231 results for Conference poster

  • Institutional Collaboration around Institutional Repositories

    Hayes, Leonie; Stevenson, Alison; Mason, Ingrid; Scott, Anne; Kennedy, Peter (2007)

    Conference poster
    The University of Auckland Library

    Three New Zealand universities have been collaborating on a project to provide open, web-based, access to research outputs through the creation of institutional repositories using the DSpace software. This poster will therefore address the theme of eResearch with particular focus on the benefits of active collaboration, intra-university, inter-university and international, in this area of activity. New Zealand has a small population of 4 million, an innovative and resourceful academic community, a newly implemented research funding model, based on performance (PBRF) and a readiness to stay competitive with the rest of the world. Institutional Repositories in New Zealand are in their infancy but a considerable body of experience already exists overseas which we can draw upon if we work in partnership with those institutions who have already implemented institutional repositories. Funding is limited but by sharing resources and working collaboratively each institution can make substantial progress towards the creation of individual repositories. This poster reports on the joint project between the University of Auckland, the University of Canterbury and Victoria University of Wellington. The three partners have been funded by the New Zealand Tertiary Education Commission to make available, via the Internet for access by Open Archives Initiative (OAI) compliant search engines, research outputs created by staff and students of the three partner institutions. This poster will present information on the work to: • Establish DSpace repositories in partner institutions that conform to the OAI-PMH standard. • Contribute to the development of linkages with the Australian DEST funded information infrastructure projects, i.e. ADT, APSR and ARROW projects. • Identify methods for increasing academic understanding of, and promoting contributions to, digital repositories the content of which is then available to enhance teaching and learning, as well as research. • Provide digital materials, either through the deposit of “born digital” material or through digitisation of material already available in print, that contribute to the developing digital content landscape as envisaged in the NZ Digital Strategy • Contribute to national research resource discovery service to be established by the National Library of New Zealand. Ensure that the content in the project repositories is visible for harvesting by global OAI-compliant search engines such as Google Scholar, OAIster, etc. Collaborate with other IR projects and communicate the lessons learned to the wider tertiary and research communities of New Zealand

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  • CellML: Cellml.org, Tools and Community

    Lawson J.; Lloyd C.; Noble P.; Hunter P.; Nielsen P. (2007)

    Conference poster
    The University of Auckland Library

    Poster presented at ICSB2007 The purpose of CellML is to store and exchange computer-based mathematical models of as wide a range of scale and subject as posssible. For example, biochemical signalling and metabolic systems can be embedded in electrophysiological models of excitable cells in CellML. The CellML language is an open standard based on the XML markup language and is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups [1]. The majority of computational biology publications aim to discuss their model but often fail to provide a comprehensive set of instructions for recreating the model, or include errors preventing reproduction of published model outputs. Publishing a paper with a link to a CellML model facilitates the wide distribution and recreation of that model, and additionally forces the modeller to carefully consider matters such as unit consistency. The CellML specification and application programming interfaces (API) are driven by a core team, but a growing international community is involved in work related to CellML. A community website (www.cellml.org) has been set up as a focal point for the community and also functions as a model repository. A number of groups are developing software tools for CellML and using the language for research in computational biology. A repository of almost 300 unique CellML models is available at www.cellml.org/models: these are computational models from peer-reviewed publications that have been coded into CellML. These models are undergoing an active curation process based on the MIRIAM standard, proposed by the international biological modelling community [2]. This process includes provision of comprehensive documentation, annotation with citation and model author metadata, maintenance of file modification histories, and correspondence with model authors to ensure that models define all required initial conditions and parameters. The CellML community strongly supports collaboration with other groups to continue to set standards for curation and distribution of biological models. A number of free / open source software tools for developing and simulating CellML models are available, including Physiome CellML Environment (PCEnv) and Cellular Open Resource (COR). Other modelling environments such as JSim and Virtual Cell also support the CellML format. Information on further tools such as validators, debuggers and simulation specific packages can be found at www.cellml.org/tools. In the near future, models in the cellml.org model repository will be completely annotated with ontologies such as BioPaX and references to databases such as UniProt. Models will be broken down into the components from which they are comprised, and these components will themselves be curated, providing a toolbox of standardised computational parts from which new models can be created, in an in silico analogy to the MIT Registry of Standard Biological parts (http://parts.mit.edu/registry/index.php/Main_Page). An API has recently been developed for software tools to allow interaction between CellML and SVG diagrams of models, such as biochemical pathway schematics, and work is also underway to standardise graphical representations of CellML models. For more information, please join the CellML community mailing list at http://www.cellml.org/mailman/listinfo/cellml-discussion. 1.) Cuellar, A.A., Lloyd, C. M., Nielsen, P. F., Bullivant, D. P., Nickerson, D. P., Hunter, P. J. "An Overview of CellML 1.1, a Biological Model Description Language" Simulation, 2003, 79, No. 12, 740-747 2.) Le Novere, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D., Wanner, B.L. "Minium information requested in the annotation of biochemical models (MIRIAM)" Nature Biotechnology, 2005, 23 1509-1515

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  • Stream Restoration: Getting the microbial ecology right.

    Lewis, Gillian; Lear, Gavin; Turner, Susan; Boothroyd, Ian; Stott, Rebecca; Roberts, Kelly; Ancion, Pierre; Dopheide, Andrew; Washington, Vidya; Knight, Duane; Smith, Joanna (2008-08-17)

    Conference poster
    The University of Auckland Library

    A comprehensive program to re-establish the structure and function of an ecosystem, including its natural diversity and aquatic habitats.

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  • Bacterially mediated manganese deposition in novel "anelli" within the biofilms of an impacted urban stream

    Smith, JP; Lewis, Gillian (2007-12-02)

    Conference poster
    The University of Auckland Library

    The purpose of this work is to identify bacteria responsible for the formation of manganese containing anelli within stream biofilms, and study their distribution. Manganese oxidising bacteria are part of a diverse group of organisms found commonly within many disparate environments, which deposit manganese and iron biominerals within biofilms and flocs [1]. The purpose of microbial manganese oxidation is poorly understood, but may be associated with energy production, mobilisation of nutrients, protection and/or detoxification [1, 2]. Manganese has a high sorptive capacity for heavy metals, metalloids, and other ions, as well as a strong oxidizing potential, and therefore frequently induces co-precipitation of cations present within the surrounding environment [1]. Within urban streams contaminants such as heavy metals may therefore potentially be concentrated within steam biofilms in the presence of manganese oxidising bacteria.

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  • A novel implantable blood pressure telemetry device: Comparison between Data Sciences and Telemetry Research systems

    Malpas, Simon; Lim, M; McCormick, John; Kirton, RS; Van Vliet, B; Easteal, Allan; Barrett, Carolyn; Guild, Sarah-Jane; Budgett, David (2008-04-05)

    Conference poster
    The University of Auckland Library

    The pending expiry (May 2008) of a Data Sciences (DSI) patent in the area of blood pressure telemetry permits the development of alternative technologies. A key aspect in providing new telemetry systems is a comparison to existing technology. Important aspects include stability of the calibration over time and the ability to capture the pulsitile blood pressure waveform. In a group of 6 rats and 5 rabbits DSI blood pressure transmitters (C40 or D70 models) were implanted in conjunction with Telemetry Research (TR) transmitters. Both systems incorporate a fluid filled catheter of similar dimensions with a biocompatible gel in the tip. The blood pressure waveform was collected via telemetry for up to 2 months after implantation. The signal was sampled at 500 Hz and digitally transmitted to a receiver up to 5 m away The battery of TR transmitter was recharged within the rat using inductive power transfer technology. The pulsitile waveform associated with each heart beat was reflected similarly in all cases although the frequency response of DSI telemeters was limited to ~40 Hz (–3 dB rolloff point). The calibrated offset level between the two transmitters was not more than 5 mmHg at all times over a 2 month period. We conclude that the Telemetry Research blood pressure transmitters offer comparable performance to existing technology but with extra design advantages (rechargeable, co-housing of animals, greater range).

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  • Effects of Storm water metal contaminats on microbial communities in stream biofilm revealed by Automated Ribosomal Intergenic Spacer Analysis (ARISA)

    Ancion, Pierre; Lear, Gavin; Lewis, Gillian (2008-08-17)

    Conference poster
    The University of Auckland Library

    Stormwater metal contaminants are known to be a threat to our freshwater environments but little is known about their effects on stream micro-organisms. This project investigates accumulation and release of the most common stormwater metal contaminants (zinc, copper and lead) in stream biofilms and their effects on bacterial populations.

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  • Molecular investigation of protozoan diversity in stream biofilms

    Dopheide, AJ; Lear, Gavin; Lewis, Gillian (2006-11-21)

    Conference poster
    The University of Auckland Library

    This research aims to test the following hypothesis: that molecular biological methods will allow description of protozoan diversity and ecology in streams.

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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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  • Blood flow redistribution following pulmonary micro-embolism

    Clark, Alys; Burrowes, KS; Tawhai, Merryn (2010)

    Conference poster
    The University of Auckland Library

    Occlusion of pulmonary arteries by autologous clot and bead emboli affect pulmonary function by elevating arterial pressures and reducing the number of functional gas exchange units in the lung. The occlusion of multiple arterioles at the acinar level can have a significant impact on pulmonary function. However, the contribution of acinar structure to perfusion distribution and the significance of arteriole occlusion is not well characterized.

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  • Pregnancy Associated Changes in Insulin Signalling in Daughters of Adolescent Ewes

    Oliver, Mark; Hancock, SN; Kenyon, PR; Blair, HT; Pain, S; Morris, S; Phua, Hui; Bloomfield, Francis (2011-09)

    Conference poster
    The University of Auckland Library

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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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  • A case study on frontline perspectives of organizational change: A practitioner-academic partnership to analyse the creation of a Youth Justice entity in Child, Youth and Family

    Webster, Michael; Herrmann, Klaus (2009-11-11)

    Conference poster
    The University of Auckland Library

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  • The development of online learning environments (OLEs) at The University of Auckland Library: collaboration, integration and usability testing

    Zdravkovic, Neda (2013-04-09)

    Conference poster
    The University of Auckland Library

    In order to meet the learning needs of a large number of in-house, flexible learning and distance-learning students from a variety of disciplines, The University of Auckland Library has enhanced the provision of information and academic literacy instruction through the design of online learning environments. Learning Services Librarians, learning designers and subject librarians from The University of Auckland Library have collaborated with faculty, Centre for Academic Development staff, graphic design professionals and web developers to design online courses and tutorials, such as: • Academic Integrity - stand-alone online academic integrity course, compulsory for all new students at the University of Auckland from Semester I 2013; • COMLAW 101: New Zealand’s Legal Framework - curriculum- integrated information literacy online tutorial designed for COMLAW 101: Law in a Business Environment academic course with 2000 students each year; • POPLHLTH 701: Research Methods in Health - curriculum- integrated online information literacy learning environment for postgraduate students completing the POPLHLTH 701: Research Methods in Health course and compulsory assessment activity bearing 15% course mark; • FTVMS 100: Assignment Research Path – curriculum-integrated information literacy online tutorial and compulsory assessment activity (10% course mark) designed for FTVMS 100: Media studies first year undergraduate course with 1000 students each year; • Understanding Your Reading List - generic information literacy online tutorial designed for all first year undergraduate students. The focus of the paper will be on the development framework of online courses, curriculum-integrated and generic tutorials and the analysis of different stages of each project, their collaborative nature and usability testing practices applied (user observation, focus group interviews, surveys) and outcomes. It will introduce CourseBuilder as a web-based tool for the design of online learning environments and activities, its features, functionalities and published outputs. CourseBuilder, developed by the University of Auckland’s Centre for Academic Development, is an authoring tool that provides customisable templates to develop online interactive activities (eg, case studies, reflections and quizzes), import text, insert media, monitor student responses and more. Finally the paper will describe issues and challenges during each development stage, as well as benefits and limitations of using an online learning environment development system.

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  • Getting Research 'Out There': ResearchSpace@Auckland

    Newton-Wade, Vanessa; Laurie, John; Hayes, Leonie (2007)

    Conference poster
    The University of Auckland Library

    A key part of the academic research process is publishing the results – ‘getting it out there’. An institutional repository such as ResearchSpace@Auckland provides authors with a channel for near-instantaneous worldwide dissemination of research. ResearchSpace@Auckland has been developed at the University of Auckland under the umbrella of the Institutional Repositories Aotearoa Project (Ira). Built using DSpace Open Source Software, the repository contains ‘research outputs’ from the University of Auckland’s staff and students, including theses, papers and reports. The PhD thesis collection is the flagship of the repository – electronic submission is compulsory for all completing PhD students from 2011. The initial 200 items in the PhD thesis collection were gathered by contacting authors of theses submitted at the University of Auckland since 2001 and inviting them to submit digital copies and consent forms. Trials are underway to digitize theses that are unavailable in digital format. The mandating of compulsory submission for PhD theses submitted at the University of Auckland ensures regulatory requirements for digital deposit are catered for. Other collections for articles, papers, and images are being developed.

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  • Registry of BioBricks models using CellML

    Rouilly, Vincent; Canton, Barry; Nielsen, Poul; Kitney, Richard (2007)

    Conference poster
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. One of the main goals in Synthetic Biology is to assess the feasibility of building novel biological systems from interchangeable and standardized parts. In order to collect and share parts, a Registry of standardized DNA BioBricks http://parts.mit.edu/registry has been established at the MIT. BioBricks can be assembled to form devices and systems to operate in living cells. Design of reliable devices and systems would benefit from accurate models of system function. To predict the function of systems built from many parts, we need to have accurate models for the parts and mechanisms to easily compose those part models into a system model. Therefore, in parallel to increasing the number of parts available and characterising them experimentally, a logical extension to the Registry would be to build a Registry of BioBrick models to complement the physical parts.

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  • Space-Time Multi-Resolution Banded Graph-Cut for Fast Segmentation. (Conference Poster)

    Vaudrey, Tobi; Gruber, Daniel; Wedel, Andreas; Klappstein, Jens (2008)

    Conference poster
    The University of Auckland Library

    Conference Details: 30th Annual Symposium of the German Association for Pattern Recognition DAGM Munich, Germany, June 2008. http://www.dagm2008.org/ Applying real-time segmentation is a major issue when processing every frame of image sequences. In this paper, we propose a modi cation of the well known graph-cut algorithm to improve speed for discrete segmentation. Our algorithm yields real-time segmentation, using graph-cut, by performing a single cut on an image with regions of di erent resolutions, combining space-time pyramids and narrow bands. This is especially suitable for image sequences, as segment borders in one image are re ned in the next image. The fast computation time allows one to use information contained in every image frame of an input image stream at 20 Hz, on a standard PC. The algorithm is applied to traf- c scenes, using a monocular camera installed in a moving vehicle. Our results show the segmentation of moving objects with similar results to standard graph-cut, but with improved speed.

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  • Goal: Real-Time Segmentation via Graph Cut Goal: Real-Time Segmentation via Graph Cut

    Vaudrey, Tobi; Wedel, Andreas; Rabe, Clemens; Klappstein, Jens; Klette, Reinhard (2008)

    Conference poster
    The University of Auckland Library

    Conference Details: 2008 23rd International Conference Image and Vision Computing New Zealand. IVCNZ 08. Lincoln University, Christchurch, 26-28 November 2008. http://www.lvl.co.nz/ivcnz2008/ The detection of moving objects is a crucial part of driver assistance systems. This paper tackles this issue using computer vision. Two approaches are investigated, monocular and stereoscopic. The base principals and implementational issues are discussed and detailed, high- lighting areas of concern. In both cases, the detection is based on motion analysis of individually tracked image points (optical ow). The monoc- ular approach relies solely on the optical ow, where as the stereoscopic approach also takes stereo depth information into account. In both ap- proaches the motion analysis provides a motion metric which corresponds to the likelihood that the tracked point is moving. Based on this metric the points are segmented into objects by employing the globally op- timal graph cut algorithm. These approaches are then compared and contrasted using real-world vehicle image sequences.

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  • Benefits of speech & language therapy for hearing impaired children

    Fairgray, Liz; Purdy, Suzanne (2008)

    Conference poster
    The University of Auckland Library

    Conference details: Reflecting Connections 2008, the second conference jointly hosted by the New Zealand Speech-Language Therapists Association and Speech Pathology Australia. Held at the SKYCITY Convention Centre in Auckland, New Zealand, from the 25th to the 29th of May, 2008. http://www.reflectingconnections.co.nz/ Although the need for speech and language therapy is widely recognized for children who are hearing impaired, there is little research evidence for improved outcomes after specific speech and language therapy interventions. With improvements in hearing aid and cochlear implant technology, and consequently improved access to the speech signal, there has been greater emphasis on listening-based therapies. The most widely used therapy is referred to as “auditory-verbal therapy” (AVT). This approach is endorsed by the Alexander Graham Bell Association, but there is paucity of research evidence for AVT effectiveness (Rhoades, 1982; Goldberg & Flexer, 1993; Wray et al., 1997; Rhoades & Chisholm, 2000). Previous studies have focused on psychosocial and educational outcomes of AVT, rather than measuring specific speech and language outcomes. The current study investigates speech and language, speech perception in noise and reading abilities before and after a 6-month period of weekly AVT with an experienced Certified Auditory-Verbal and Speech-language Therapist. Participants are eight children aged 5 to 17 years with moderate-profound sensorineural hearing loss using cochlear implants (CI) and/or hearing aids.

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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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