Organizational Unit:
Wallace H. Coulter Department of Biomedical Engineering

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Now showing 1 - 10 of 1168
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    Flux driven fly-throughs
    (Georgia Institute of Technology, 2003-06) Bouix, Sylvain ; Siddiqi, Kaleem ; Tannenbaum, Allen R. ; Georgia Institute of Technology. Dept. of Biomedical Engineering ; Emory University. Dept. of Biomedical Engineering ; McGill University. School of Computer Science
    We present a fast, robust and automatic method for computing central paths through tubular structures for application to virtual endoscopy. The key idea is to utilize a medial surface algorithm, which exploits properties of the average outward flux of the gradient vector field of a Euclidean distance function the boundary of the structure of interest. The algorithm is modified to yield a collection of 3D curves, each of which is locally centered. The approach requires no user interaction, and is virtually parameter free and has low computational complexity. We illustrate the approach on segmented colon and vessel data.
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    On the spectra and invertibility of certain operators in systems theory
    (Georgia Institute of Technology, 1987-12) Foias, Ciprian ; Tannenbaum, Allen R. ; University of Minnesota. Dept. of Electrical Engineering ; Universiṭat Ben-Guryon ba-Negev ; Indiana University, Bloomington. Dept. of Mathematics
    In this paper we study the following kind of problem. Let T be an arbitrary contraction. We will define a certain function which will lead to an explicit procedure for the computation of the isolated spectrum of w(T)w(T)', T any contraction. We will then show how this generalizes the results of [l-31. (See (2.1) and (2.2) below.) We will moreover apply our theory to operators TϵC.₀ and in particular derive a relatively simple expression for the calculation of the discrete spectrum of w (T). We should note that from the control engineering point of view, this means that one can now solve an important special case of the general model-matching problem discussed in [SI for multivariate distributed systems as a well as treat a whole new range of Hankel norm approximation problems. We plan to return to these topics in a future applications oriented paper.
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    GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences
    (Georgia Institute of Technology, 2013) Antonov, Ivan ; Baranov, Pavel ; Borodovsky, Mark ; Georgia Institute of Technology. School of Computational Science and Engineering ; University College, Cork. Biochemistry Dept. ; Moskovskiĭ fiziko-tekhnicheskiĭ institut
    Database annotations of prokaryotic genomes and eukaryotic mRNA sequences pay relatively low attention to frame transitions that disrupt protein-coding genes. Frame transitions (frameshifts) could be caused by sequencing errors or indel mutations inside protein-coding regions. Other observed frameshifts are related to recoding events (that evolved to control expression of some genes). Earlier, we have developed an algorithm and software program GeneTack for ab initio frameshift finding in intronless genes. Here, we describe a database (freely available at http://topaz.gatech. edu/GeneTack/db.html) containing genes with frameshifts (fs-genes) predicted by GeneTack. The database includes 206 991 fs-genes from 1106 complete prokaryotic genomes and 45 295 frameshifts predicted in mRNA sequences from 100 eukaryotic genomes. The whole set of fs-genes was grouped into clusters based on sequence similarity between fs-proteins (conceptually translated fs-genes), conservation of the frameshift position and frameshift direction (_1, +1). The fs-genes can be retrieved by similarity search to a given query sequence via a web interface, by fs-gene cluster browsing, etc. Clusters of fs-genes are characterized with respect to their likely origin, such as pseudogenization, phase variation, etc. The largest clusters contain fs-genes with programed frameshifts (related to recoding events).
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    Dynamic Geodesic Snakes for Visual Tracking
    (Georgia Institute of Technology, 2004) Niethammer, Marc ; Tannenbaum, Allen R. ; Georgia Institute of Technology. School of Electrical and Computer Engineering
    Visual tracking using active contours is usually accomplished in a static framework. The active contour tracks the object of interest in a given frame of an image sequence, and then a subsequent prediction step ensures good initial placement for the next frame. This approach is unnatural, the curve evolution gets decoupled from the actual dynamics of the objects to be tracked. True dynamic approaches exist, all being marker particle based, and thus prone to the shortcomings of such particle-based implementations. In particular, topological changes are not handled naturally in this framework. The now "classical" level set approach is tailored for codimension one evolutions. However, dynamic curve evolution is at least of codimension two. We propose a natural, efficient, level set based approach for dynamic curve evolution which removes the artificial separation of segmentation and prediction, while retaining all the desirable properties of level set formulations. This is based on a new energy minimization functional which for the first time puts dynamics into the geodesic active contour framework.
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    The Role of Noise-Induced Excitable Dynamics of Rho Family GTPases in the Regulation of Actin Cytoskeleton
    (Georgia Institute of Technology, 2021-12) Rahman, Farhan S. ; Tsygankov, Denis ; Hladyshau, Siarhei ; Biomedical Engineering (Joint GT/Emory Department)
    Rho GTPases, a family of signaling proteins, play a pivotal role by acting as molecular switches to regulate F-actin cytoskeletal and cell adhesion. Recent studies have shown that reaction-diffusion (RD) models have the ability to exhibit a wide variety of characteristic patterns of wave propagations of Rho GTPases. This study uses computational modeling to investigate a particular dynamic behavior directly relevant to the observed protrusive activity of motile cells: a single decaying traveling wave of actin polymerization. The model is conducted in a 2D cell of an arbitrarily complex shape. It reveals that the inhibitor decay rate controls the transition from reflecting waves to a single decaying wave and helps to avoid the formation of spiral waves. For noise, we observe that it controls the propagation of wavefronts, such that higher amplitudes of noise induce a greater number of waves. Additionally, the model distinguishes that noise induces waves at different time points. These findings serve as a framework for further comprehensive representation of actin polymerization during cellular morphogenesis.
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    Point Set Registration via Particle Filtering and Stochastic Dynamics
    (Georgia Institute of Technology, 2009-07-16) Sandhu, Romeil ; Dambreville, Samuel ; Tannenbaum, Allen R. ; Georgia Institute of Technology. School of Electrical and Computer Engineering ; Georgia Institute of Technology. Dept. of Biomedical Engineering ; Emory University. Dept. of Biomedical Engineering
    In this paper, we propose a particle filtering approach for the problem of registering two point sets that differ by a rigid body transformation. Typically, registration algorithms compute the transformation parameters by maximizing a metric given an estimate of the correspondence between points across the two sets of interest. This can be viewed as a posterior estimation problem, in which the corresponding distribution can naturally be estimated using a particle filter. In this work, we treat motion as a local variation in pose parameters obtained by running a few iterations of a certain local optimizer. Employing this idea, we introduce stochastic motion dynamics to widen the narrow band of convergence often found in local optimizer approaches for registration. Experimental results are provided that demonstrate the robustness of the algorithm to initialization, noise, missing structures or differing point densities in each sets, on challenging 2D and 3D registration tasks.
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    Finite Element Simulations of Comprehensive Mitral Valve Model
    (Georgia Institute of Technology, 2015-01-27) Pena, Marcel ; Yoganathan, Ajit ; Behravesh, Essy ; Toma, Milan ; Biomedical Engineering (Joint GT/Emory Department)
    Mitral regurgitation (MR) is an increasingly prevalent disorder of the heart in which the mitral valve (MV) does not close properly causing blood to flow backward (leak) into the upper heart chamber when the left lower heart chamber contracts. MR is the most common type of heart valve insufficiency, often requiring open-heart surgical repair. After age 55, some degree of MR is found in almost 20% of men and women. MV repair is considered superior to mitral valve replacement, and there are many surgical techniques utilized to address differing pathologies. One approach to assess the effects of pathology and proposed surgical repair is to utilize a computational model, in which pathologic or surgical alterations can be assessed systematically. However, current models are limited by assumptions related to geometry and material properties and importantly, none have been validated with detailed experimental data. In the present work, an advanced fluid-structure interaction (FSI) model of the MV system is utilized without the limitation of geometry and material properties. This model allows analysis of the valve in the normal, diseased, or repaired states.
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    Conformal Flattening of Brain Ventricles
    (Georgia Institute of Technology, 2006-10) Melonakos, John ; Gao, Yi ; Tannenbaum, Allen R. ; Georgia Institute of Technology. School of Electrical and Computer Engineering
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    Superoxide dismutase delivery and cardiac progenitor cell characterization for myocardial regeneration applications
    (Georgia Institute of Technology, 2011-11-07) Iyer, Gokulakrishnan Seshadri ; Davis, Michael E. ; Harrison, David ; Murthy, Niren ; Nerem, Robert ; Taylor, Robert ; Biomedical Engineering
    Cardiovascular diseases are the leading cause of death throughout the world and various estimates predict that heart disease will remain the number one killer in the world. Pharmacotherapies have not shown significant long term survival benefits to the patients, therefore alternate therapeutic strategies such as bioactive agent delivery and cell therapy based approaches are being investigated. One of the major causes of heart failure is the disease progression after an ischemic event and any successful therapy will be needed over the course of several days/weeks. Oxidative stress is greatly increased in the myocardium following infarction. This plays a significant role in cardiac disease progression and it has also been implicated in the failure of implanted cell therapy. Therefore, reducing oxidative stress in damaged tissue using antioxidants may have broad clinical implications for both the treatment of cardiac dysfunction and for cardiac regeneration applications. This dissertation work examines the effect of sustained delivery of endogenous antioxidant superoxide dismutase (SOD) to the rat myocardium following ischemia/reperfusion (IR) using polyketal polymers as drug carriers. The second major objective of this dissertation is to examine the effects of oxidative stress on cardiac progenitor cells - a promising endogenous adult stem cell in cardiac cell therapy applications
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    Wavy-Walled Bioreactor Supports Increased Cell Proliferation and Matrix Deposition in Engineered Cartilage Constructs
    (Georgia Institute of Technology, 2005-11) Bueno, Ericka M. ; Bilgen, Bahar ; Barabino, Gilda A. ; Northeastern University. Dept. of Chemical Engineering
    Hydrodynamic forces in bioreactors can decisively influence extracellular matrix deposition in engineered cartilage constructs. In the present study, the reduced fluid shear, high-axial mixing environment provided by a wavy-walled bioreactor was exploited in the cultivation of cartilage constructs using polyglycolic acid scaffolds seeded with bovine articular chondrocytes. Increased growth as defined by weight, cell proliferation and extracellular matrix deposition was observed in cartilage constructs from wavy-walled bioreactors in comparison with those from spinner flasks cultured under the same conditions. The wet weight composition of 4-week constructs from the wavy-walled bioreactor was similar to that of spinner flask constructs, but the former were 60% heavier due to equally higher incorporation of extracellular matrix and 30% higher cell population. It is most likely that increased construct matrix incorporation was a result of increased mitotic activity of chondrocytes cultured in the environment of the wavy-walled bioreactor. A layer of elongated cells embedded in type I collagen formed at the periphery of wavy-walled bioreactor and spinner flask constructs, possibly as a response to local shear forces. On the basis of the robustness and reproducibility of the extracellular matrix composition of cartilage constructs, the wavy-walled bioreactor demonstrated promise as an experimental cartilage tissue-engineering vessel. Increased construct growth in the wavy-walled bioreactor may lead to enhanced mechanical properties and expedited in vitro cultivation.