Coupled agent-based and finite-element models for predicting scar structure following myocardial infarction

Pre-Processing techniques and artificial intelligence algorithms for electrocardiogram (ECG) signals analysis: A comprehensive review

Electrocardiogram (ECG) are the physiological signals and a standard test to measure the heart's electrical activity that depicts the movement of cardiac muscles. A review study has been conducted on ECG signals analysis with the help of artificial intelligence (AI) methods over the last ten years i.e., 2012-22. Primarily, the method of ECG analysis by software systems was divided into classical signal processing (e.g. spectrograms or filters), machine learning (ML) and deep learning (DL), including recursive models, transformers and hybrid. Secondly, the data sources and benchmark datasets were depicted. Authors grouped resources by ECG acquisition methods into hospital-based portable machines and wearable devices. Authors also included new trends like advanced pre-processing, data augmentation, simulations and agent-based modeling. The study found improvement in ECG examination perfection made each year through ML, DL, hybrid models, and transformers. Convolutional neural networks and hybrid models were more targeted and proved efficient. The transformer model extended the accuracy from 90% to 98%. The Physio-Net library helps acquire ECG signals, including the popular benchmark databases such as MIT-BIH, PTB, and challenging datasets. Similarly, wearable devices have been established as a appropriate option for monitoring patient health without the time and place limitations and are also helpful for AI model calibration with so far accuracy of 82%-83% on Samsung smartwatch. In the pre-processing signals, spectrogram generation through Fourier and wavelet transformations are erected leading approaches promoting on average accuracy of 90%-95%. Likewise, data enhancement using geometrical techniques is well-considered; however, extraction and concatenation-based methods need attention. As the what-if analysis in healthcare or cardiac issues can be performed using a complex simulation, the study reviews agent-based modeling and simulation approaches for cardiovascular risk event assessment.

Bioengineering and the cervix: The past, current, and future for addressing preterm birth

The uterine cervix plays two important but opposing roles during pregnancy - as a mechanical barrier that maintains the fetus for nine months and as a compliant structure that dilates to allow for the delivery of a baby. In some pregnancies, however, the cervix softens and dilates prematurely, leading to preterm birth. Bioengineers have addressed and continue to address the lack of reduction in preterm birth rates by developing novel technologies to diagnose, prevent, and understand premature cervical remodeling. This article highlights these existing and emerging technologies and concludes with open areas of research related to the cervix and preterm birth that bioengineers are currently well-positioned to address.

Vaginal Fibroblast Behavior as a Function of Stiffness Changes in a Polyisocyanide Hydrogel for Prolapse Repair

There is an urgent need for improved outcomes in the treatment of pelvic organ prolapse (POP). Success of primary surgery relies on the load bearing capacity of plicated connective tissue underneath the vaginal wall, which is compromised due to an altered vaginal fibroblast function and collagen composition. There is an important factor in connective tissue repair that relates to changes in stiffness of the vaginal fibroblast microenvironment, which influences cell activity through cellular mechanosensing. The aim of this study is to investigate the effect of stiffness changes on vaginal fibroblast functions that relate to connective tissue healing in prolapse repair. The substrate stiffness was controlled by changing the polymer concentration in the fibrous and strongly biomimetic polyisocyanide (PIC) hydrogel. We analyzed stiffness during cell culture and assessed the consequential fibroblast proliferation, morphology, collagen deposition, and contraction. Our results show that increasing stiffness coincides with vaginal fibroblast alignment, promotes collagen deposition, and inhibits PIC gel contraction. These findings suggest that the matrix stiffness directly influences vaginal fibroblast functionality. Moreover, we observed a buildup in stiffness and collagen, with an enhanced fibroblast and collagen organization on the PIC-substrate, which indicate an enhanced structural integrity of the hydrogel-cell construct. An improved tissue structure during healing is relevant in the functional repair of POP. Therefore, this study encourages future research in the use of PIC gels as a supplement in prolapse surgery, whereby the hydrogel stiffness should be considered.

An agent-based model of tissue maintenance and self-repair

We hypothesized that a system that possesses the capacity for ongoing maintenance of its tissues will necessarily also have the capacity to self-heal following a perturbation. We used an agent-based model of tissue maintenance to investigate this idea, and in particular to determine the extent to which the current state of the tissue must influence cell behavior in order for tissue maintenance and self-healing to be stable. We show that a mean level of tissue density is robustly maintained when catabolic agents digest tissue at a rate proportional to local tissue density, but that the spatial heterogeneity of the tissue at homeostasis increases with the rate at which tissue is digested. The rate of self-healing is also increased by increasing either the amount of tissue removed or deposited at each time step by catabolic or anabolic agents, respectively, and by increasing the density of both agent types on the tissue. We also found that tissue maintenance and self-healing are stable with an alternate rule in which cells move preferentially to tissue regions of low density. The most basic form of self-healing can thus be achieved with cells that follow very simple rules of behavior, provided these rules are based in some way on the current state of the local tissue. Straightforward mechanisms can accelerate the rate of self-healing, as might be beneficial to the organism.

Mechano-biological and bio-mechanical pathways in cutaneous wound healing

Injuries to the skin heal through coordinated action of fibroblast-mediated extracellular matrix (ECM) deposition, ECM remodeling, and wound contraction. Defects involving the dermis result in fibrotic scars featuring increased stiffness and altered collagen content and organization. Although computational models are crucial to unravel the underlying biochemical and biophysical mechanisms, simulations of the evolving wound biomechanics are seldom benchmarked against measurements. Here, we leverage recent quantifications of local tissue stiffness in murine wounds to refine a previously-proposed systems-mechanobiological finite-element model. Fibroblasts are considered as the main cell type involved in ECM remodeling and wound contraction. Tissue rebuilding is coordinated by the release and diffusion of a cytokine wave, e.g. TGF-β, itself developed in response to an earlier inflammatory signal triggered by platelet aggregation. We calibrate a model of the evolving wound biomechanics through a custom-developed hierarchical Bayesian inverse analysis procedure. Further calibration is based on published biochemical and morphological murine wound healing data over a 21-day healing period. The calibrated model recapitulates the temporal evolution of: inflammatory signal, fibroblast infiltration, collagen buildup, and wound contraction. Moreover, it enables in silico hypothesis testing, which we explore by: (i) quantifying the alteration of wound contraction profiles corresponding to the measured variability in local wound stiffness; (ii) proposing alternative constitutive links connecting the dynamics of the biochemical fields to the evolving mechanical properties; (iii) discussing the plausibility of a stretch- vs. stiffness-mediated mechanobiological coupling. Ultimately, our model challenges the current understanding of wound biomechanics and mechanobiology, beside offering a versatile tool to explore and eventually control scar fibrosis after injury.

Tropoelastin Improves Post-Infarct Cardiac Function

BACKGROUND

Myocardial infarction (MI) is among the leading causes of death worldwide. Following MI, necrotic cardiomyocytes are replaced by a stiff collagen-rich scar. Compared to collagen, the extracellular matrix protein elastin has high elasticity and may have more favorable properties within the cardiac scar. We sought to improve post-MI healing by introducing tropoelastin, the soluble subunit of elastin, to alter scar mechanics early after MI.

METHODS AND RESULTS

We developed an ultrasound-guided direct intramyocardial injection method to administer tropoelastin directly into the left ventricular anterior wall of rats subjected to induced MI. Experimental groups included shams and infarcted rats injected with either PBS vehicle control or tropoelastin. Compared to vehicle treated controls, echocardiography assessments showed tropoelastin significantly improved left ventricular ejection fraction (64.7±4.4% versus 46.0±3.1% control) and reduced left ventricular dyssynchrony (11.4±3.5 ms versus 31.1±5.8 ms control) 28 days post-MI. Additionally, tropoelastin reduced post-MI scar size (8.9±1.5% versus 20.9±2.7% control) and increased scar elastin (22±5.8% versus 6.2±1.5% control) as determined by histological assessments. RNA sequencing (RNAseq) analyses of rat infarcts showed that tropoelastin injection increased genes associated with elastic fiber formation 7 days post-MI and reduced genes associated with immune response 11 days post-MI. To show translational relevance, we performed immunohistochemical analyses on human ischemic heart disease cardiac samples and showed an increase in tropoelastin within fibrotic areas. Using RNA-seq we also demonstrated the tropoelastin gene ELN is upregulated in human ischemic heart disease and during human cardiac fibroblast-myofibroblast differentiation. Furthermore, we showed by immunocytochemistry that human cardiac fibroblast synthesize increased elastin in direct response to tropoelastin treatment.

CONCLUSIONS

We demonstrate for the first time that purified human tropoelastin can significantly repair the infarcted heart in a rodent model of MI and that human cardiac fibroblast synthesize elastin. Since human cardiac fibroblasts are primarily responsible for post-MI scar synthesis, our findings suggest exciting future clinical translation options designed to therapeutically manipulate this synthesis.

MicroRNAs in Mechanical Homeostasis

Mechanical variables such as stiffness, stress, strain, and fluid shear stress are central to tissue functions, thus, must be maintained within the proper range. Mechanics are especially important in the cardiovascular system and lung, the functions of which are essentially mechanical. Mechanical homeostasis is characterized by negative feedback in which deviations from the optimal value or set point activates mechanisms to return the system to the correct range. In chronic diseases, homeostatic mechanisms are generally overcome or replaced with positive feedback loops that promote disease progression. Recent work has shown that microRNAs (miRNAs) are essential to mechanical homeostasis in a number of biological systems and that perturbations to miRNA biogenesis play key roles in cardiovascular and pulmonary diseases. In this review, we integrate current knowledge of miRNAs in mechanical homeostasis and how these mechanisms are altered in disease.

A Lumped Two-Compartment Model for Simulation of Ventricular Pump and Tissue Mechanics in Ischemic Heart Disease

Introduction: Computational modeling of cardiac mechanics and hemodynamics in ischemic heart disease (IHD) is important for a better understanding of the complex relations between ischemia-induced heterogeneity of myocardial tissue properties, regional tissue mechanics, and hemodynamic pump function. We validated and applied a lumped two-compartment modeling approach for IHD integrated into the CircAdapt model of the human heart and circulation.

Methods: Ischemic contractile dysfunction was simulated by subdividing a left ventricular (LV) wall segment into a hypothetical contractile and noncontractile compartment, and dysfunction severity was determined by the noncontractile volume fraction (NCVF). Myocardial stiffness was determined by the zero-passive stress length (Ls0,pas) and nonlinearity (kECM) of the passive stress-sarcomere length relation of the noncontractile compartment. Simulated end-systolic pressure volume relations (ESPVRs) for 20% acute ischemia were qualitatively compared between a two- and one-compartment simulation, and parameters of the two-compartment model were tuned to previously published canine data of regional myocardial deformation during acute and prolonged ischemia and reperfusion. In six patients with myocardial infarction (MI), the NCVF was automatically estimated using the echocardiographic LV strain and volume measurements obtained acutely and 6 months after MI. Estimated segmental NCVF values at the baseline and 6-month follow-up were compared with percentage late gadolinium enhancement (LGE) at 6-month follow-up.

Results: Simulation of 20% of NCVF shifted the ESPVR rightward while moderately reducing the slope, while a one-compartment simulation caused a leftward shift with severe reduction in the slope. Through tuning of the NCVF, Ls0,pas, and kECM, it was found that manipulation of the NCVF alone reproduced the deformation during acute ischemia and reperfusion, while additional manipulations of Ls0,pas and kECM were required to reproduce deformation during prolonged ischemia and reperfusion. Out of all segments with LGE>25% at the follow-up, the majority (68%) had higher estimated NCVF at the baseline than at the follow-up. Furthermore, the baseline NCVF correlated better with percentage LGE than NCVF did at the follow-up.

Conclusion: We successfully used a two-compartment model for simulation of the ventricular pump and tissue mechanics in IHD. Patient-specific optimizations using regional myocardial deformation estimated the NCVF in a small cohort of MI patients in the acute and chronic phase after MI, while estimated NCVF values closely approximated the extent of the myocardial scar at the follow-up. In future studies, this approach can facilitate deformation imaging–based estimation of myocardial tissue properties in patients with cardiovascular diseases.

Multiscale Computational Modeling of Vascular Adaptation: A Systems Biology Approach Using Agent-Based Models

The widespread incidence of cardiovascular diseases and associated mortality and morbidity, along with the advent of powerful computational resources, have fostered an extensive research in computational modeling of vascular pathophysiology field and promoted in-silico models as a support for biomedical research. Given the multiscale nature of biological systems, the integration of phenomena at different spatial and temporal scales has emerged to be essential in capturing mechanobiological mechanisms underlying vascular adaptation processes. In this regard, agent-based models have demonstrated to successfully embed the systems biology principles and capture the emergent behavior of cellular systems under different pathophysiological conditions. Furthermore, through their modular structure, agent-based models are suitable to be integrated with continuum-based models within a multiscale framework that can link the molecular pathways to the cell and tissue levels. This can allow improving existing therapies and/or developing new therapeutic strategies. The present review examines the multiscale computational frameworks of vascular adaptation with an emphasis on the integration of agent-based approaches with continuum models to describe vascular pathophysiology in a systems biology perspective. The state-of-the-art highlights the current gaps and limitations in the field, thus shedding light on new areas to be explored that may become the future research focus. The inclusion of molecular intracellular pathways (e.g., genomics or proteomics) within the multiscale agent-based modeling frameworks will certainly provide a great contribution to the promising personalized medicine. Efforts will be also needed to address the challenges encountered for the verification, uncertainty quantification, calibration and validation of these multiscale frameworks.

A Comparison of Fiber Based Material Laws for Myocardial Scar

The mechanics of most soft tissues in the human body are determined by the organization of their collagen fibers. Predicting how mechanics will change during growth and remodeling of those tissues requires constitutive laws that account for the density and dispersion of collagen fibers. Post-infarction scar in the heart, a mechanically and structurally complex material, does not yet have a validated fiber-based constitutive model. In this study, we tested four different constitutive laws employing exponential or polynomial strain-energy functions and accounting for either mean fiber orientation alone or the details of the fiber distribution about that mean. We quantified the goodness of fit of each law to mechanical testing data from 6-week-old myocardial scar in the rat using both sum of squared error (SSE) and the Akaike Information Criterion (AIC) to account for differences in the number of material parameters within the constitutive laws. We then compared their ability to prospectively predict the mechanics of independent myocardial scar samples from other time points during healing. Our analysis suggests that a constitutive law with a polynomial form that incorporates detailed information about collagen fiber distribution using a structure tensor provides excellent fits with just two parameters and reasonable predictions of myocardial scar mechanics from measured structure alone in scars containing sufficiently high collagen content.

Notch in mechanotransduction - from molecular mechanosensitivity to tissue mechanostasis

Tissue development and homeostasis are controlled by mechanical cues. Perturbation of the mechanical equilibrium triggers restoration of mechanostasis through changes in cell behavior, while defects in these restorative mechanisms lead to mechanopathologies, for example, osteoporosis, myopathies, fibrosis or cardiovascular disease. Therefore, sensing mechanical cues and integrating them with the biomolecular cell fate machinery is essential for the maintenance of health. The Notch signaling pathway regulates cell and tissue fate in nearly all tissues. Notch activation is directly and indirectly mechanosensitive, and regulation of Notch signaling, and consequently cell fate, is integral to the cellular response to mechanical cues. Fully understanding the dynamic relationship between molecular signaling, tissue mechanics and tissue remodeling is challenging. To address this challenge, engineered microtissues and computational models play an increasingly large role. In this Review, we propose that Notch takes on the role of a 'mechanostat', maintaining the mechanical equilibrium of tissues. We discuss the reciprocal role of Notch in the regulation of tissue mechanics, with an emphasis on cardiovascular tissues, and the potential of computational and engineering approaches to unravel the complex dynamic relationship between mechanics and signaling in the maintenance of cell and tissue mechanostasis.

Biomechanics of infarcted left ventricle: a review of modelling

Mathematical modelling in biomechanics of infarcted left ventricle (LV) serves as an indispensable tool for remodelling mechanism exploration, LV biomechanical property estimation and therapy assessment after myocardial infarction (MI). However, a review of mathematical modelling after MI has not been seen in the literature so far. In the paper, a systematic review of mathematical models in biomechanics of infarcted LV was established. The models include comprehensive cardiovascular system model, essential LV pressure-volume and stress-stretch models, constitutive laws for passive myocardium and scars, tension models for active myocardium, collagen fibre orientation optimization models, fibroblast and collagen fibre growth/degradation models and integrated growth-electro-mechanical model after MI. The primary idea, unique characteristics and key equations of each model were identified and extracted. Discussions on the models were provided and followed research issues on them were addressed. Considerable improvements in the cardiovascular system model, LV aneurysm model, coupled agent-based models and integrated electro-mechanical-growth LV model are encouraged. Substantial attention should be paid to new constitutive laws with respect to stress-stretch curve and strain energy function for infarcted passive myocardium, collagen fibre orientation optimization in scar, cardiac rupture and tissue damage and viscoelastic effect post-MI in the future.

An in-silico study of cancer cell survival and spatial distribution within a 3D microenvironment

3D cell cultures are in-vitro models representing a significant improvement with respect to traditional monolayers. Their diffusion and applicability, however, are hampered by the complexity of 3D systems, that add new physical variables for experimental analyses. In order to account for these additional features and improve the study of 3D cultures, we here present SALSA (ScAffoLd SimulAtor), a general purpose computational tool that can simulate the behavior of a population of cells cultured in a 3D scaffold. This software allows for the complete customization of both the polymeric template structure and the cell population behavior and characteristics. In the following the technical description of SALSA will be presented, together with its validation and an example of how it could be used to optimize the experimental analysis of two breast cancer cell lines cultured in collagen scaffolds. This work contributes to the growing field of integrated in-silico/in-vitro analysis of biological systems, which have great potential for the study of complex cell population behaviours and could lead to improve and facilitate the effectiveness and diffusion of 3D cell culture models.

Stretch-activated current in human atrial myocytes and Na+ current and mechano-gated channels' current in myofibroblasts alter myocyte mechanical behavior: a computational study

Background

The activation of stretch-activated channels (SACs) in cardiac myocytes, which changes the phases of action potential repolarization, is proven to be highly efficient for the conversion of atrial fibrillation. The expression of Na⁺ current in myofibroblasts (Mfbs) regenerates myocytes’ action potentials, suggesting that Mfbs play an active role in triggering cardiac rhythm disturbances. Moreover, the excitation of mechano-gated channels (MGCs) in Mfbs depolarizes their membrane potential and contributes to the increased risk of post-infarct arrhythmia. Although these electrophysiological mechanisms have been largely known, the roles of these currents in cardiac mechanics are still debated. In this study, we aimed to investigate the mechanical influence of these currents via mathematical modeling. A novel mathematical model was developed by integrating models of human atrial myocyte (including the stretch-activated current, Ca²⁺–force relation, and mechanical behavior of a single segment) and Mfb (including our formulation of Na⁺ current and mechano-gated channels’ current). The effects of the changes in basic cycle length, number of coupled Mfbs and intercellular coupling conductance on myocyte mechanical properties were compared.

Results

Our results indicated that these three currents significantly regulated myocyte mechanical parameters. In isosarcometric contraction, these currents increased segment force by 13.8–36.6% and dropped element length by 12.1–31.5%. In isotonic contraction, there are 2.7–5.9% growth and 0.9–24% reduction. Effects of these currents on the extremum of myocyte mechanical parameters become more significant with the increase of basic cycle length, number of coupled Mfbs and intercellular coupling conductance.

Conclusions

The results demonstrated that stretch-activated current in myocytes and Na⁺ current and mechano-gated channels’ current in Mfbs significantly influenced myocyte mechanical behavior and should be considered in future cardiac mechanical mathematical modeling.

Detailed structural assessment of healthy interventricular septum in the presence of remodeling infarct in the free wall - A finite element model

Purpose

Computational modelling may improve the fundamental understanding of various mechanisms of diseases more particularly related to clinical challenges. In this study the effect of remodeling infarct presence in the left ventricle on the interventricular septal wall is studied using the finite element methods.

Methods

In this study, two rat heart (one model with healthy myocardium and one model with remodeling free wall and healthy septal wall) with magnetic resonance imaging data was gathered to reconstruct three-dimensional (3D) rat heart models. 3D data points from Segment® were imported into SolidEdge® for creation of 3D rat heart models. Abaqus® was used for finite element modeling.

Results

The strain in the healthy interventricular septum of the infarcted left ventricle wall increased when compared to the healthy interventricular septum in the healthy left ventricle. Similarly, the average stress in the healthy left ventricle was observed to have increased on the healthy the interventricular septum where the free wall is subjected to remodeling infarct. When comparing the infarcted models to the healthy model, it was found that the average strain had greatly increased by up to 50.0 %.

Conclusions

The remodeling infarct in the left ventricle has an impact on the healthy interventricular septal wall. Even though the interventricular septal wall was modelled as healthy, it was observed that it has undergone considerable changes in stresses and strains in circumferential and longitudinal direction. The observed changes in myocardial stresses and strains may result in poor global functioning of the heart.

Mechanical regulation of gene expression in cardiac myocytes and fibroblasts

The intact heart undergoes complex and multiscale remodelling processes in response to altered mechanical cues. Remodelling of the myocardium is regulated by a combination of myocyte and non-myocyte responses to mechanosensitive pathways, which can alter gene expression and therefore function in these cells. Cellular mechanotransduction and its downstream effects on gene expression are initially compensatory mechanisms during adaptations to the altered mechanical environment, but under prolonged and abnormal loading conditions, they can become maladaptive, leading to impaired function and cardiac pathologies. In this Review, we summarize mechanoregulated pathways in cardiac myocytes and fibroblasts that lead to altered gene expression and cell remodelling under physiological and pathophysiological conditions. Developments in systems modelling of the networks that regulate gene expression in response to mechanical stimuli should improve integrative understanding of their roles in vivo and help to discover new combinations of drugs and device therapies targeting mechanosignalling in heart disease.

Spatial scaling in multiscale models: methods for coupling agent-based and finite-element models of wound healing

Multiscale models that couple agent-based modeling (ABM) and finite-element modeling (FEM) allow the dynamic simulation of tissue remodeling and wound healing, with mechanical environment influencing cellular behaviors even as tissue remodeling modifies mechanics. One of the challenges in coupling ABM to FEM is that these two domains typically employ grid or element sizes that differ by several orders of magnitude. Here, we develop and demonstrate an interpolation-based method for mapping between ABM and FEM domains of different resolutions that is suitable for linear and nonlinear FEM meshes and balances accuracy with computational demands. We then explore the effects of refining the FEM mesh and the ABM grid in the setting of a fully coupled model. ABM grid refinement studies showed unexpected effects of grid size whenever cells were present at a high enough density for crowding to affect proliferation and migration. In contrast to an FE-only model, refining the FE mesh in the coupled model increased strain differences between adjacent finite elements. Allowing strain-dependent feedback on collagen turnover magnified the effects of regional heterogeneity, producing highly nonlinear spatial and temporal responses. Our results suggest that the choice of both ABM grid and FEM mesh density in coupled models must be guided by experimental data and accompanied by careful grid and mesh refinement studies in the individual domains as well as the fully coupled model.

Coupled agent-based and hyperelastic modelling of the left ventricle post-myocardial infarction

Understanding the healing and remodelling processes induced by myocardial infarction (MI) of the heart is important, and the mechanical properties of the myocardium post-MI can be indicative for effective treatments aimed at avoiding eventual heart failure. MI remodelling is a multiscale feedback process between the mechanical loading and cellular adaptation. In this paper, we use an agent-based model to describe collagen remodelling by fibroblasts regulated by chemical and mechanical cues after acute MI, and upscale into a finite element 3D left ventricular model. We model the dispersed collagen fibre structure using the angular integration method and have incorporated a collagen fibre tension-compression switch in the left ventricle (LV) model. This enables us to study the scar healing (collagen deposition, degradation, and reorientation) of a rat heart post-MI. Our results, in terms of collagen accumulation and alignment, compare well with published experimental data. In addition, we show that different shapes of the MI region can affect the collagen remodelling, and in particular, the mechanical cue plays an important role in the healing process.

A fully coupled framework for in silico investigation of in-stent restenosis

Finite element analysis (FEA) can be implemented along with Agent-based model (ABM) to investigate the biomechanical and mechanobiological mechanisms of pathophysiological processes. However, traditional ABM-FEA approaches are often partially coupled and lack the feedback responses from biological analysis. To overcome this problem, a fully coupled ABM-FEA framework is developed in this paper by linking the macro-scale and cell-scale modules bi-directionally. Numerical studies of the in-stent restenosis process are conducted using the proposed approach and comparisons are made between the two types of frameworks. A reduction in lumen loss rate, which is possibly caused by the time-varying stresses, is observed in the fully coupled simulations. The re-endothelialisation process is also simulated under different frameworks and the simulation results show strong inhibition of endothelial cells to vascular restenosis. The proposed method is proved to be effective to explain the biomechanical-mechanobiological coupling characteristics of the restenosis problem and can be utilized for stent design and optimization.

Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading

Mechanical stimulation of the healing tendon is thought to regulate scar anisotropy and strength and is relatively easy to modulate through physical therapy. However, in vivo studies of various loading protocols in animal models have produced mixed results. To integrate and better understand the available data, we developed a multiscale model of rat Achilles tendon healing that incorporates the effect of changes in the mechanical environment on fibroblast behavior, collagen deposition, and scar formation. We modified an OpenSim model of the rat right hindlimb to estimate physiologic strains in the lateral/medial gastrocnemius and soleus musculo-tendon units during loading and unloading conditions. We used the tendon strains as inputs to a thermodynamic model of stress fiber dynamics that predicts fibroblast alignment, and to determine local collagen synthesis rates according to a response curve derived from in vitro studies. We then used an agent-based model (ABM) of scar formation to integrate these cell-level responses and predict tissue-level collagen alignment and content. We compared our model predictions to experimental data from ten different studies. We found that a single set of cellular response curves can explain features of observed tendon healing across a wide array of reported experiments in rats–including the paradoxical finding that repairing transected tendon reverses the effect of loading on alignment–without fitting model parameters to any data from those experiments. The key to these successful predictions was simulating the specific loading and surgical protocols to predict tissue-level strains, which then guided cellular behaviors according to response curves based on in vitro experiments. Our model results provide a potential explanation for the highly variable responses to mechanical loading reported in the tendon healing literature and may be useful in guiding the design of future experiments and interventions.

Tendons and ligaments transmit force between muscles and bones throughout the body and are comprised of highly aligned collagen fibers that help bear high loads. The Achilles tendon is exposed to exceptionally high loads and is prone to rupture. When damaged Achilles tendons heal, they typically have reduced strength and stiffness, and while most believe that appropriate physical therapy can help improve these mechanical properties, both clinical and animal studies of mechanical loading following injury have produced highly variable and somewhat disappointing results. To help better understand the effects of mechanical loading on tendon healing and potentially guide future therapies, we developed a computational model of rat Achilles tendon healing and showed that we could predict the main effects of different mechanical loading and surgical repair conditions reported across a wide range of published studies. Our model offers potential explanations for some surprising findings of prior studies and for the high variability observed in those studies and may prove useful in designing future therapies or experiments to test new therapies.

Surgical reinforcement alters collagen alignment and turnover in healing myocardial infarcts

Previous studies have suggested that the composition and global mechanical properties of the scar tissue that forms after a myocardial infarction (MI) are key determinants of long-term survival, and emerging therapies such as biomaterial injection are designed in part to alter those mechanical properties. However, recent evidence suggests that local mechanics regulate scar formation post-MI, so that perturbing infarct mechanics could have unexpected consequences. We therefore tested the effect of changes in local mechanical environment on scar collagen turnover, accumulation, and alignment in 77 Sprague-Dawley rats at 1, 2, 3 and 6 wk post-MI by sewing a Dacron patch to the epicardium to eliminate circumferential strain while permitting continued longitudinal stretching with each heart beat. We found that collagen in healing infarcts aligned parallel to regional strain and perpendicular to the preinfarction muscle and collagen fiber direction, strongly supporting our hypothesis that mechanical environment is the primary determinant of scar collagen alignment. Mechanical reinforcement reduced levels of carboxy-terminal propeptide of type I procollagen (PICP; a biomarker for collagen synthesis) in samples collected by microdialysis significantly, particularly in the first 2 wk. Reinforcement also reduced carboxy-terminal telopeptide of type I collagen (ICTP; a biomarker for collagen degradation), particularly at later time points. These alterations in collagen turnover produced no change in collagen area fraction as measured by histology but significantly reduced wall thickness in the reinforced scars compared with untreated controls. Our findings confirm the importance of regional mechanics in regulating scar formation after infarction and highlight the potential for therapies that reduce stretch to also reduce wall thickness in healing infarcts. NEW & NOTEWORTHY This study shows that therapies such as surgical reinforcement, which reduce stretch in healing infarcts, can also reduce collagen synthesis and wall thickness and modify collagen alignment in postinfarction scars.

Mechanosensitivity of Jagged-Notch signaling can induce a switch-type behavior in vascular homeostasis

Hemodynamic forces and Notch signaling are both known as key regulators of arterial remodeling and homeostasis. However, how these two factors integrate in vascular morphogenesis and homeostasis is unclear. Here, we combined experiments and modeling to evaluate the impact of the integration of mechanics and Notch signaling on vascular homeostasis. Vascular smooth muscle cells (VSMCs) were cyclically stretched on flexible membranes, as quantified via video tracking, demonstrating that the expression of Jagged1, Notch3, and target genes was down-regulated with strain. The data were incorporated in a computational framework of Notch signaling in the vascular wall, where the mechanical load was defined by the vascular geometry and blood pressure. Upon increasing wall thickness, the model predicted a switch-type behavior of the Notch signaling state with a steep transition of synthetic toward contractile VSMCs at a certain transition thickness. These thicknesses varied per investigated arterial location and were in good agreement with human anatomical data, thereby suggesting that the Notch response to hemodynamics plays an important role in the establishment of vascular homeostasis.

Personalised computational cardiology: Patient-specific modelling in cardiac mechanics and biomaterial injection therapies for myocardial infarction

Predictive computational modelling in biomedical research offers the potential to integrate diverse data, uncover biological mechanisms that are not easily accessible through experimental methods and expose gaps in knowledge requiring further research. Recent developments in computing and diagnostic technologies have initiated the advancement of computational models in terms of complexity and specificity. Consequently, computational modelling can increasingly be utilised as enabling and complementing modality in the clinic—with medical decisions and interventions being personalised. Myocardial infarction and heart failure are amongst the leading causes of death globally despite optimal modern treatment. The development of novel MI therapies is challenging and may be greatly facilitated through predictive modelling. Here, we review the advances in patient-specific modelling of cardiac mechanics, distinguishing specificity in cardiac geometry, myofibre architecture and mechanical tissue properties. Thereafter, the focus narrows to the mechanics of the infarcted heart and treatment of myocardial infarction with particular attention on intramyocardial biomaterial delivery.

Emergence of Collagen Orientation Heterogeneity in Healing Infarcts and an Agent-Based Model

Spatial heterogeneity of matrix structure can be an important determinant of tissue function. Although bulk properties of collagen structure in healing myocardial infarcts have been characterized previously, regional heterogeneity in infarct structure has received minimal attention. Herein, we quantified regional variations of collagen and nuclear orientations over the initial weeks of healing after infarction in rats, and employed a computational model of infarct remodeling to test potential explanations for the heterogeneity we observed in vivo. Fiber and cell orientation maps were generated from infarct samples acquired previously at 1, 2, 3, and 6 weeks postinfarction in a rat ligation model. We analyzed heterogeneity by calculating the dot product of each fiber or cell orientation vector with every other fiber or cell orientation vector, and plotting that dot product versus distance between the fibers or cells. This analysis revealed prominent regional heterogeneity, with alignment of both fibers and cell nuclei in local pockets far exceeding the global average. Using an agent-based model of fibroblast-mediated collagen remodeling, we found that similar levels of heterogeneity can spontaneously emerge from initially isotropic matrix via locally reinforcing cell-matrix interactions. Specifically, cells that sensed fiber orientation at a distance or remodeled fibers at a distance by traction-mediated reorientation or aligned deposition gave rise to regionally heterogeneous structures. However, only the simulations in which cells deposited collagen fibers aligned with their own orientation reproduced experimentally measured patterns of heterogeneity across all time points. These predictions warrant experimental follow-up to test the role of such mechanisms in vivo and identify opportunities to control heterogeneity for therapeutic benefit.

Ventricular wall biomaterial injection therapy after myocardial infarction: Advances in material design, mechanistic insight and early clinical experiences

Intramyocardial biomaterial injection therapy for myocardial infarction has made significant progress since concept initiation more than 10 years ago. The interim successes and progress in the first 5 years have been extensively reviewed. During the last 5 years, two phase II clinical trials have reported their long term follow up results and many additional biomaterial candidates have reached preclinical and clinical testing. Also in recent years deeper investigations into the mechanisms behind the beneficial effects associated with biomaterial injection therapy have been pursued, and a variety of process and material parameters have been evaluated for their impact on therapeutic outcomes. This review explores the advances made in this biomaterial-centered approach to ischemic cardiomyopathy and discusses potential future research directions as this therapy seeks to positively impact patients suffering from one of the world's most common sources of mortality.

In vivo assessment of regional mechanics post-myocardial infarction: A focus on the road ahead

Cardiovascular disease, particularly the occurrence of myocardial infarction (MI), remains a leading cause of morbidity and mortality (Go et al., Circulation 127: e6-e245, 2013; Go et al. Circulation 129: e28-e292, 2014). There is growing recognition that a key factor for post-MI outcomes is adverse remodeling and changes in the regional structure, composition, and mechanical properties of the MI region itself. However, in vivo assessment of regional mechanics post-MI can be confounded by the species, temporal aspects of MI healing, as well as size, location, and extent of infarction across myocardial wall. Moreover, MI regional mechanics have been assessed over varying phases of the cardiac cycle, and thus, uniform conclusions regarding the material properties of the MI region can be difficult. This review assesses past studies that have performed in vivo measures of MI mechanics and attempts to provide coalescence on key points from these studies, as well as offer potential recommendations for unifying approaches in terms of regional post-MI mechanics. A uniform approach to biophysical measures of import will allow comparisons across studies, as well as provide a basis for potential therapeutic markers.

μCT of ex-vivo stained mouse hearts and embryos enables a precise match between 3D virtual histology, classical histology and immunochemistry

The small size of the adult and developing mouse heart poses a great challenge for imaging in preclinical research. The aim of the study was to establish a phosphotungstic acid (PTA) ex-vivo staining approach that efficiently enhances the x-ray attenuation of soft-tissue to allow high resolution 3D visualization of mouse hearts by synchrotron radiation based μCT (SRμCT) and classical μCT. We demonstrate that SRμCT of PTA stained mouse hearts ex-vivo allows imaging of the cardiac atrium, ventricles, myocardium especially its fibre structure and vessel walls in great detail and furthermore enables the depiction of growth and anatomical changes during distinct developmental stages of hearts in mouse embryos. Our x-ray based virtual histology approach is not limited to SRμCT as it does not require monochromatic and/or coherent x-ray sources and even more importantly can be combined with conventional histological procedures. Furthermore, it permits volumetric measurements as we show for the assessment of the plaque volumes in the aortic valve region of mice from an ApoE-/- mouse model. Subsequent, Masson-Goldner trichrome staining of paraffin sections of PTA stained samples revealed intact collagen and muscle fibres and positive staining of CD31 on endothelial cells by immunohistochemistry illustrates that our approach does not prevent immunochemistry analysis. The feasibility to scan hearts already embedded in paraffin ensured a 100% correlation between virtual cut sections of the CT data sets and histological heart sections of the same sample and may allow in future guiding the cutting process to specific regions of interest. In summary, since our CT based virtual histology approach is a powerful tool for the 3D depiction of morphological alterations in hearts and embryos in high resolution and can be combined with classical histological analysis it may be used in preclinical research to unravel structural alterations of various heart diseases.

Agent-Based Modelling in Multicellular Systems Biology

This chapter aims at discussing the content of multi-agent based simulation (MABS) applied to computational biology i.e., to modelling and simulating biological systems by means of computational models, methodologies, and frameworks. In particular, the adoption of agent-based modelling (ABM) in the field of multicellular systems biology is explored, focussing on the challenging scenarios of developmental biology. After motivating why agent-based abstractions are critical in representing multicellular systems behaviour, MABS is discussed as the source of the most natural and appropriate mechanism for analysing the self-organising behaviour of systems of cells. As a case study, an application of MABS to the development of Drosophila Melanogaster is finally presented, which exploits the ALCHEMIST platform for agent-based simulation.

Novel therapeutic strategies targeting fibroblasts and fibrosis in heart disease

Our understanding of the functions of cardiac fibroblasts has moved beyond their roles in heart structure and extracellular matrix generation and now includes their contributions to paracrine, mechanical and electrical signalling during ontogenesis and normal cardiac activity. Fibroblasts also have central roles in pathogenic remodelling during myocardial ischaemia, hypertension and heart failure. As key contributors to scar formation, they are crucial for tissue repair after interventions including surgery and ablation. Novel experimental approaches targeting cardiac fibroblasts are promising potential therapies for heart disease. Indeed, several existing drugs act, at least partially, through effects on cardiac connective tissue. This Review outlines the origins and roles of fibroblasts in cardiac development, homeostasis and disease; illustrates the involvement of fibroblasts in current and emerging clinical interventions; and identifies future targets for research and development.

Multi-scale Modeling of the Cardiovascular System: Disease Development, Progression, and Clinical Intervention

Cardiovascular diseases (CVDs) are the leading cause of death in the western world. With the current development of clinical diagnostics to more accurately measure the extent and specifics of CVDs, a laudable goal is a better understanding of the structure-function relation in the cardiovascular system. Much of this fundamental understanding comes from the development and study of models that integrate biology, medicine, imaging, and biomechanics. Information from these models provides guidance for developing diagnostics, and implementation of these diagnostics to the clinical setting, in turn, provides data for refining the models. In this review, we introduce multi-scale and multi-physical models for understanding disease development, progression, and designing clinical interventions. We begin with multi-scale models of cardiac electrophysiology and mechanics for diagnosis, clinical decision support, personalized and precision medicine in cardiology with examples in arrhythmia and heart failure. We then introduce computational models of vasculature mechanics and associated mechanical forces for understanding vascular disease progression, designing clinical interventions, and elucidating mechanisms that underlie diverse vascular conditions. We conclude with a discussion of barriers that must be overcome to provide enhanced insights, predictions, and decisions in pre-clinical and clinical applications.

Computational modeling of cardiac fibroblasts and fibrosis

Altered fibroblast behavior can lead to pathologic changes in the heart such as arrhythmia, diastolic dysfunction, and systolic dysfunction. Computational models are increasingly used as a tool to identify potential mechanisms driving a phenotype or potential therapeutic targets against an unwanted phenotype. Here we review how computational models incorporating cardiac fibroblasts have clarified the role for these cells in electrical conduction and tissue remodeling in the heart. Models of fibroblast signaling networks have primarily focused on fibroblast cell lines or fibroblasts from other tissues rather than cardiac fibroblasts, specifically, but they are useful for understanding how fundamental signaling pathways control fibroblast phenotype. In the future, modeling cardiac fibroblast signaling, incorporating -omics and drug-interaction data into signaling network models, and utilizing multi-scale models will improve the ability of in silico studies to predict potential therapeutic targets against adverse cardiac fibroblast activity.

Augmenting Surgery via Multi-scale Modeling and Translational Systems Biology in the Era of Precision Medicine: A Multidisciplinary Perspective

In this era of tremendous technological capabilities and increased focus on improving clinical outcomes, decreasing costs, and increasing precision, there is a need for a more quantitative approach to the field of surgery. Multiscale computational modeling has the potential to bridge the gap to the emerging paradigms of Precision Medicine and Translational Systems Biology, in which quantitative metrics and data guide patient care through improved stratification, diagnosis, and therapy. Achievements by multiple groups have demonstrated the potential for (1) multiscale computational modeling, at a biological level, of diseases treated with surgery and the surgical procedure process at the level of the individual and the population; along with (2) patient-specific, computationally-enabled surgical planning, delivery, and guidance and robotically-augmented manipulation. In this perspective article, we discuss these concepts, and cite emerging examples from the fields of trauma, wound healing, and cardiac surgery.

Biomechanics of Cardiac Function

The heart pumps blood to maintain circulation and ensure the delivery of oxygenated blood to all the organs of the body. Mechanics play a critical role in governing and regulating heart function under both normal and pathological conditions. Biological processes and mechanical stress are coupled together in regulating myocyte function and extracellular matrix structure thus controlling heart function. Here, we offer a brief introduction to the biomechanics of left ventricular function and then summarize recent progress in the study of the effects of mechanical stress on ventricular wall remodeling and cardiac function as well as the effects of wall mechanical properties on cardiac function in normal and dysfunctional hearts. Various mechanical models to determine wall stress and cardiac function in normal and diseased hearts with both systolic and diastolic dysfunction are discussed. The results of these studies have enhanced our understanding of the biomechanical mechanism in the development and remodeling of normal and dysfunctional hearts. Biomechanics provide a tool to understand the mechanism of left ventricular remodeling in diastolic and systolic dysfunction and guidance in designing and developing new treatments.

Physiological Implications of Myocardial Scar Structure

Once myocardium dies during a heart attack, it is replaced by scar tissue over the course of several weeks. The size, location, composition, structure, and mechanical properties of the healing scar are all critical determinants of the fate of patients who survive the initial infarction. While the central importance of scar structure in determining pump function and remodeling has long been recognized, it has proven remarkably difficult to design therapies that improve heart function or limit remodeling by modifying scar structure. Many exciting new therapies are under development, but predicting their long-term effects requires a detailed understanding of how infarct scar forms, how its properties impact left ventricular function and remodeling, and how changes in scar structure and properties feed back to affect not only heart mechanics but also electrical conduction, reflex hemodynamic compensations, and the ongoing process of scar formation itself. In this article, we outline the scar formation process following a myocardial infarction, discuss interpretation of standard measures of heart function in the setting of a healing infarct, then present implications of infarct scar geometry and structure for both mechanical and electrical function of the heart and summarize experiences to date with therapeutic interventions that aim to modify scar geometry and structure. One important conclusion that emerges from the studies reviewed here is that computational modeling is an essential tool for integrating the wealth of information required to understand this complex system and predict the impact of novel therapies on scar healing, heart function, and remodeling following myocardial infarction.

Building a better infarct: Modulation of collagen cross-linking to increase infarct stiffness and reduce left ventricular dilation post-myocardial infarction

Matrix metalloproteinase-9 (MMP-9) deletion attenuates collagen accumulation and dilation of the left ventricle (LV) post-myocardial infarction (MI); however the biomechanical mechanisms underlying the improved outcome are poorly understood. The aim of this study was to determine the mechanisms whereby MMP-9 deletion alters collagen network composition and assembly in the LV post-MI to modulate the mechanical properties of myocardial scar tissue. Adult C57BL/6J wild-type (WT; n=88) and MMP-9 null (MMP-9(-/-); n=92) mice of both sexes underwent permanent coronary artery ligation and were compared to day 0 controls (n=42). At day 7 post-MI, WT LVs displayed a 3-fold increase in end-diastolic volume, while MMP-9(-/-) showed only a 2-fold increase (p<0.05). Biaxial mechanical testing revealed that MMP-9(-/-) infarcts were stiffer than WT infarcts, as indicated by a 1.3-fold reduction in predicted in vivo circumferential stretch (p<0.05). Paradoxically, MMP-9(-/-) infarcts had a 1.8-fold reduction in collagen deposition (p<0.05). This apparent contradiction was explained by a 3.1-fold increase in lysyl oxidase (p<0.05) in MMP-9(-/-) infarcts, indicating that MMP-9 deletion increased collagen cross-linking activity. Furthermore, MMP-9 deletion led to a 3.0-fold increase in bone morphogenetic protein-1, the metalloproteinase that cleaves pro-collagen and pro-lysyl oxidase (p<0.05) and reduced fibronectin fragmentation by 49% (p<0.05) to enhance lysyl oxidase activity. We conclude that MMP-9 deletion increases infarct stiffness and prevents LV dilation by reducing collagen degradation and facilitating collagen assembly and cross-linking through preservation of the fibronectin network and activation of lysyl oxidase.

Systems approach to the study of stretch and arrhythmias in right ventricular failure induced in rats by monocrotaline

We demonstrate the synergistic benefits of using multiple technologies to investigate complex multi-scale biological responses. The combination of reductionist and integrative methodologies can reveal novel insights into mechanisms of action by tracking changes of in vivo phenomena to alterations in protein activity (or vice versa). We have applied this approach to electrical and mechanical remodelling in right ventricular failure caused by monocrotaline-induced pulmonary artery hypertension in rats. We show arrhythmogenic T-wave alternans in the ECG of conscious heart failure animals. Optical mapping of isolated hearts revealed discordant action potential duration (APD) alternans. Potential causes of the arrhythmic substrate; structural remodelling and/or steep APD restitution and dispersion were observed, with specific remodelling of the Right Ventricular Outflow Tract. At the myocyte level, [Ca(2+)]i transient alternans were observed together with decreased activity, gene and protein expression of the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA). Computer simulations of the electrical and structural remodelling suggest both contribute to a less stable substrate. Echocardiography was used to estimate increased wall stress in failure, in vivo. Stretch of intact and skinned single myocytes revealed no effect on the Frank-Starling mechanism in failing myocytes. In isolated hearts acute stretch-induced arrhythmias occurred in all preparations. Significant shortening of the early APD was seen in control but not failing hearts. These observations may be linked to changes in the gene expression of candidate mechanosensitive ion channels (MSCs) TREK-1 and TRPC1/6. Computer simulations incorporating MSCs and changes in ion channels with failure, based on altered gene expression, largely reproduced experimental observations.