Imaging and biophysical modelling of thrombogenic mechanisms in atrial fibrillation and stroke

Atrial fibrillation (AF) underlies almost one third of all ischaemic strokes, with the left atrial appendage (LAA) identified as the primary thromboembolic source. Current stroke risk stratification approaches, such as the CHA2DS2-VASc score, rely mostly on clinical comorbidities, rather than thrombogenic mechanisms such as blood stasis, hypercoagulability and endothelial dysfunction—known as Virchow’s triad. While detection of AF-related thrombi is possible using established cardiac imaging techniques, such as transoesophageal echocardiography, there is a growing need to reliably assess AF-patient thrombogenicity prior to thrombus formation. Over the past decade, cardiac imaging and image-based biophysical modelling have emerged as powerful tools for reproducing the mechanisms of thrombogenesis. Clinical imaging modalities such as cardiac computed tomography, magnetic resonance and echocardiographic techniques can measure blood flow velocities and identify LA fibrosis (an indicator of endothelial dysfunction), but imaging remains limited in its ability to assess blood coagulation dynamics. In-silico cardiac modelling tools—such as computational fluid dynamics for blood flow, reaction-diffusion-convection equations to mimic the coagulation cascade, and surrogate flow metrics associated with endothelial damage—have grown in prevalence and advanced mechanistic understanding of thrombogenesis. However, neither technique alone can fully elucidate thrombogenicity in AF. In future, combining cardiac imaging with in-silico modelling and integrating machine learning approaches for rapid results directly from imaging data will require development under a rigorous framework of verification and clinical validation, but may pave the way towards enhanced personalised stroke risk stratification in the growing population of AF patients. This Review will focus on the significant progress in these fields

In Silico Modeling of Shear-Stress-Induced Nitric Oxide Production in Endothelial Cells through Systems Biology

Nitric oxide (NO) produced by vascular endothelial cells is a potent vasodilator and an antiinflammatory mediator. Regulating production of endothelial-derived NO is a complex undertaking, involving multiple signaling and genetic pathways that are activated by diverse humoral and biomechanical stimuli. To gain a thorough understanding of the rich diversity of responses observed experimentally, it is necessary to account for an ensemble of these pathways acting simultaneously. In this article, we have assembled four quantitative molecular pathways previously proposed for shear-stress-induced NO production. In these pathways, endothelial NO synthase is activated 1), via calcium release, 2), via phosphorylation reactions, and 3), via enhanced protein expression. To these activation pathways, we have added a fourth, a pathway describing actual NO production from endothelial NO synthase and its various protein partners. These pathways were combined and simulated using CytoSolve, a computational environment for combining independent pathway calculations. The integrated model is able to describe the experimentally observed change in NO production with time after the application of fluid shear stress. This model can also be used to predict the specific effects on the system after interventional pharmacological or genetic changes. Importantly, this model reflects the up-to-date understanding of the NO system, providing a platform upon which information can be aggregated in an additive way.National Institutes of Health (U.S.) (Grant R01HL090856)Singapore-MIT Alliance Computational and Systems Biology Progra

Generalized super-resolution 4D Flow MRI \unicode{x2013} using ensemble learning to extend across the cardiovascular system

4D Flow Magnetic Resonance Imaging (4D Flow MRI) is a non-invasive measurement technique capable of quantifying blood flow across the cardiovascular system. While practical use is limited by spatial resolution and image noise, incorporation of trained super-resolution (SR) networks has potential to enhance image quality post-scan. However, these efforts have predominantly been restricted to narrowly defined cardiovascular domains, with limited exploration of how SR performance extends across the cardiovascular system; a task aggravated by contrasting hemodynamic conditions apparent across the cardiovasculature. The aim of our study was to explore the generalizability of SR 4D Flow MRI using a combination of heterogeneous training sets and dedicated ensemble learning. With synthetic training data generated across three disparate domains (cardiac, aortic, cerebrovascular), varying convolutional base and ensemble learners were evaluated as a function of domain and architecture, quantifying performance on both in-silico and acquired in-vivo data from the same three domains. Results show that both bagging and stacking ensembling enhance SR performance across domains, accurately predicting high-resolution velocities from low-resolution input data in-silico. Likewise, optimized networks successfully recover native resolution velocities from downsampled in-vivo data, as well as show qualitative potential in generating denoised SR-images from clinical level input data. In conclusion, our work presents a viable approach for generalized SR 4D Flow MRI, with ensemble learning extending utility across various clinical areas of interest.Comment: 10 pages, 5 figure

Non-invasive pressure difference estimation from PC-MRI using the work-energy equation

Pressure difference is an accepted clinical biomarker for cardiovascular disease conditions such as aortic coarctation. Currently, measurements of pressure differences in the clinic rely on invasive techniques (catheterization), prompting development of non-invasive estimates based on blood flow. In this work, we propose a non-invasive estimation procedure deriving pressure difference from the work-energy equation for a Newtonian fluid. Spatial and temporal convergence is demonstrated on in silico Phase Contrast Magnetic Resonance Image (PC-MRI) phantoms with steady and transient flow fields. The method is also tested on an image dataset generated in silico from a 3D patient-specific Computational Fluid Dynamics (CFD) simulation and finally evaluated on a cohort of 9 subjects. The performance is compared to existing approaches based on steady and unsteady Bernoulli formulations as well as the pressure Poisson equation. The new technique shows good accuracy, robustness to noise, and robustness to the image segmentation process, illustrating the potential of this approach for non-invasive pressure difference estimation

A displacement-based finite element formulation for incompressible and nearly-incompressible cardiac mechanics

AbstractThe Lagrange Multiplier (LM) and penalty methods are commonly used to enforce incompressibility and compressibility in models of cardiac mechanics. In this paper we show how both formulations may be equivalently thought of as a weakly penalized system derived from the statically condensed Perturbed Lagrangian formulation, which may be directly discretized maintaining the simplicity of penalty formulations with the convergence characteristics of LM techniques. A modified Shamanskii–Newton–Raphson scheme is introduced to enhance the nonlinear convergence of the weakly penalized system and, exploiting its equivalence, modifications are developed for the penalty form. Focusing on accuracy, we proceed to study the convergence behavior of these approaches using different interpolation schemes for both a simple test problem and more complex models of cardiac mechanics. Our results illustrate the well-known influence of locking phenomena on the penalty approach (particularly for lower order schemes) and its effect on accuracy for whole-cycle mechanics. Additionally, we verify that direct discretization of the weakly penalized form produces similar convergence behavior to mixed formulations while avoiding the use of an additional variable. Combining a simple structure which allows the solution of computationally challenging problems with good convergence characteristics, the weakly penalized form provides an accurate and efficient alternative to incompressibility and compressibility in cardiac mechanics

An efficient and accurate method for modeling nonlinear fractional viscoelastic biomaterials

Computational biomechanics plays an important role in biomedical engineering: using modeling to understand pathophysiology, treatment and device design. While experimental evidence indicates that the mechanical response of most tissues is viscoelastic, current biomechanical models in the computational community often assume hyperelastic material models. Fractional viscoelastic constitutive models have been successfully used in literature to capture viscoelastic material response; however, the translation of these models into computational platforms remains limited. Many experimentally derived viscoelastic constitutive models are not suitable for three-dimensional simulations. Furthermore, the use of fractional derivatives can be computationally prohibitive, with a number of current numerical approximations having a computational cost that is [Formula: see text] and a storage cost that is (N(T)) (N(T) denotes the number of time steps). In this paper, we present a novel numerical approximation to the Caputo derivative which exploits a recurrence relation similar to those used to discretize classic temporal derivatives, giving a computational cost that is (N(T)) and a storage cost that is fixed over time. The approximation is optimized for numerical applications, and an error estimate is presented to demonstrate the efficacy of the method. The method, integrated into a finite element solid mechanics framework, is shown to be unconditionally stable in the linear viscoelastic case. It was then integrated into a computational biomechanical framework, with several numerical examples verifying the accuracy and computational efficiency of the method, including in an analytic test, in an analytic fractional differential equation, as well as in a computational biomechanical model problem

Non-invasive estimation of relative pressure in turbulent flow using virtual work-energy

Vascular pressure differences are established risk markers for a number of cardiovascular diseases. Relative pressures are, however, often driven by turbulence-induced flow fluctuations, where conventional non-invasive methods may yield inaccurate results. Recently, we proposed a novel method for non-turbulent flows, nu WERP, utilizing the concept of virtual work-energy to accurately probe relative pressure through complex branching vasculature. Here, we present an extension of this approach for turbulent flows: nu WERP-t. We present a theoretical method derivation based on flow covariance, quantifying the impact of flow fluctuations on relative pressure. nu WERP-t is tested on a set of in-vitro stenotic flow phantoms with data acquired by 4D flow MRI with six-directional flow encoding, as well as on a patientspecific in-silico model of an acute aortic dissection. Over all tests nu WERP-t shows improved accuracy over alternative energy-based approaches, with excellent recovery of estimated relative pressures. In particular, the use of a guaranteed divergence-free virtual field improves accuracy in cases where turbulent flows skew the apparent divergence of the acquired field. With the original nu WERP allowing for assessment of relative pressure into previously inaccessible vasculatures, the extended nu WERP-t further enlarges the methods clinical scope, underlining its potential as a novel tool for assessing relative pressure in-vivo. (C) 2019 The Authors. Published by Elsevier B.V.Funding Agencies|Hans Werthen foundation of the Royal Academy of Engineering Sciences; Galostiftelsen; Erik and Edith Fernstrom Foundation for Medical Research; Basic Science Research Program through the National Research Foundation of Korea (NRF) - Ministry of Education [2018R1D1A1A02043249]; Kangwon National University [D1001679-01-01]; European Unions Horizon 2020 research and Innovation programme under the Marie Sklodowska-Curie grant [764739]; Engineering and Physical Sciences Research CouncilUK Research &amp; Innovation (UKRI)Engineering &amp; Physical Sciences Research Council (EPSRC) [EP/N011554/1, EP/R003866/1]; Wellcome TrustWellcome TrustEuropean Commission [209450/Z/17/Z]; Swedish Research CouncilSwedish Research CouncilEuropean Commission [2018-04454]; Swedish Heart-Lung FoundationSwedish Heart-Lung Foundation [2018-0657]; Wellcome ESPRC Centre for Medical Engineering at Kings College LondonUK Research &amp; Innovation (UKRI)Engineering &amp; Physical Sciences Research Council (EPSRC) [WT 203148/Z/16/Z]; British Heart FoundationBritish Heart Foundation [TG/17/3/33406]</p