MBI Publications

MBI Publications for 2008 (47)

  • Y. Guo, J. Rubin, C. McIntyre, J. Vitek and D. Terman
    Thalamocortical Relay Fidelity Varies Across Subthalamic Nucleus Deep Brain Stimulation Protocols in a Data-Driven Computational Model
    J. NeurophysiolVol. 99 (2008) pp. 1477-1492

    Abstract

  • M. Djordjevic and R. Bundschuh
    Open complex formation by bacterial RNA polymerase – a quantitative model
    Biophys JVol. 94 No. 11 (2008) pp. 4233

    Abstract

  • I. Basawa, U. Bhat and J. Zhou
    Parameter estimation using partial information with applications to queueing and related models
    Statistics & Probability LettersVol. 78 No. 12 (2008) pp. 1349-1682

    Abstract

  • B. Szomolay, T. Eubank, R. Roberts, C. Marsh and A. Friedman
    Modeling Inhibition of breast cancer growth by GM-CSF: A mathematical model
    Bulletin of Mathematical Biology (2008) (Submitted)

    Abstract

  • A. Nevai and R. Vance
    The role of leaf height in plant competition for sunlight: analysis of a canopy partitioning model
    Math. Biosci. Eng.Vol. 5 (2008) pp. 101-124

    Abstract

  • E. Bogdanova, M. Djordjevic, I. Papapanagiotou, T. Heyduk, G. Kneale and K. Severinov
    Transcription regulation of the type II restriction-modification system AhdI
    Nucl Acids ResVol. 36 No. 5 (2008) pp. 1429

    Abstract

  • Y. Kim, S. Lawler, M. Nowicki, E. Chiocca and A. Friedman
    A mathematical model of Brain tumor: pattern formation of glioma cells outside the tumor spheroid core
    J Theo BiolVol. 260 (2008) pp. 259-371 (Submitted)

    Abstract

  • G. Wright, S. Kottcamp and M. Thomson
    Generalization mediates sensitivity to complex odor features in the honeybee
    PLoS ONEVol. 3 No. 2 (2008)

    Abstract

  • L. Allen, B. Bolker, Y. Lou and A. Nevai
    Asymptotic profile of the steady states for an SIS epidemic reaction-diffusion model
    Discr. Cont. Dyn. Sys.Vol. 21 (2008) pp. 1-20

    Abstract

  • H. Lin, T. Zuo, C. Kuo, S. Liyanarachchi, S. Sun, R. Shen, D. Deatherage, D. Potter, L. Asamoto, S. Lin, P. Yan, A. Cheng, M. Ostrowski and T. Huang
    Breast cancer-associated fibroblasts confer AKT1-mediated epigenetic silencing of cystatin M in epithelial cells
    Cancer ResearchVol. 68 (2008) pp. 10257-10266

    Abstract

  • J. Zhou, S. Lin, V. Melfi and J. Verducci
    Composite microRNA predictions and comparisons of several prediction algorithms
    (2008) (Submitted)

    Abstract

  • W. Just and A. Nevai
    A Kolmogorov-type competition model with multiple coexistence states and its applications to plant competition for sunlight
    J. Math. Anal. Appl.Vol. 348 (2008) pp. 620-636

    Abstract

  • R. Laubenbacher and B. Stigler
    Design of Experiments and Biochemical Network Inference
    Algebraic and Geometric Methods in Statistics (2008)

    Abstract

  • M. Rempe, N. Spruston, W. Kath and D. Chopp
    Compartmental Neural Simulations with Spatial Adaptivity
    J Comp NeuroVol. 25 No. 3 (2008) pp. 465-480

    Abstract

  • B. Szomolay
    Analysis of a moving boundary value problem arising in biofilm modeling
    Math. Meth. Appl. Sc.Vol. 31 No. 15 (2008) pp. 1835-1859

    Abstract

  • M. Clendenning, L. Senter, H. Hampel, K. Robinson, S. Sun, D. Buchanan, M. Walsh, M. Nilbert, J. Green, J. Potter, A. Lindblom and A. De La Chapelle
    A frame-shift mutation of PMS2 is a widespread cause of Lynch syndrome
    Journal of Medical GeneticsVol. 45 (2008) pp. 340-345

    Abstract

  • P. Grajdeanu, R. Schugart, A. Friedman, C. Valentine and B. Rovin
    A mathematical model of venous neointimal hyperplasia
    Theoretical Biology and Medical ModellingVol. 5 (2008)

    Abstract

  • E. Green and A. Friedman
    The extensional flow of a thin sheet of incompressible, transversely isotropic fluid
    European Journal of Applied MathematicsVol. 19 No. 3 (2008) pp. 225-257

    Abstract

    Motivated by the aim of modelling the mechanical behaviour of biological gels (such as collagen gels) which have a fibrous microstructure, we consider the extensional flow of a thin two-dimensional film of incompressible, transversely isotropic viscous fluid. Neglecting inertia, and the effects of gravity and surface tension, leading-order equations are derived from a perturbation expansion of the full flow problem in powers of the (small) inverse aspect ratio. The existence and uniqueness of the solution of the reduced system of equations for small times is then proven. Special cases, in which the solution may be determined explicitly, are considered and we discuss the physical interpretation of the results.
  • B. Szomolay, I. Klapper and M. Dindos
    Analysis of Adaptive Response to Dosing Protocols for Biofilm Control
    in SIAM Appl. Math. (2008) (Under Review)

    Abstract

  • K. Robenack and P. Goel
    A combined observer and filter based approach for the determination of unknown parameters
    International Journal of Systems Science (2008)

    Abstract

  • E. Jung, E. Jung, S. Lim, S. Lee and W. Lee
    Computational models of valveless pumping using the immersed boundary method
    Computer Methods in Applied Mechanics and EngineeringVol. 197 No. Series 25-28 (2008) pp. 2329-2339

    Abstract

  • S. Lim, A. Ferent, X. Wang and C. Peskin
    dynamics of a closed rod with twist and bend in fluid
    SIAM Journal on Scientific ComputingVol. 31 No. 1 (2008) pp. 273-302

    Abstract

  • Y. Kim, S. Lim, S. Raman, O. Simonetti and A. Friedman
    Blood flow in a compliant vessel by the immersed boundary method
    Annals of Biomedical Engineering (2008) (Submitted)

    Abstract

  • I. Basawa, U. Bhat and J. Zhou
    Parameter estimation using partial information with applications to queueing and related models
    Statistics & Probability LettersVol. 78 No. 12 (2008) pp. 1349-1682

    Abstract

  • R. Zhao, A. Friedman, R. Schugart and C. Sen
    Wound angiogenesis as a function of tissue oxygen tension - a mathematical model
    PNAS USAVol. 105 (2008) pp. 2628-2633

    Abstract

  • M. Clendenning, M. Baze, S. Sun, K. Walsh, S. Liyanarachchi, D. Fix, V. Schumemann, I. Comeras, M. Deacon, J. Wenstrup, S. Thibodeau, H. Lynch, H. Hampel and A. De La Chapelle
    New haplotype and genealogical data give important implications for the origins and prevalence of the American Founder Mutation of MSH2
    Cancer ResearchVol. 68 No. 7 (2008) pp. 2145-2153

    Abstract

  • A. Friedman, J. Turner and B. Szomolay
    A model on the influence of age on immunity with Mycobacterium tuberculosis
    Exp. GerontolVol. 43 No. 4 (2008) pp. 275-285

    Abstract

  • S. Sun, D. Potter, P. Yan, T. Huang and S. Lin
    A quantile approach to analyzing differential methylation hybridization (DMH) microarrays
    Poster proceedings of the 4th International Symposium on Bioinformatics Research and Applications (ISBRA) (2008) pp. 87-90

    Abstract

  • B. Aguda, Y. Kim, M. Piper-Hunter, A. Friedman and C. Marsh
    MicroRNA Regulation of a Cancer Network: Consequences of the Feedback Loops Involving miR-17-92, E2F, and Myc
    PNASVol. 105 No. 50 (2008) pp. 19678-19683

    Abstract

  • G. Enciso
    On a Smale theorem and nonhomogeneous equilibria in cooperative systems
    Proceedings of the American Mathematical SocietyVol. 136 (2008) pp. 2901-2909

    Abstract

  • G. Enciso and E. Sontag
    Monotone Bifurcation Graphs
    Journal of Biological DynamicsVol. 2 (2008) pp. 121-139 (Submitted)

    Abstract

  • P. Grajdeanu, R. Schugart, A. Friedman, D. Birmingham, D. Birmingham and B. Rovin
    The dynamics of SLE nephritis under immunosuppressive therapy: A mathematical model
    (2008) (Submitted)

    Abstract

  • P. Grajdeanu, R. Schugart, A. Friedman, C. Valentine, A. Agarwal and B. Rovin
    A mathematical model of venous neointimal hyperplasia formation
    Theoretical Biology and Medical ModellingVol. 5 No. 2 (2008)

    Abstract

  • X. Liu, P. Srinivasan, E. Collard, P. Grajdeanu, J. Zweier and A. Friedman
    Nitric oxide diffusion rate is reduced in the aortic wall
    Biophysical JournalVol. 94 No. 5 (2008) pp. 1880-1889

    Abstract

  • P. Srinivasan, R. Muniyappa, T. Aougab, A. Sherman and M. Quon
    Endothelial dysfunction due to pathway-selective impairment of PI3K-dependent insulin signaling in vascular endothelium: Insights from Mathematical modeling
    68th Scientific Sessions, American Diabetes Association (2008)

    Abstract

  • J. Day, J. Rubin, Y. Vodovotz, C. Chow and G. Clermont
    Using nonlinear model predictive control to optimize inflammation-modulating therapy.
    (2008) (In Preparation)

    Abstract

  • P. Federico, D. Dimitrov and G. McCracken
    Bat Population Dynamics: Multi-level Model Based on Individuals' Energetics
    Math Biosciences and Engineering JournalVol. 5 No. 4 (2008) pp. 734-756

    Abstract

  • D. Janies and D. Pol
    Large-scale Phylogenetic Analysis of Emerging Infectious diseases
    Lecture Notes in Mathematics (Mathematical Biosciences SubseriesVol. 1922 (2008) pp. 39-76

    Abstract

  • K. Robenack and P. Goel
     A combined observer and filter based approach for the determination of unknown parameters
    International Journal of Systems Science (2008)

    Abstract

  • D. Janies, F. Habib, B. Alexandrov, A. Hill and D. Pol
    Evolution of genomes, host shifts, and the geographic spread of SARS-CoV and related coronaviruses
    CladisticsVol. 23 (2008) pp. 1-20

    Abstract

  • A. Sacan, H. Ferhatosmanoglu and H. Coskun
    CellTrack: an open-source software for cell tracking and motility analysis
    BioinformaticsVol. 24 No. 14 (2008) pp. 1647-1649

    Abstract

  • B. Aguda, Y. Kim, M. Piper-Hunter, A. Friedman and C. Marsh
    MicroRNA Regulation of a Cancer Network: Consequences of the Feedback Loops Involving miR-17-92, E2F, and Myc
    PNASVol. 105 No. 50 (2008) pp. 19678-19683

    Abstract

    The transcription factors E2F and Myc participate in the control of cell proliferation and apoptosis, and can act as oncogenes or tumor suppressors depending on their levels of expression. Positive feedback loops in the regulation of these factors are predicted-and recently shown experimentally-to lead to bistability, which is a phenomenon characterized by the existence of low and high protein levels ("off" and "on" levels, respectively), with sharp transitions between levels being inducible by, for example, changes in growth factor concentrations. E2F and Myc are inhibited at the posttranscriptional step by members of a cluster of microRNAs (miRs) called miR-17-92. In return, E2F and Myc induce the transcription of miR-17-92, thus forming a negative feedback loop in the interaction network. The consequences of the coupling between the E2F/Myc positive feedback loops and the E2F/Myc/miR-17-92 negative feedback loop are analyzed using a mathematical model. The model predicts that miR-17-92 plays a critical role in regulating the position of the off-on switch in E2F/Myc protein levels, and in determining the on levels of these proteins. The model also predicts large-amplitude protein oscillations that coexist with the off steady state levels. Using the concept and model prediction of a "cancer zone," the oncogenic and tumor suppressor properties of miR-17-92 is demonstrated to parallel the same properties of E2F and Myc.
  • P. Grajdeanu, R. Schugart, A. Friedman, C. Valentine, A. Agarwal and B. Rovin
    A mathematical model of venous neointimal hyperplasia formation
    Theoretical Biology and Medical ModellingVol. 5 No. 2 (2008)

    Abstract

    In hemodialysis patients, the most common cause of vascular access failure is neointimal hyperplasia of vascular smooth muscle cells at the venous anastomosis of arteriovenous fistulas and grafts. The release of growth factors due to surgical injury, oxidative stress and turbulent flow has been suggested as a possible mechanism for neointimal hyperplasia.
    In this work, we construct a mathematical model which analyzes the role that growth factors might play in the stenosis at the venous anastomosis. The model consists of a system of partial differential equations describing the influence of oxidative stress and turbulent flow on growth factors, the interaction among growth factors, smooth muscle cells, and extracellular matrix, and the subsequent effect on the stenosis at the venous anastomosis, which, in turn, affects the level of oxidative stress and degree of turbulent flow. Computer simulations suggest that our model can be used to predict access stenosis as a function of the initial concentration of the growth factors inside the intimal-luminal space.
    The proposed model describes the formation of venous neointimal hyperplasia, based on pathogenic mechanisms. The results suggest that interventions aimed at specific growth factors may be successful in prolonging the life of the vascular access, while reducing the costs of vascular access maintenance. The model may also provide indication of when invasive access surveillance to repair stenosis should be undertaken.
  • E. Jung, S. Lim, S. Lee and W. Lee
    Computational models of valveless pumping using the immersed boundary method
    Computer Methods in Applied Mechanics and EngineeringVol. 197 No. Series 25-28 (2008) pp. 2329-2339

    Abstract

    Mathematical models of valveless pumping can be represented by either a closed loop system or an open tube system. In this paper, we present a three-dimensional model of valveless pumping in a closed loop system. We also present a two-dimensional model using an open elastic cylinder contained in a rigid tank. In both models, we take the periodic compress-and-release action at the asymmetric location of the soft tube and observe the existence of a net flow and the important features of valveless pumping that have been reported in the previous models or experiments. The innovative idea of this work is that we explain the existence of a net flow by introducing the concept of the signed area of the flow-pressure loop over one cycle, which represents the power in the system. The direction and the magnitude of a net flow can also be explained by the sign and the amount of power, which is work done on the fluid by the fluid pressure and the elastic wall over one period, respectively.
  • S. Lim, A. Ferent, X. Wang and C. Peskin
    Dynamics of a closed rod with twist and bend in fluid
    SIAM Journal on Scientific ComputingVol. 31 No. 1 (2008) pp. 273-302

    Abstract

    We investigate the instability and subsequent dynamics of a closed rod with twist and bend in a viscous, incompressible fluid. A new version of the immersed boundary (IB) method is used in which the immersed boundary applies torque as well as force to the surrounding fluid and in which the equations of motion of the immersed boundary involve the local angular velocity as well as the local linear velocity of the fluid. An important feature of the IB method in this context is that self-crossing of the rod is automatically avoided because the rod moves in a continuous (interpolated) velocity field. A rod with a uniformly distributed twist that has been slightly perturbed away from its circular equilibrium configuration is used as an initial condition, with the fluid initially at rest. If the twist in the rod is sufficiently small, the rod simply returns to its circular equilibrium configuration, but for larger twists that equilibrium configuration becomes unstable, and the rod undergoes large excursions before relaxing to a stable coiled configuration.
  • X. Liu, P. Srinivasan, E. Collard, P. Grajdeanu, J. Zweier and A. Friedman
    Nitric Oxide Diffusion Rate is Reduced in the Aortic Wall
    Biophysical JournalVol. 94 No. 5 (2008) pp. 1880-1889q

    Abstract

    Endogenous nitric oxide (NO) plays important physiological roles in the body. As a small diatomic molecule, NO has been assumed to freely diffuse in tissues with a diffusion rate similar to that in water. However, this assumption has not been tested experimentally. In this study, a modified Clark-type NO electrode attached with a customized aorta holder was used to directly measure the flux of NO diffusion across the aortic wall at 37°C. Experiments were carefully designed for accurate measurements of the apparent NO diffusion coefficient D and the partition coefficient α in the aortic wall. A mathematical model was presented for analyzing experimental data. It was determined that α = 1.15 ± 0.11 and D = 848 ± 45 μm2/s (n = 12). The NO diffusion coefficient in the aortic wall is nearly fourfold smaller than the reported diffusion coefficient in solution at 37°C, indicating that NO diffusion in the vascular wall is no longer free, but markedly dependent on the environment in the tissue where these NO molecules are. These results imply that the NO diffusion rate in the vascular wall may be upregulated and downregulated by certain physiological and/or pathophysiological processes affecting the composition of tissues.
  • D. Schmidt and R. Durrett
    Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution
    GeneticsVol. 180 (2008) pp. 1501-1509

    Abstract

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