DOI: 10.5061/dryad.n2z34tn86
title: Data from: STAR locally prolongs effective refractory period and increases ventricular tachycardia cycle length without short-term scar formation or functional decline: Insights from a translational porcine model study

description: This dataset contains data required to reproduce computational simulations
 presented in the 2025 paper by Zenger et al. This data set comprises (1)
 Geometric descriptions of the simulation domain (whole heart, tissue
 wedge, etc.), with point clouds interconnected by finite elements, each of
 which is associated with a vector encoding local myofiber orientation. (2)
 Parameter files describing functional cell- and tissue-scale properties of
 different tissue regions, perturbations to be applied to the model during
 the simulation (e.g., electrical stimuli), and numerical solver settings.
 (3) Initial condition state files describing the functional state of the
 model at the beginning of the simulation, if these conditions differ from
 the cell-scale default parameters. All of the above are stored in plain
 text or binary formats compatible with the openCARP framework, which is
 freely available for non-commercial use.
description: # STAR locally prolongs effective refractory period and increases
 ventricular tachycardia cycle length without short-term scar formation or
 functional decline: Insights from a translational porcine model study
 Please contact Dr. Patrick M. Boyle
 ([pmjboyle@uw.edu](mailto:pmjboyle@uw.edu)) with any questions, concerns,
 complaints, or difficulties. This dataset contains data required to
 reproduce computational simulations presented in the 2025 paper by Zenger
 et al. #### Description of the data and file structure The repository
 contains all finite element model files needed to rerun simulations in
 openCARP. These files have the basename ring_hemi_26mm. or
 ring_hemi_28mm.*, depending on model dimensions. Specific finite element
 mesh file types: .pts: description of points in Cartesian coordinates
 (spacial unit: microns) .elem: description of how nodes (zero indexed) are
 interconnected by elements .lon: fiber orientations for each element
 .surf: description of mesh surface (zero indexed) triangulation .xfrm /
 .mshz: saved transform / state files for model visualization The .sv files
 contain initial conditions for all cell-scale ionic models used in
 simulation studies. The file ring_hemi_TT2_final.par provides the baseline
 parameters used to run all simulations in this study. The file
 ReproduceResults.sh is a driver script that can be run from the command
 line to produce the six exact simulations presented in Fig. 8A of the
 paper. Modifications to this script may be necessary to account for local
 machine settings. See documentation in script for more detail. Key for
 interpreting filenames:  * **Finite element mesh filenames:** *
 **ring_hemi prefix:** This refers to a model of a tissue ring subdivided
 into upper and lower hemispheres. * **26mm / 28mm suffix:** This refers to
 the outer diameter of the ring model. * **Specific file extensions:** *
 .pts: Finite element nodes in Cartesian coordinates (x, y, z); units of
 microns * .elem: Finite element tetrahedral connectedness specifications,
 four nodes per element * .lon: Finite element fiber orientation vectors,
 assigned on an element-wise basis * .surf: Surface file containing node
 information for surfaces to be visualized * .xfrm: Geometric transform
 file for visualizing data in meshalyzer * \_RenderVm.mshz: Saved state
 file for visualizing membrane voltage (Vm) in meshalyzer * **.sv
 extension:** Save state data for OpenCARP ionic models * **GTT2_fast
 prefix for .sv files:** refers to the TT2 ionic model * **[factor]xIKrIKs
 token:** refers to the scaling factor applied to rapid and slow delayed
 rectifier potassium currents (IKr and IKs, respectively) in the TT2 ionic
 model * **Normal / GrayZone token:** Refers to model settings associated
 with normal human ventricular myocardium vs. tissue  in the vicinity of
 infarcted regions, which is affected by ionic remodeling (i.e., Gray Zone,
 Peri-Infarct Zone, Border Zone, etc.) * **10x1Hz_Prepace token:**
 Describes the prepacing stimulation protocol, which involves delivery of
 10 electrical stimuli at 1 Hz frequency; after the response from the final
 stimulus has resolved, the state of the ionic model is written into the
 .sv file * **ring_hemi_TT2_final.par:** OpenCARP parameter file for
 running simulations in the ring model with the ten Tusscher 2006 (TT2)
 human ventricular ionic model (DOI: 10.1152/ajpheart.00109.2006) *
 **ReproduceResults.sh:** Bash script to invoke commands for reproducing
 results #### Example usage -- tested using openCARP v8.2 on Ubuntu 22.04.5
 The command below (text following $) can be executed on a properly
 configured system. Example output of the script is also included. $ bash
 -u ReproduceResults.sh; Fig8A 2.6 cm Control -- last act. = 1499 ms;
 reentry: period = 413.2 ms, freq = 2.420 Hz Fig8A 2.6 cm +20% ERP -- last
 act. = 1499 ms; reentry: period = 430.1 ms, freq = 2.325 Hz Fig8A 2.6 cm
 +40% ERP -- last act. = 849 ms [simulation terminated before 1000 ms
 post-stim] Fig8A 2.8 cm Control -- last act. = 1464 ms; reentry: period =
 422.1 ms, freq = 2.369 Hz Fig8A 2.8 cm +20% ERP -- last act. = 1499 ms;
 reentry: period = 441.4 ms, freq = 2.266 Hz Fig8A 2.8 cm +40% ERP -- last
 act. = 1499 ms; reentry: period = 464.1 ms, freq = 2.155 Hz #### Data
 visualization -- tested using meshalyzer v5.2 on Ubuntu 22.04.5 The
 command below can be executed on a properly configure system to visualize
 the results of a particular simulation; modify the mesh name provided and
 the path to the relevant vm.igb file to visualize results of different
 simulations. $ meshalyzer \ mesh/ring_hemi_26mm.pts \
 ReproduceResults/Ring_26mm/1.00xIKrIKs/S2_374/vm.igb \
 mesh/ring_hemi_26mm_RenderVm.mshz; The first line after the invocation of
 the visualization program is the path to the .pts file associated with the
 relevant mesh. The second line is the path to the vm.igb file containing
 membrane voltage over time. The third line is the path to a meshalyzer
 state file compatible with v5.2 of the software. #### Sharing/access
 information All files contained in this repository are published under the
 Creative Commons CC0 license. Future users are thus allowed and encouraged
 to distribute, remix, adapt, and build upon the material in any medium or
 format, with no conditions. Although CC0 does not require attribution, we
 encourage all parties who reuse this dataset in any way to cite the paper
 with which it was published (Zenger et al. 2025). #### Code/software
 information * openCARP and meshalyzer information can be found at:
 [https://opencarp.org/](https://opencarp.org/)