DOI: 10.5061/dryad.g79cnp62q
title: Data from: Systematic computational assessment of atrial function impairment due to fibrotic remodeling in electromechanical properties

description: This dataset supports our study “Systematic computational assessment of
 atrial function impairment due to fibrotic remodeling in electromechanical
 properties,” which explores the impact of electromechanical remodeling in
 the fibrotic left atrium. It contains deidentified, patient-specific left
 atrial geometries; complete parameter sets for baseline and fibrotic
 combinations; scripts used to perform the simulations; and the resulting
 output files. Each geometry includes fibrosis patterns, fiber
 orientations, region tags, and pacing sites. Parameter files specify
 alterations in nine fibrosis-associated properties—conduction velocities,
 ion channel conductances, active tension scaling, myofilament kinetics,
 and tissue stiffness—across one-factor-at-a-time and fractional factorial
 sensitivity analysis setups. Simulation and preprocessing scripts are
 provided for reproducibility and can be executed using the Carpentry
 software framework (Numericor). Output data, provided in CSV format,
 include left atrial pressure–volume (PV) loop recordings and hemodynamic
 variables from the coupled 3D electromechanical–0D circulatory model for
 all simulated conditions. These data quantify atrial work and contractile
 performance under varied remodeling scenarios. The dataset is structured
 to enable replication of the published results and to support further
 investigations into the biophysical determinants of atrial dysfunction and
 stroke risk.
description: # Data from: Systematic computational assessment of atrial function
 impairment due to fibrotic remodeling in electromechanical properties
 Dataset DOI: [10.5061/dryad.g79cnp62q](10.5061/dryad.g79cnp62q) ##
 Description of the data and file structure This data set contains
 deidentified patient LA geometries, parameters and scripts used to run
 electromechanical simumulations for these in two sensitivity analysis
 setups, and resulting output PV loop data. ### Files and variables ####
 File: geometries.zip **Description:** vtk files for all LA geometries,
 with fiber orientations and tags (tag file attached in main folder) + vtx
 files for pacing areas for each patient. Structured in folders for Patient
 1, Patient 2, and Patient 3; for original and extended fibrosis levels.
 #### File: parameters_OFAT_FFD.csv **Description:** parameter changes
 imposed in fibrotic regions in geometries above in the various sensitivity
 analysis simulations (baseline; 9 one-factor-at-a-time simulations, and 32
 fractional factorial analysis simulations)  ##### Variables * Simulation:
 Given sensitivity analysis combination this parameter combination was
 applied for * CV_L (P1): Longitudinal conduction velocity (CV) for Patient
 1 * CV_T (P1): Transverse CV for Patient 1 (cm/s) * CV_L (P2):
 Longitudinal CV for Patient 2 (cm/s) * CV_T (P2): Transverse CV for
 Patient 2 (cm/s) * CV_L (P3): Longitudinal CV for Patient 3 (cm/s) * CV_T
 (P3): Transverse CV for Patient 3 (cm/s) * GK1: Conductance for IK1
 (mS/cm^2) * GCaL: Conductance for ICaL (mS/cm^2) * GNa: Conductance for
 INa (mS/cm^2) * Ta: Active tension scaling factor (kPa) * mu: Myofilament
 binding rate (-) * a: Isotropic stiffness parameter (kPa) * af: Additional
 fiber direction stiffness parameter (kPa) #### File:
 pv_loops_all_simulations.zip **Description:** pv_loops_all_simulations.zip
 – output files for LA measurements from the coupled biomechanical-0D
 circulatory model; for all sensitivity analysis combinations; also this
 per patient and per fibrosis level Each txt file contains these variables:
 * Time: Time step for simulated values; note that it starts with 50
 "minus" steps which corresponds to the unloading procedure. 10
 cycles with 2000 steps in each; pacing happens at 30 ms (ms). * Pressure:
 Recorded LA pressure in the coupled biomechanical - 0D circulatory model
 (mmHg) * Volume: Recorded LA volume in the coupled biomechanical - 0D
 circulatory model (mL) * State: descriptive state; load (for preloading),
 eject (for active contraction), or fill (for passive blood filling) *
 P_out (mmHg), Q_out (mL/s), D_P_out (mmHg), P_in (mmHg), Q_in (mL/s),
 D_P_in (mmHg) – additional parameters tracked by the coupled
 biomechanical-0D circulatory model (see details in Augustin et al., 2021,
 Comput. Methods Appl. Mech. Eng.) #### File:
 sensitivity_analysis_scripts.zip **Description:**  bash scripts used to
 run all the sensitivity analysis simulations; for all 3 patients and both
 fibrosis levels (note: in these Patient 1=AF2, Patient 2=AF4, and Patient
 3=AF5). These can be run with Carpentry software (Numericor;
 [https://numericor.at/rlb/wordpress/](https://numericor.at/rlb/wordpress/)), or opened as txt files to see specific parameter assignments. #### File: unloading_scripts.zip **Description:** bash scripts used to run the unloading/reloading procedure, producing pre-systolic inflated volumes with a constant pressure of 10 mmHg; these were run prior to the organ-level simulations, for all 4 possible stiffness parameter combinations, for all 3 patients and both fibrosis levels. These can be run with Carpentry software (Numericor; [https://numericor.at/rlb/wordpress/](https://numericor.at/rlb/wordpress/)), or opened as txt files to see specific parameter assignments. #### File: cv_calibration.sh **Description:** Bash script used to calculate all CV value combinations. It can be run in the terminal with a Patient ID string (e.g., "P1") and target longitudinal CV as parameters, and outputs all fibrotic value combinations for that patient/value. Builds on OpenCarp's tuneCV functionality. ## Code/software Geometries (vtk files; [https://vtk.org/](https://vtk.org/)) files can be opened by a number of softwares; e.g. Paraview. Parameter documentation and pv loop output data come as csv files (text files). Scripts used to analyze and plot results are published here: [https://github.com/aashildte/sensitivity_analysis_pvloops](https://github.com/aashildte/sensitivity_analysis_pvloops). Scripts are bash scripts used to run simulations on the University of Washington Hyak supercomputer cluster, with Carpentry (commercial software from [https://numericor.at/](https://numericor.at/)) installed. The cv calibration script can be used with the open-source OpenCarp installed (see [https://opencarp.org/documentation/examples/02_ep_tissue/03a_study_prep_tunecv](https://opencarp.org/documentation/examples/02_ep_tissue/03a_study_prep_tunecv) for documentation and examples on how to use tuneCV). ## Human subjects data This repository contains computational meshes of human left atria segmented from late gadolinium enhanced cardiac magnetic resonance imaging. These meshes support the replication of our findings while protecting confidential patient information. This study was approved by the University of Washington Institutional Review Board. All participants provided written informed consent.