R; Chu, XC; Kobialka, T; Kazmierczak, E; Moss, R; Appelbe, W; Hunter, Peter; Thomas, SR (2009-06-13)

    Journal article
    The University of Auckland Library

    The Virtual Kidney uses a web interface and distributed computing to provide experimental scientists and analysts with access to computational simulations and knowledge databases hosted in geographically separated laboratories. Users can explore a variety of complex models without requiring the specific programming environment in which applications have been developed. This initiative exploits high-bandwidth communication networks for collaborative research and for shared access to knowledge resources. The Virtual Kidney has been developed within a specialist community of renal scientists but is transferable to other areas of research requiring interaction between published literature and databases, theoretical models and simulations and the formulation of effective experimental designs. A web-based three-dimensional interface provides access to experimental data, a parameter database and mathematical models. A multi-scale kidney reconstruction includes blood vessels and serially sectioned nephrons. Selection of structures provides links to the database, returning parameter values and extracts from the literature. Models are run locally or remotely with a Grid resource broker managing scheduling, monitoring and visualization of simulation results and application, credential and resource allocation. Simulation results are viewed graphically or as scaled colour gradients on the Virtual Kidney structures, allowing visual and quantitative appreciation of the effects of simulated parameter changes.

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  • The cardiac atlas project: Rationale, design and procedures

    Fonseca, CG; Backhaus, M; Do Chung, J; Tao, W; Medrano Gracia, Pau; Cowan, Brett; Hunter, Peter; Finn, JP; Shivkumar, K; Lima, JAC; Bluemke, DA; Kadish, AH; Lee, DC; Young, Alistair (2010)

    Conference item
    The University of Auckland Library

    The Cardiac Atlas Project (CAP) is a NIH sponsored international collaboration to establish a web-accessible structural and functional atlas of the normal and pathological heart as a resource for the clinical, research and educational communities. An initial goal of the atlas is to facilitate statistical analysis of regional heart shape and wall motion characteristics, and characterization of remodeling, between and within population groups. The two main early contributing studies are the Multi Ethnic Study of Atherosclerosis (MESA) and the Defibrillators to Reduce Risk by Magnetic Resonance Imaging Evaluation (DETERMINE) clinical trial. De-identified image and text data from 2864 asymptomatic volunteers from MESA, and 470 myocardial infarction cases from DETERMINE, are currently available in the CAP database. DICOM images were de-identified using HIPAA compliant software based on tools provided by the Center for Computational Biology at UCLA. Only those cases with informed consent and IRB approval compatible with the CAP were included. Researchers requesting permission to access CAP data can apply through the CAP website (www.cardiacatlas.org). All proposals for data access must be approved by the data contributors, and applicants must sign a data transfer agreement with each study from which data is requested. Software to visualize cardiac images and create 3D mathematical models, developed in the CAP, is available open-source from the website.

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  • Practitioner research: collaboration and knowledge production

    Lunt, N; Shaw, I; Fouche, Christa (2010)

    Journal article
    The University of Auckland Library

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  • Recovery of myocardial kinematic function without the time history of external loads

    Zhang, Heye; Li, Bo; Young, Alistair; Hunter, Peter (2010)

    Journal article
    The University of Auckland Library

    A time-domain filtering algorithm is proposed to recover myocardial kinematic function using output-only measurements without the time history of external loads. The main contribution of this work is that the overall effect of all the external loads on the myocardium is treated as a random variable disturbed by the Gaussian white noise because the external loads of the myocardium are usually unknown in practical exercises. The kernel of our proposed algorithm is an iterative, multiframe, and sequential filtering procedure consisting of a Kalman filter and a least-squares filter. In our proposed implementation, the initial guess of myocardial kinematic function and residual innovation of all the state variables are first computed using a Kalman filter via state space equations only driven by the Gaussian white noise, and then the residual innovation is fed into a least-squares filter to estimate the total external loads of the myocardium. In the end, the initial guess of myocardial kinematic function is corrected using external loads provided by the least-squares filter. After the introduction of the whole structure of our algorithm, we demonstrate the ability of the framework on synthetic data and MR image sequences.

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  • Practitioner research made easier: A report on the GRIP project

    Beddoe, Elizabeth; Yates, D; Fouche, Christa; Harington, Philip (2010)

    Journal article
    The University of Auckland Library

    An article in this journal in 2007 outlined an innovative programme in progress in Auckland at that time. Growing Research in Practice (GRIP) involved groups of social service practitioners who carried out small and manageable research projects on topics that piqued their interest within the workplace. The main aim of the GRIP programme was to nurture a culture of practitioner enquiry in social service agencies in Auckland, in an attempt at facilitating meaningful change and service improvement in the longer term. This article reports on the findings from the second phase of the evaluation of the programme where seven participants were interviewed about their reflections on GRIP and the outcomes of the programme. The article offers recommendations for social service practitioners in this regard.

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  • FieldML: Concepts and implementation

    Christie, Gerald; Nielsen, Poul; Blackett, Shane; Bradley, Christopher; Hunter, Peter (2009-05)

    Journal article
    The University of Auckland Library

    The field modelling language FieldML is being developed as a standard for modelling and interchanging field descriptions in software, suitable for a wide range of computation techniques. It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems. It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems. This paper describes the concepts behind FieldML, including a simple example of a spatially varying finite-element field. It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience.

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  • Does anyone die from AIDS in South Africa?

    Fouche, Christa; Riffe, H (2007)

    Journal article
    The University of Auckland Library

    Despite staggering statistics on AIDS, South African respondents to a study about perceptions surrounding HIV/AIDS from populations at risk claim little knowledge about people dying of AIDS or even of attendance at funerals for someone who has died of AIDS. Using data from focus groups, the authors discuss possible reasons for lack of knowledge of deaths related to HIV/AIDS, including: reticence to publicly admit knowledge; avoidance of contact with affected persons; denial of the impact/extent of the disease; and ignorance of disease symptoms or culturally-consistent diagnoses (i.e., familiar explanations consistent with the culture). Speculation about possible implications of this for people infected and affected by AIDS-related deaths in South Africa lead to the conclusion that all aspects of society must be interwoven and mobilized to develop effective responses to HIV infection. Copyright ?? 2007 by The Haworth Press, Inc. All rights reserved.

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  • An invitation to dialogue: The World Cafe in Social Work Research

    Fouche, Christa; Light, GL (2010)

    Journal article
    The University of Auckland Library

    In the context of discussions about the potential of collaborative research, a practice-based project was implemented in Auckland, New Zealand during 2006 and 2007, aimed to help develop a culture of enquiry among practitioners in social service. One design variable in this project was the World Cafe?? , a conversational process that helps groups to engage in constructive dialogue around critical questions, to build personal relationships, and to foster collaborative learning. In relation to other collaborative approaches, the World Cafe?? is powerful in terms of the use of cross-pollination of ideas through evolving rounds of information exchange and the use of a cafe?? -style social context that allows the sharing of information in an equitable and nonthreatening manner. This article reports on the design and implementation of a World Cafe?? approach, located in the philosophy of appreciative inquiry, through ???Cafe?? Hear and Now???. The authors reflect on the perceived value of this initiative and invite dialogue on the implementation of the World Cafe?? in social work research.

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  • Meeting Report on the 2nd MEI International Symposium - The Worldwide Challenge to Physiome and Systems Biology and Osaka Accord -.

    Hunter, Peter; Kurachi, Y; Noble, D; Viceconti, M (2008-12)

    Journal article
    The University of Auckland Library

    The integration of knowledge from many disciplines and the vast amount of biological data in the post-genome era, together with new techniques from the mathematical and information sciences, are moving the world towards a new generation of life sciences where physiological and pathological information from the living human body can be quantitatively described in silico across multiple scales of time and size and through diverse hierarchies of organization.

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  • A finite element method for an eikonal equation model of myocardial excitation wavefront propagation

    Tomlinson, KA; Hunter, Peter; Pullan, Andrew (2002)

    Journal article
    The University of Auckland Library

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  • CELLULAR OPEN RESOURCE (COR): current status and future directions

    Garny, A; Noble, D; Hunter, Peter; Kohl, P (2009-05-28)

    Journal article
    The University of Auckland Library

    The need for tools to aid the description and sharing of biological models was highlighted at the launch of the International Union of Physiological Sciences Physiome Project in 1997. This has resulted in the release, in 2001, of the CellML specifications (http://www. cellml.org/specifications/). CELLULAR OPEN RESOURCE (COR) was among the early adopters of this standard, eventually forming the first publicly available CellML-based modelling and collaboration environment. From the onset, COR was designed to provide an environment that could not only be used by experienced modellers, but also by experimentalists, teachers and students. It therefore tries to combine a user-friendly interface with a computationally efficient numerical engine. In this paper, we introduce the philosophy behind COR, explain its user interface and current functionality, including the editing and running of CellML files, highlight lessons learned from user feedback and problems experienced during the development of COR and conclude by exploring future development potential.

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  • Action research for developing social workers' research capacity

    Lunt, N; Fouche, Christa (2009)

    Journal article
    The University of Auckland Library

    We reflect on the action research process implemented in assisting the development of a culture of practitioner enquiry amongst social workers in social services agencies, and highlight the overall outcomes of the intervention. The paper outlines the rationale and process for undertaking an action research process with social services professionals in an attempt to stimulate practitioner research. It discusses the project experiences in two separate sections, particularly highlighting the ripple effects of the initiative, and the development of ???networked mentoring??? within the learning nest of the project.

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  • Computer simulation of vertebral artery occlusion in endovascular procedures

    Ho, Harvey; Mithraratne, Premakumar; Sands, Gregory; Hunter, Peter (2010)

    Journal article
    The University of Auckland Library

    Objective The aim of this work is to establish a computational pipeline for the simulation of blood flow in vasculatures and apply this pipeline to endovascular interventional scenarios, e.g. ngioplasty in vertebral arteries. Methods A patient-specific supra-aortal vasculature is digitized from a 3D CT angiography image. By coupling a reduced formulation of the governing Navier???Stokes equations with a wall constitutive equation we are able to solve the transient flow in elastic vessels. By further incorporating a bifurcation model the blood flow across vascular branches can be evaluated, thus flow in a large vasculature can be modeled. Vascular diseases are simulated by modifying the arterial tree configurations, e.g. the effective diameters, schematic connectivity, etc. Occlusion in an artery is simulated by removing that artery from the arterial tree. Results It takes about 2min per cardiac cycle to compute blood flow in an arterial tree consisting of 38 vessels and 18 bifurcations on a laptop PC. The simulation results show that blood supply in the posterior region is compensated from the contralateral vertebral artery and the anterior cerebral arteries if one of the vertebral arteries is occluded. Conclusion The computational pipeline is computationally efficient and can capturemain flowpatterns at any point in the arterial tree.With further improvement it can serve as a powerful tool for the haemodynamic analysis in patient-specific vascular structures.

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  • Computational multiscale modeling in the IUPS Physiome Project: modeling cardiac electromechanics

    Nickerson, David; Nash, Martyn; Nielsen, Poul; Smith, N; Hunter, Peter (2006)

    Journal article
    The University of Auckland Library

    We present a computational modeling and numerical simulation framework that enables the integration of multiple physics and spatiotemporal scales in models of physiological systems. This framework is the foundation of the IUPS (International Union of Physiological Sciences) Physiome Project. One novel aspect is the use of CellML, an annotated mathematical representation language, to specify model- and simulation-specific equations. Models of cardiac electromechanics at the cellular, tissue, and organ spatial scales are outlined to illustrate the development and implementation of the framework. We quantify the computational demands of performing simulations using such models and compare models of differing biophysical detail. Applications to other physiological systems are also discussed.

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  • CellML metadata standards, associated tools and repositories

    Beard, DA; Britten, Randall; Cooling, Michael; Garny, A; Halstead, MDB; Hunter, Peter; Lawson, James; Lloyd, Catherine; Marsh, Justin; Miller, Andrew; Nickerson, David; Nielsen, Poul; Nomura, T; Subramanium, S; Wimalaratne, Sarala; Yu, Yan Hei (2009-05-28)

    Journal article
    The University of Auckland Library

    The development of standards for encoding mathematical models is an important component of model building and model sharing among scientists interested in understanding multi-scale physiological processes. CellML provides such a standard, particularly for models based on biophysical mechanisms, and a substantial number of models are now available in the CellML Model Repository. However, there is an urgent need to extend the current CellML metadata standard to provide biological and biophysical annotation of the models in order to facilitate model sharing, automated model reduction and connection to biological databases. This paper gives a broad overview of a number of new developments on CellML metadata and provides links to further methodological details available from the CellML website.

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