In Silico Assessment of Arrhythmic Risk Following the Implantation of Engineered Heart Tissues in Porcine Hearts - Dataset

This repository contains the modeling data and simulation settings for the paper entitled “In Silico Assessment of Arrhythmic Risk Following the Implantation of Engineered Heart Tissues in Porcine Hearts with Varying Infarct Locations” by Ricardo M. Rosales, Gonzalo R. Ríos-Muñoz, Ana María Sánchez de la Nava, María Eugenia Fernández-Santos, Javier Bermejo, Manuel Doblaré, Ana Mincholé, and Esther Pueyo. The paper can be found here. The preprocessing and postprocessing code is available in the repositories HeartModelling and simOmPP, respectively. All simulations were performed using ELECTRA. Data Structure Cells:Contains all cell-related initialization files. Models:There are 9 infarcted biventricular porcine models, which were generated in our previous work integrating multi-modal data in models of the pig heart (4-7 are infarcted in the left circumflex coronary artery and 8-12 are infarcted in the left anterior descending (LAD) coronary artery, see the paper for reference). In this work, engineered heart tissues (EHTs) were computationally added to these models for assessing arrhythmia inducibility (see Paper for reference). EHT1 and EHT2 in the file name indicates if the location of implantation was central (EHT1: L1 in Paper) or lateral (EHT2: L2 in Paper) to the infarction. Every pigX_EHTX folder has: mesh_no_scar.* files: Mesh data for visualization (.vtk) or simulation input (.inp). The scar is excluded as it was simulated as an insulator (see Paper for reference). Mesh regions are labeled, fibers can be visualized in Paraview from the .vtk file, and the AHA segment-based stimulation sites are saved as well. s_RBM_EHTrandom file: Rule-based fiber alignment data for simulation input. The fiber direction was obtained using a standard fiber field (s_RBM: +60/-60 endo-epi degrees) for the biventricular tissue and random orientation for the EHT. final_mipatch_surfmesh.obj file: This is the superficial, triangular mesh of the biventricles and the EHT in case a new meshing is nedeed. The used conduction systems (ap_CS) and biventricular meshes without the EHT (infarction only) can be download from here Optical Mapping (OM) Contains the OM data under ventricular trachycardia for all LAD pigs: Videos: Raw and filtered optical mapping recordings in MATLAB (.mat) format. Metadata (info.xlsx): Detailed stimulation parameters, spatial resolution, sampling frequency, and specified Regions of Interest (ROIs). ROIs: Defined regions for analysis. Usage: the script getOMVideos2.py in simOmPP can be used after filtering the OM videos for obtaining the tissue-level electrophysiological videos presented in the paper. Simulations: settings_CL600_1800ms_stimAHAX_first3beats: Generic configuration file for simulation of the first three S1 beats of the S1-S2 protocol presented. settings_CL600_1800ms_stimAHAX_S2_X: Generic configuration file for simulation of the fourth S1 beat and the S2 beat of the S1-S2 protocol presented. Note: File paths and possible typographical errors should be reviewed and adjusted as needed. For additional details, please refer to the paper and the related software repositories. The previous paper can be found here.