2011 Conference Abstracts: Annual Undergraduate Research Conference at the Interface of Biology and Mathematics

Abstract book for the Third Annual Undergraduate Research Conference at the Interface of Biology and Mathematics Date: October 21-22, 2011Plenary speaker: J. Carl Panetta, Department of Pharmaceutical Sciences, St. Jude Children\u27s Research HospitalFeatured Speaker: John Jungck, Mead Chair of the Sciences and Professor of Biology, Beloit Colleg

The LifeV library: engineering mathematics beyond the proof of concept

LifeV is a library for the finite element (FE) solution of partial differential equations in one, two, and three dimensions. It is written in C++ and designed to run on diverse parallel architectures, including cloud and high performance computing facilities. In spite of its academic research nature, meaning a library for the development and testing of new methods, one distinguishing feature of LifeV is its use on real world problems and it is intended to provide a tool for many engineering applications. It has been actually used in computational hemodynamics, including cardiac mechanics and fluid-structure interaction problems, in porous media, ice sheets dynamics for both forward and inverse problems. In this paper we give a short overview of the features of LifeV and its coding paradigms on simple problems. The main focus is on the parallel environment which is mainly driven by domain decomposition methods and based on external libraries such as MPI, the Trilinos project, HDF5 and ParMetis. Dedicated to the memory of Fausto Saleri.Comment: Review of the LifeV Finite Element librar

Exploring clinical phenotypes of open-angle glaucoma and their significance in practice

There are several enduring questions regarding the differentiation of clinical phenotypes of glaucoma which clinicians may derive clinical meaning directed towards patient’s management and prognostication. This thesis seeks to address the following issues relating to distinguishing clinical phenotypes of glaucoma: “Evaluating the impact of changing visual field test density on macular structure-function relationships to identify central-involving glaucoma phenotypes”; and “Identifying quantitative structural and functional clinical parameters that may distinguish between intraocular pressure (IOP) defined glaucoma phenotypes”; Two studies were undertaken to examine clinical phenotypes of glaucoma. The first study utilised systematic approach to assessing the impact of test point density in macular visual field (VF) testing on structure-function concordance for identifying centrally-involving glaucoma phenotypes. The second study used multivariate regression analysis and principal component analysis (PCA) to examine quantitative structural (using optical coherence tomography) and functional (VF) clinical data of newly-diagnosed glucoma patients to determine if there are clinically meaningful distinctions between IOP-defined phenotypes (i.e. low-tension vs high-tension glaucoma). Study 1) Using a systematic approach of test point addition and subtraction, we identified a critical number of test locations (8-14) in macular VF testing where binarised structure-function concordance is maximised, and discordance minimised. This methodology provides a framework for optimising macular VF test patterns for detection of centrally-involving glaucoma phenotypes. Study 2) Despite statistical significance in differences between low- and high-tension glaucoma, PCA applied to quantitative clinical structural and functional parameters returned no groups of clinical parameters that reliably distinguished between patients in IOP-defined glaucoma phenotypes. The present work provides a framework to identify phenotypic groups of glaucoma, the clinical significance of which may vary. We identified the minimum number of test points required to detect central-involving glaucoma in visual field testing. We also demonstrate that IOP-defined phenotypes are not clinically distinguishable at the point of diagnosis, suggesting that these phenotypes form part of a continuum of open-angle glaucoma. These findings have implications for disease staging and preferred treatment modality

Optical coherence tomography angiography

Optical coherence tomography (OCT) was one of the biggest advances in ophthalmic imaging. Building on that platform, OCT angiography (OCTA) provides depth resolved images of blood flow in the retina and choroid with levels of detailed far exceeding that obtained with older forms of imaging. This new modality is challenging because of the need for new equipment and processing techniques, current limitations of imaging capability, and rapid advancements in both imaging and in our understanding of the imaging and applicable pathophysiology of the retina and choroid, and the requirement for understanding the origins of image artifacts. These factors lead to a steep learning curve, even for those with a working understanding dye-based ocular angiography. All for a method of imaging that is a little more than 10 years old. This review begins with a historical account of the development of OCTA, and the methods used in OCTA, including signal processing, image generation, and display techniques. This forms the basis to understand what OCTA images show as well as how image artifacts arise. The anatomy and imaging of specific vascular layers of the eye are reviewed. The integration of OCTA in multimodal imaging in the evaluation of retinal vascular occlusive diseases, diabetic retinopathy, uveitis, inherited diseases, age-related macular degeneration, and disorders of the optic nerve is presented. OCTA is an exciting, disruptive technology. Its use is rapidly expanding in clinical practice as well as for research into the pathophysiology of diseases of the posterior pole

Roadmap on signal processing for next generation measurement systems

Signal processing is a fundamental component of almost any sensor-enabled system, with a wide range of applications across different scientific disciplines. Time series data, images, and video sequences comprise representative forms of signals that can be enhanced and analysed for information extraction and quantification. The recent advances in artificial intelligence and machine learning are shifting the research attention towards intelligent, data-driven, signal processing. This roadmap presents a critical overview of the state-of-the-art methods and applications aiming to highlight future challenges and research opportunities towards next generation measurement systems. It covers a broad spectrum of topics ranging from basic to industrial research, organized in concise thematic sections that reflect the trends and the impacts of current and future developments per research field. Furthermore, it offers guidance to researchers and funding agencies in identifying new prospects.AerodynamicsMicrowave Sensing, Signals & System

Micro/Nano Devices for Blood Analysis, Volume II

The development of micro- and nanodevices for blood analysis continues to be a growing interdisciplinary subject that demands the careful integration of different research fields. Following the success of the book “Micro/Nano Devices for Blood Analysis”, we invited more authors from the scientific community to participate in and submit their research for a second volume. Researchers from different areas and backgrounds cooperated actively and submitted high-quality research, focusing on the latest advances and challenges in micro- and nanodevices for diagnostics and blood analysis; micro- and nanofluidics; technologies for flow visualization and diagnosis; biochips, organ-on-a-chip and lab-on-a-chip devices; and their applications to research and industry