DOI: 10.5281/zenodo.5105724
title: Simulations of focal and reentrant sources with Acetylcholine regulation in atrial fibrillation

description: <strong>Simulations of focal and reentrant sources with Acetylcholine regulation in atrial fibrillation</strong> This contains focal and reentrant sources with Acetylcholine regulation in atrial fibrillation simulations used in the manuscript <strong>Detection of focal source and arrhythmogenic substrate from body surface potentials to guide atrial fibrillation ablation (</strong>https://doi.org/10.1371/journal.pcbi.1009893<strong>)</strong>. <strong>Please cite our manuscript if you use our code</strong>. Detailed simulation files for focal and reentrant sources with Acetylcholine regulation in CARPentry. Tested with CARP GIT commit hash: 2e280733.<br> The formats of .elem, .lon, .pts, .dat and .igb used or produced by carp can be found in the CARPentry website. <strong>Data (<code>data/</code>)</strong> <code>Mesh1(.elem, .lon, .pts)</code>: files (elements, fibres, nodes) of a mesh Mesh1 with basic tagging of atrial structures. <code>Mesh1_FS_L22.vtx</code>: vertices of a focal site at (αLA=0.2,βLA=0.2\alpha_{LA} = 0.2, \beta_{LA} = 0.2αLA=0.2,βLA=0.2). <code>Mesh1_L22_r0(.elem, .lon, .pts)</code>: files (elements, fibres, nodes) of a mesh Mesh1 with basic tagging of atrial structures and tagging of regions (Section 1 - 48) for reentrant sources. <code>Mesh1_UAC*.dat</code>: plain text files where each row specifies a Universal Atrial Coordinate ( <code>Mesh1_UAC1.dat</code>: alpha, <code>Mesh1_UAC2.dat</code> : beta, <code>Mesh1_UAC3.dat</code> : LA or RA) of Mesh1 in Roney et al. 2019, which could be used to select vertices and tag elements. We annotated elements with tags of 1-4 and 11-28 for the Universal Atrial Coordinate. <code>vest.pts</code>: a <code>.pts</code> file specifying the locations of 252 vest leads. <code>Mesh1_ACh_islands.adj</code>: adjustment file specifying the node indices (first column) and concentration of the ACh (second column) for ACh islands. <strong>Par files: parameter files for CARPentry software.</strong> <code>Focal_source.par</code>: to simulate a focal source with a CL of 180 ms on the left atrial focal site lasting for 3000 ms. <code>Focal_source_ACh.par</code>: to simulate a focal source with a CL of 180 ms lasting for 3000 ms with ACh. <code>Reentrant_source.par</code>: to simulate a reentrant source around a left atrial core of (αLA=0.2,βLA=0.2\alpha_{LA} = 0.2, \beta_{LA} = 0.2αLA=0.2,βLA=0.2). To run this file in CARP, the user is advised to compute the initial state files of each segment (<code>init/*.sv</code>) using <code>Reentrant_source_get_init_states.py</code>. This serves as initial states for regions with tags 100 - 147 for the left atral sections of a phase distribution method (Section 100 - 147 refers to the Section 1 - 48 in the main article Fig S1) in <code>Mesh1_L22_r0.elem</code>. <strong>Ionic model</strong> <code>CRN_ACH.model</code>: an ionic model file with Acetylcholine introduction of Bayer et al. (2019), with Acetylcholine concentration 0 by default. <strong>Initial conditions for reentrant sources</strong> <code>Reentrant_source_get_init_states.py</code>: Python script that output Linux commands to call <code>bench</code> software in CARPentry to initiate the reentrant sources. The produced initial state files <code>init/*.sv</code> are to be used by <code>Reentrant_source.par</code>. <strong>Tags for the atrial structures in the element file (specified in <code>.elem</code>)</strong> 1 - Right atrial body 2 - Right atrial appendage 3 - Sinoatrial node 4 - Line of block 5 - Coronary sinus 6 - Superior vena cava 7 - Inferior vena cava 8 - Crist terminalis 9 - Pectinate muscle 10 - Bachman Bundle 11- Left atrial body endocardial layer 12 - Left atrial body epicardial layer 13 - Left atrial appendage endocardial layer 14 - Left atrial appendage epicardial layer 21, 23, 25 & 27 - endocardial layer of four left atrial PVs 22, 24, 26 & 28 - epicardial layer of four left atrial PVs <strong>References</strong> Feng Y, Roney CH, Bayer JD, Niederer SA, Hocini M, Vigmond EJ (2022) Detection of focal source and arrhythmogenic substrate from body surface potentials to guide atrial fibrillation ablation. PLoS Comput Biol 18(3): e1009893.<strong> </strong>https://doi.org/10.1371/journal.pcbi.1009893 Roney CH, Pashaei A, Meo M, Dubois R, Boyle PM, Trayanova NA, et al. Universal atrial coordinates applied to visualisation, registration and construction of patient specific meshes. Medical Image Analysis. 2019 Jul 1;55:65–75. https://10.1016/j.media.2019.04.004 Bayer, et al. (2019). Acetylcholine Delays Atrial Activation to Facilitate Atrial Fibrillation. Frontiers in Physiology, 10, 1105. https://doi.org/10.3389/fphys.2019.01105
description: {"references": ["Roney CH, Pashaei A, Meo M, Dubois R, Boyle PM, Trayanova NA, et al. Universal atrial coordinates applied to visualisation, registration and construction of patient specific meshes. Medical Image Analysis. 2019 Jul 1;55:65\u201375. https://10.1016/j.media.2019.04.004", "Bayer, et al. (2019). Acetylcholine Delays Atrial Activation to Facilitate Atrial Fibrillation. Frontiers in Physiology, 10, 1105. https://doi.org/10.3389/fphys.2019.01105"]}