A simultaneous solution procedure for fully coupled fluid flows with structural interactions

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1999.Includes bibliographical references (p. 85-88).by Sandra Rugonyi.S.M

Characterization of the dynamic response of continuous system discretized using finite element methods

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2001.Includes bibliographical references (leaves 122-125).Nonlinear dynamic physical systems exhibit a rich variety of behaviors. In many cases, the system response is unstable, and the behavior may become unpredictable. Since an unstable or unpredictable response is usually undesirable in engineering practice, the stability characterization of a system's behavior becomes essential. In this work, a numerical procedure to characterize the dynamic stability of continuous solid media, discretized using finite element methods, is proposed. The procedure is based on the calculation of the maximum Lyapunov characteristic exponent (LCE), which provides information about the asymptotic stability of the system response. The LCE is a measure of the average divergence or convergence of nearby trajectories in the system phase space, and a positive LCE indicates that the system asymptotic behavior is chaotic, or, in other words, asymptotically dynamically unstable. In addition, a local temporal stability indicator is proposed to reveal the presence of local dynamic instabilities in the response. Using the local stability indicator, dynamic instabilities can be captured shortly after they occur in a numerical calculation. The indicator can be obtained from the successive approximations of the response LCE calculated at each discretized time step. Both procedures can also be applied to fluid-structure interaction problems in which the analysis focuses on the behavior of the structural part.(cont.) The response of illustrative structural systems and fluid flow-structure interaction systems, in which the fluid is modeled using the Navier-Stokes equations, was calculated. The systems considered present both stable and unstable behaviors, and their LCEs and local stability indicators were computed using the proposed procedures. The stability of the complex behaviors exhibited by the problems considered was properly captured by both approaches, confirming the validity of the procedures proposed in this work.by Sandra Rugonyi.Ph.D

4-D Computational Modeling of Cardiac Outflow Tract Hemodynamics over Looping Developmental Stages in Chicken Embryos

Cardiogenesis is interdependent with blood flow within the embryonic system. Recently, a number of studies have begun to elucidate the effects of hemodynamic forces acting upon and within cells as the cardiovascular system begins to develop. Changes in flow are picked up by mechanosensors in endocardial cells exposed to wall shear stress (the tangential force exerted by blood flow) and by myocardial and mesenchymal cells exposed to cyclic strain (deformation). Mechanosensors stimulate a variety of mechanotransduction pathways which elicit functional cellular responses in order to coordinate the structural development of the heart and cardiovascular system. The looping stages of heart development are critical to normal cardiac morphogenesis and have previously been shown to be extremely sensitive to experimental perturbations in flow, with transient exposure to altered flow dynamics causing severe late stage cardiac defects in animal models. This paper seeks to expand on past research and to begin establishing a detailed baseline for normal hemodynamic conditions in the chick outflow tract during these critical looping stages. Specifically, we will use 4-D (3-D over time) optical coherence tomography to create in vivo geometries for computational fluid dynamics simulations of the cardiac cycle, enabling us to study in great detail 4-D velocity patterns and heterogeneous wall shear stress distributions on the outflow tract endocardium. This information will be useful in determining the normal variation of hemodynamic patterns as well as in mapping hemodynamics to developmental processes such as morphological changes and signaling events during and after the looping stages examined here

Few-shot hypercolumn-based mitochondria segmentation in cardiac and outer hair cells in focused ion beam-scanning electron microscopy (FIB-SEM) data

We present a novel AI-based approach to the few-shot automated segmentation of mitochondria in large-scale electron microscopy images. Our framework leverages convolutional features from a pre-trained deep multilayer convolutional neural network, such as VGG-16. We then train a binary gradient boosting classifier on the resulting high-dimensional feature hypercolumns. We extract VGG-16 features from the first four convolutional blocks and apply bilinear upsampling to resize the obtained maps to the input image size. This procedure yields a 2688-dimensional feature hypercolumn for each pixel in a 224 x 224 input image. We then apply L1-regularized logistic regression for supervised active feature selection to reduce dependencies among the features, to reduce overfitting, as well as to speed-up gradient boosting-based training. During inference we block process 1728 x 2022 large microscopy images. Our experiments show that in such a formulation of transfer learning our processing pipeline is able to achieve high-accuracy results on very challenging datasets containing a large number of irregularly shaped mitochondria in cardiac and outer hair cells. Our proposed few-shot training approach gives competitive performance with the state-of-the-art using far less training data

Transient Increase in VEGF-A Leads to Cardiac Tube Anomalies and Increased Risk of Congenital Heart Malformations.

Vascular Endothelial Growth Factor (VEGF) plays a critical role during early heart development. Clinical evidence shows that conditions associated with changes in VEGF signaling in utero are correlated with an increased risk of congenital heart defects (CHD) in newborns. However, how malformations develop after abnormal VEGF exposure is unknown. During embryogenesis, a primitive heart, consisting of an endocardial tube enveloped by a myocardial mantle, is the first organ to function. This tubular heart ultimately transforms into a four-chambered heart. To determine how a transient increase in VEGF prior to heart tube formation affects heart development leading to CHD, we applied exogenous VEGF or a control (vehicle) solution to quail embryos in ovo at Hamburger-Hamilton (HH) stage 8 (28-30 hrs of incubation), right before heart tube formation. Light microscopy analysis of embryos re-incubated after treatment for 13 hrs (to approximately HH11/HH12) showed that increased VEGF leads to impaired heart tube elongation accompanied by diameter expansion. Micro-CT analysis of embryos re-incubated for 9 days (to approximately HH38), when the heart is fully formed, showed that VEGF treatment increased the rate of cardiac malformations in surviving embryos. However, despite no sex differences in survival, female embryos were more likely to develop cardiac malformations. Our results further suggest that heart tube malformations after a transient increase in VEGF right before heart tube formation may be reversible, leading to normal hearts. This article is protected by copyright. All rights reserved

Visualization of chicken embryo heart motion

<p>We present a geometric surface parameterisation algorithm and multiple visualisation techniques (cross-sectional area and shape change, peristaltic motion, stress/strain, volume change, surface curvature change several visualisation techniques) adapted to the problem of understanding the 4D peristaltic-like motion of the outflow tract (OFT) in an embryonic chick heart. We illustrated the techniques using data from hearts under normal conditions (four embryos), and hearts in which blood flow conditions are altered through OFT banding (four embryos). The overall goal is to create quantitative measures of the temporal heart shape change both within a single subject and between multiple subjects. These measures will help elucidate how altering hemodynamic conditions changes the shape and motion of the OFT walls, which in turn influence the stresses and strains on the developing heart, causing it to develop differently. We take advantage of the tubular shape and periodic motion of the OFT to produce successively lower dimensional visualisations of the cardiac motion (e.g. curvature, volume and cross section) over time, and quantifications of such visualisations. These visualisations enable a more fine-grained understanding of how the contraction wave moves through the OFT and the cross-sectional shape change that accompanies it.</p