The LifeV library: engineering mathematics beyond the proof of concept

LifeV is a library for the finite element (FE) solution of partial differential equations in one, two, and three dimensions. It is written in C++ and designed to run on diverse parallel architectures, including cloud and high performance computing facilities. In spite of its academic research nature, meaning a library for the development and testing of new methods, one distinguishing feature of LifeV is its use on real world problems and it is intended to provide a tool for many engineering applications. It has been actually used in computational hemodynamics, including cardiac mechanics and fluid-structure interaction problems, in porous media, ice sheets dynamics for both forward and inverse problems. In this paper we give a short overview of the features of LifeV and its coding paradigms on simple problems. The main focus is on the parallel environment which is mainly driven by domain decomposition methods and based on external libraries such as MPI, the Trilinos project, HDF5 and ParMetis. Dedicated to the memory of Fausto Saleri.Comment: Review of the LifeV Finite Element librar

Master of Science

thesisThis study introduces a pipeline for the temporal dilation of canine cardiac signals following registration to human torsos. Performing registration of data attained from canine electrophysiology studies to human torso geometries allows for a larger database for the investigation of human-like arrhythmias that cannot be readily obtained otherwise. However, during registration, the canine cardiac signals must be adjusted to correct spatially dependent aspects of propagation, such as conduction velocity (CV), that are influenced by increased heart size. We refer to this correction process as "temporal dilation'' as it includes resampling of the cardiac signals. We acquired 10 canine cardiac recordings from electrodes built into socks that covered the epicardial surface of the ventricles. The sock geometries were registered to two human torsos. From this spatial transform, we calculated both global and local scaling factors needed to adjust the time signals. Signals were then dilated with both scaling types using linear and nonlinear techniques. The linear method homogeneously dilated the entire signal and the nonlinear technique dilated segments of the signals outside the QRS and T wave. Dilated cardiac signals were validated by comparison of calculated values of CV, total activation time (TAT), and activation recovery interval (ARI). Activation maps also served as a means of qualitative comparison. The observed ECG metrics of canine cardiac signals after temporal dilation using global scaling closely resembled those from human recordings in terms of CV, ARI, and TAT. Temporally dilated signals using local scaling, in contrast, caused the observed ECG metrics to no longer remain within a physiologically relevant range. A realistic activation pattern was maintained after temporal dilation using global scaling. Though temporal dilation using locally calculated scaling factors did not result in physiologically relevant cardiac signals to humans, homogenous temporal dilation could be used to correct the spatially dependent aspects of propagation after geometric registration of canine hearts to human torso geometries. Homogenous temporal dilation, therefore, is a technique that can be used to generate human-like cardiac signals useful for validation of devices used to diagnose, monitor, or intervene in cases of cardiac arrhythmias

The Application of Computer Techniques to ECG Interpretation

This book presents some of the latest available information on automated ECG analysis written by many of the leading researchers in the field. It contains a historical introduction, an outline of the latest international standards for signal processing and communications and then an exciting variety of studies on electrophysiological modelling, ECG Imaging, artificial intelligence applied to resting and ambulatory ECGs, body surface mapping, big data in ECG based prediction, enhanced reliability of patient monitoring, and atrial abnormalities on the ECG. It provides an extremely valuable contribution to the field

Computer-Aided Clinical Decision Support Systems for Atrial Fibrillation

Clinical decision support systems (clinical DSSs) are widely used today for various clinical applications such as diagnosis, treatment, and recovery. Clinical DSS aims to enhance the end‐to‐end therapy management for the doctors, and also helps to provide improved experience for patients during each phase of the therapy. The goal of this chapter is to provide an insight into the clinical DSS associated with the highly prevalent heart rhythm disorder, atrial fibrillation (AF). The use of clinical DSS in AF management is ubiquitous, starting from detection of AF through sophisticated electrophysiology treatment procedures, all the way to monitoring the patient\u27s health during follow‐ups. Most of the software associated with AF DSS are developed based on signal processing, image processing, and artificial intelligence techniques. The chapter begins with a brief description of DSS in general and then introduces DSS that are used for various clinical applications. The chapter continues with a background on AF and some relevant mechanisms. Finally, a couple of clinical DSS used today in regard with AF are discussed, along with some proposed methods for potential implementation of clinical DSS for detection of AF, prediction of an AF treatment outcome, and localization of AF targets during a treatment procedure

Intracoronary electrocardiogram as a direct measure of myocardial ischemia

The electrocardiogram is a valuable diagnostic method providing insight into pathologies of the heart, especially rhythm disorders or insufficient myocardial blood supply (myocardial ischemia). The commonly used surface ECG is, however, limited in detecting short-lasting myocardial ischemia, in particular in the territory of the left circumflex coronary artery supplying the postero-lateral wall of the left ventricle. Conversely, an ECG recorded in close vicinity to the myocardium, i.e., within a coronary artery (intracoronary ECG, icECG) has been thought to overcome these limitations. Since its first implementation during cardiac catheterization in 1985, icECG has shown ample evidence for its diagnostic value given the higher sensitivity for myocardial ischemia detection when compared to the surface ECG. In addition, icECG has been demonstrated to be a direct measure of myocardial ischemia in real-time, thus, providing valuable information during percutaneous coronary diagnostics and interventions. However, a lack of analysing systems to obtain and quantify icECG in real-time discourages routine use. The goals of this MD-PhD thesis are two-fold: First, to determine the diagnostic accuracy of icECG ST-segment shift during pharmacologic inotropic stress in comparison to established indices for coronary lesion severity assessment using quantitative angiographic percent diameter stenosis as reference (Project I). Second, to determine the optimal icECG parameter for myocardial ischemia detection and quantification (Project II and III). In essence, this thesis demonstrates that the icECG is an easy available diagnostic method providing highly accurate information on the amount of myocardial ischemia in real-time. Quantitative assessment of acute, transmural myocardial ischemia by icECG is most accurately performed by measuring ST-segment shift at the J-point, while the quantitative assessment during physical exercise, respectively its pharmacologic simulation, is most accurately performed by measuring ST-segment shift 60ms after the J-point

Three-dimensional Multiscale Modelling and Simulation of Atria and Torso Electrophysiology

A better understanding of the electrical activity of the heart under physiological and pathological conditions has always been key for clinicians and researchers. Over the last years, the information in the P-wave signals has been extensively analysed to un-cover the mechanisms underlying atrial arrhythmias by localizing ectopic foci or high-frequency rotors. However, the relationship between the activation of the different areas of the atria and the characteristics of the P-wave signals or body surface poten-tial maps are still far from being completely understood. Multiscale anatomical and functional models of the heart are a new technological framework that can enable the investigation of the heart as a complex system. This thesis is centred in the construction of a multiscale framework that allows the realistic simulation of atrial and torso electrophysiology and integrates all the anatom-ical and functional descriptions described in the literature. The construction of such model involves the development of heterogeneous cellular and tissue electrophysiolo-gy models fitted to empirical data. It also requires an accurate 3D representation of the atrial anatomy, including tissue fibre arrangement, and preferential conduction axes. This multiscale model aims to reproduce faithfully the activation of the atria under physiological and pathological conditions. We use the model for two main applica-tions. First, to study the relationship between atrial activation and surface signals in sinus rhythm. This study should reveal the best places for recording P-waves signals in the torso, and which are the regions of the atria that make the most significant contri-bution to the body surface potential maps and determine the main P-wave characteris-tics. Second, to spatially cluster and classify ectopic atrial foci into clearly differenti-ated atrial regions by using the body surface P-wave integral map (BSPiM) as a bi-omarker. We develop a machine-learning pipeline trained from simulations obtained from the atria-torso model aiming to validate whether ectopic foci with similar BSPiM naturally cluster into differentiated non-intersected atrial regions, and whether new BSPiM could be correctly classified with high accuracy.En la actualidad, una mejor compresión de la actividad eléctrica del corazón en condi-ciones fisiológicas y patológicas es clave para médicos e investigadores. A lo largo de los últimos años, la información derivada de la onda P se ha utilizado para intentar descubrir los mecanismos subyacentes a las arritmias auriculares mediante la localiza-ción de focos ectópicos y rotores de alta frecuencia. Sin embargo, la relación entre la activación de distintas regiones auriculares y las características tanto de las ondas P como de la distribución de potencial en la superficie del torso está lejos de entenderse completamente. Los modelos cardíacos funcionales y anatómicos son una nueva he-rramienta que puede facilitar la investigación relativa al corazón entendido como sis-tema complejo. La presente tesis se centra en la construcción de un modelo multiescala para la simula-ción realista de la electrofisiología cardíaca tanto a nivel auricular como de torso, integrando toda la información anatómica y funcional disponible en la literatura. La construcción de este modelo implica el desarrollo, en base a datos experimentales, de modelos electrofisiológicos heterogéneos tanto celulares como tisulares. Así mismo, es imprescindible una representación tridimensional precisa de la anatomía auricular, incluyendo la dirección de fibras y los haces de conducción preferentes. Este modelo multiescala busca reproducir fielmente la activación auricular en condiciones fisiológi-cas y patológicas. Su uso se ha centrado fundamentalmente en dos aplicaciones. En primer lugar, estudiar la relación entre la activación auricular en ritmo sinusal y las señales en la superficie del torso. Este estudio busca definir la mejor ubicación para el registro de las ondas P en el torso así como determinar aquellas regiones auriculares que contribuyen fundamentalmente a la formación y distribución de potenciales super-ficiales así como a las características de las ondas P. En segundo lugar, agrupar y cla-sificar espacialmente los focos ectópicos en regiones auriculares claramente diferen-ciables empleando como biomarcador los mapas superficiales de integral de la onda P (BSPiM). Se ha desarrollado para ello una metodología de aprendizaje automático en la que las simulaciones obtenidas con el modelo multiescala aurícula-torso sirven de entrenamiento, permitiendo validar si los focos ectópicos cuyos BSPiMs son similares se agrupan de forma natural en regiones auriculares no intersectadas y si BSPiMs nue-vos podrían ser clasificados prospectivamente con gran precisión.Avui en dia, una millor comprenssió de l'activitat elèctrica del cor en condicions fisio-lògiques i patològiques és clau per a metges i investigadors. Al llarg dels últims anys, la informació derivada de l'ona P s'ha utilitzat per intentar descobrir els mecanismes subjacents a les arítmies auriculars mitjançant la localització de focus ectòpics i rotors d'alta freqüència. No obstant això, la relació entre l'activació de diferents regions auri-culars i les característiques tant de les ones P com de la distribució de potencial en la superfície del tors està lluny d'entendre's completament. Els models cardíacs funcionals i anatòmics són una nova eina que pot facilitar la recerca relativa al cor entès com a sistema complex. La present tesi es centra en la construcció d'un model multiescala per a la simulació realista de la electrofisiologia cardíaca tant a nivell auricular com de tors, integrant tota la informació anatòmica i funcional disponible en la literatura. La construcció d'aquest model implica el desenvolupament, sobre la base de dades experimentals, de models electrofisiològics heterogenis, tant cel·lulars com tissulars. Així mateix, és imprescindible una representació tridimensional precisa de l'anatomia auricular, in-cloent la direcció de fibres i els feixos de conducció preferents. Aquest model multies-cala busca reproduir fidelment l'activació auricular en condicions fisiològiques i pa-tològiques. El seu ús s'ha centrat fonamentalment en dues aplicacions. En primer lloc, estudiar la relació entre l'activació auricular en ritme sinusal i els senyals en la superfí-cie del tors. A més a més, amb aquest estudi també es busca definir la millor ubicació per al registre de les ones P en el tors, així com, determinar aquelles regions auriculars que contribueixen fonamentalment a la formació i distribució de potencials superfi-cials a l'hora que es caracteritzen les ones P. En segon lloc, agrupar i classificar espa-cialment els focus ectòpics en regions auriculars clarament diferenciables emprant com a biomarcador els mapes superficials d'integral de l'ona P (BSPiM). És per això que s'ha desenvolupat una metodologia d'aprenentatge automàtic en la qual les simulacions obtingudes amb el model multiescala aurícula-tors serveixen d'entrenament, la qual cosa permet validar si els focus ectòpics, llurs BSPiMs són similars, s'agrupen de for-ma natural en regions auriculars no intersectades i si BSPiMs nous podrien ser classifi-cats de manera prospectiva amb precisió.Ferrer Albero, A. (2017). Three-dimensional Multiscale Modelling and Simulation of Atria and Torso Electrophysiology [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/88402TESI

Interactive Training System for Interventional Electrocardiology Procedures

International audienceRecent progress in cardiac catheterization and devices has allowed the development of new therapies for severe cardiac diseases like arrhythmias and heart failure. The skills required for such interventions are very challenging to learn, and are typically acquired over several years. Virtual reality simulators may reduce this burden by allowing trainees to practice such procedures without risk to patients. In this paper, we propose the first training system dedicated to cardiac electrophysiology, including pacing and ablation procedures. Our framework involves the simulation of a catheter navigation that reproduces issues intrinsic to intra-cardiac catheterization, and a graphics processing unit (GPU)-based electrophysiological model. A multi-threading approach is proposed to compute both physical simulations (navigation and electrophysiology) asynchronously. With this method, we reach computational performances that account for user interactions in real-time. Based on a scenario of cardiac arrhythmia, we demonstrate the ability of the user-guided simulator to navigate inside vessels and cardiac cavities with a catheter and to reproduce an ablation procedure involving: extra-cellular potential measurements, endocardial surface reconstruction, electrophysiol-ogy mapping, radio-frequency (RF) ablation, as well as electrical stimulation. A clinical evaluation assessing the different aspects of the simulation is presented. This works is a step towards computerized medical learning curriculum

A personalized real-time virtual model of whole heart electrophysiology

Computer models capable of representing the intrinsic personal electrophysiology (EP) of the heart in silico are termed virtual heart technologies. When anatomy and EP are tailored to individual patients within the model, such technologies are promising clinical and industrial tools. Regardless of their vast potential, few virtual technologies simulating the entire organ-scale EP of all four-chambers of the heart have been reported and widespread clinical use is limited due to high computational costs and difficulty in validation. We thus report on the development of a novel virtual technology representing the electrophysiology of all four-chambers of the heart aiming to overcome these limitations. In our previous work, a model of ventricular EP embedded in a torso was constructed from clinical magnetic resonance image (MRI) data and personalized according to the measured 12 lead electrocardiogram (ECG) of a single subject under normal sinus rhythm. This model is then expanded upon to include whole heart EP and a detailed representation of the His-Purkinje system (HPS). To test the capacities of the personalized virtual heart technology to replicate standard clinical morphological ECG features under such conditions, bundle branch blocks within both the right and the left ventricles under two different conduction velocity settings are modeled alongside sinus rhythm. To ensure clinical viability, model generation was completely automated and simulations were performed using an efficient real-time cardiac EP simulator. Close correspondence between the measured and simulated 12 lead ECG was observed under normal sinus conditions and all simulated bundle branch blocks manifested relevant clinical morphological features