Cell to Whole Organ Global Sensitivity Analysis on a Four-chamber Heart Electromechanics Model Using Gaussian Processes Emulators - Training Datasets
Strocchi M, Longobardi S, Augustin CM, Gsell MAF, Petras A, Rinaldi CA, et al. (2023) Cell to whole organ global sensitivity analysis on a four-chamber heart electromechanics model using Gaussian processes emulators. PLoS Comput Biol 19(6): e1011257. https://doi.org/10.1371/journal.pcbi.1011257
This database contains all training datasets for the Gaussian processes emulators (GPEs) trained in the study entitled "Cell to Whole Organ Global Sensitivity Analysis on a Four-chamber Electromechanics Model Using Gaussian Processes Emulators", submitted to PLOS Computational Biology.
Paper , Training dataset (Zenodo) , CodeWhole Torso Computational Models
Qian S, Monaci S, Mendonca-Costa C, Campos F, Gemmell P, Zaidi HA, Rajani R, Whitaker J, Rinaldi CA, Bishop MJ. Additional coils mitigate elevated defibrillation threshold in right-sided implantable cardioverter defibrillator generator placement: a simulation study. Europace. 2023 Jun;25(6):euad146.
Whole torso computational models generated from high-resolution CT data.
Paper , Meshes (Zenodo)Predicting Atrial Fibrillation Recurrence by Combining Population Data and Virtual Cohorts of Patient-Specific Left Atrial Models
Roney, Caroline H., Iain Sim, Jin Yu, Marianne Beach, Arihant Mehta, Jose Alonso Solis-Lemus, Irum Kotadia et al. Predicting Atrial Fibrillation Recurrence by Combining Population Data and Virtual Cohorts of Patient-Specific Left Atrial Models. Circulation: Arrhythmia and Electrophysiology (2021): CIRCEP-121.
We include surface meshes in vtk format, consisting of the nodes, triangular elements, the atrial coordinate fields defined on the nodes, and the endocardial and epicardial fibre fields defined on the elements.
Paper , Meshes (Zenodo) , Data governanceVirtual cohort of 1000 synthetic heart meshes from adult human healthy population
Rodero C, Strocchi M, Marciniak M, Longobardi S, Whitaker J, O’Neill MD, Gillette K, Augustin C, Plank G, Vigmond EJ, Lamata P. Linking statistical shape models and simulated function in the healthy adult human heart. PLoS computational biology. 2021 Apr 15;17(4):e1008851.
Paper , Meshes (Zenodo)Virtual cohort of extreme and average four-chamber heart meshes from statistical shape model
Rodero C, Strocchi M, Marciniak M, Longobardi S, Whitaker J, O’Neill MD, Gillette K, Augustin C, Plank G, Vigmond EJ, Lamata P. Linking statistical shape models and simulated function in the healthy adult human heart. PLoS computational biology. 2021 Apr 15;17(4):e1008851.
Paper , Meshes (Zenodo)Virtual cohort of adult healthy four-chamber heart meshes from CT images
Rodero C, Strocchi M, Marciniak M, Longobardi S, Whitaker J, O’Neill MD, Gillette K, Augustin C, Plank G, Vigmond EJ, Lamata P. Linking statistical shape models and simulated function in the healthy adult human heart. PLoS computational biology. 2021 Apr 15;17(4):e1008851.
Paper , Meshes (Zenodo)A publicly available virtual cohort of four-chamber heart meshes for cardiac electro-mechanics simulations
Strocchi M, Augustin CM, Gsell MAF, Karabelas E, Neic A, et al. (2020) A publicly available virtual cohort of four-chamber heart meshes for cardiac electro-mechanics simulations. PLOS ONE 15(6): e0235145
Paper , Meshes (Zenodo)The Impact of Wall Thickness and Curvature on Wall Stress in Patient-Specific Electromechanical Models of the Left Atrium
Augustin CM, Fastl TE, Neic A, et al. The impact of wall thickness and curvature on wall stress in patient-specific electromechanical models of the left atrium. Biomech Model Mechanobiol. 2020;19(3):1015‐1034. doi:10.1007/s10237-019-01268-5
Paper , Meshes (Zenodo)Constructing a Human Atrial Fibre Atlas
Roney, C.H., Bendikas, R., Pashakhanloo, F. et al. Constructing a Human Atrial Fibre Atlas. Ann Biomed Eng 49, 233–250 (2021). https://doi.org/10.1007/s10439-020-02525-w
Paper , Meshes (Zenodo)A Virtual Cohort of Twenty-four Left-ventricular Models of Ischemic Cardiomyopathy Patients
Mendonca Costa, Caroline, Neic, Aurel Medical University of Graz, and Kerfoot, Eric King’s College London. A Virtual Cohort of Twenty-four Left-ventricular Models of Ischemic Cardiomyopathy Patients (2020)
KCL Library ArchivePersonalized computational finite element models for left atrial electromechanics
Fastl, Thomas E, Tobon-Gomez, Catalina King's College London, Crozier, Andrew Medical University of Graz, and McCarthy, Karen P Royal Brompton Hospital. Personalized Computational Finite Element Models for Left Atrial Electromechanics (2018).
KCL Library ArchiveA model of cardiac contraction based on novel measurements of tension development in human cardiomyocytes.
S Land, SJ Park-Holohan, NP Smith, CG Dos Remedios, JC Kentish, SA Niederer. JMCC, 2017
A model of human cardiac contraction intended for multi-scale modelling applications. Download includes relevant experimental data, and C++ code is available on request.
Pubmed , MatlabA Biophysical Systems Approach to Identifying the Pathways of Acute and Chronic Doxorubicin Mitochondrial Cardiotoxicity
de Oliveira BL, Niederer S. A biophysical systems approach to identifying the pathways of acute and chronic doxorubicin mitochondrial cardiotoxicity. PLoS Computational Biology. 2016 Nov 21;12(11):e1005214.
The clinical use of the anthracycline doxorubicin is limited by its cardiotoxicity which is associated with mitochondrial dysfunction. Redox cycling, mitochondrial DNA damage and electron transport chain inhibition have been identified as potential mechanisms of toxicity. However, the relative roles of each of these proposed mechanisms are still not fully understood. The purpose of this study is to identify which of these pathways independently or in combination are responsible for doxorubicin toxicity. A state of the art mathematical model of the mitochondria including the citric acid cycle, electron transport chain and ROS production and scavenging systems was extended by incorporating a novel representation for mitochondrial DNA damage and repair. In silico experiments were performed to quantify the contributions of each of the toxicity mechanisms to mitochondrial dysfunction during the acute and chronic stages of toxicity. Simulations predict that redox cycling has a minor role in doxorubicin cardiotoxicity. Electron transport chain inhibition is the main pathway for acute toxicity for supratherapeutic doses, being lethal at mitochondrial concentrations higher than 200μM. Direct mitochondrial DNA damage is the principal pathway of chronic cardiotoxicity for therapeutic doses, leading to a progressive and irreversible long term mitochondrial dysfunction.
PLoS Computational Biology , MatlabVerification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour
Land S, Gurev V, Arens S, Augustin CM, Baron L, Blake R, Bradley C, Castro S, Crozier A, Favino M, Fastl TE. Verification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2015 Dec 8;471(2184):20150641.
To aid in the verification of current and future cardiac mechanics solvers, this study provides three benchmark problems for cardiac mechanics. These benchmark problems test the ability to accurately simulate pressure-type forces that depend on the deformed objects geometry, anisotropic and spatially varying material properties similar to those seen in the left ventricle and active contractile forces.
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences , BitbucketA Spatially Detailed Model of Isometric Contraction Based on Competitive Binding of Troponin I Explains Cooperative Interactions between Tropomyosin and Crossbridges
Land S, Niederer SA. PLoS Computational Biology, 2015
A spatially detailed ODE model of contraction based on continuous flexible chain model of the thin filament. Includes explicit TnI kinetics and a biophysically detailed representation of RU-RU, RU-XB, and XB-XB cooperativity.
PLOS , MatlabAn analysis of deformation-dependent electromechanical coupling in the mouse heart
Land S, Niederer SA, Aronsen JM, Espe EK, Zhang L, Louch WE, Sjaastad I, Sejersted OM, Smith NP. J Physiol. 2012 15;590(Pt 18):4553-69. Epub 2012 May 21. PubMed ID: 22615436
A model of contraction fitted to mouse data at physiological temperature and frequency, including length and velocity dependent tension generation.
Journal of Physiology , cellML , MatlabA mathematical model of the murine ventricular myocyte: a data-driven biophysically based approach applied to mice overexpressing the canine NCX isoform A Mathematical Model of the Slow Force Response to Stretch in Rat Ventricular Myocytes
L. Li , S. A. Niederer , W. Idigo , Y. H. Zhang , P. Swietach , B. Casadei , N. P. Smith, 2010 American Journal of Physiology, Voume 299 no. H1045-H1063
A mouse electrophysiology model fitted to mouse data at physiological temperatures and capable of pacing to physiological pacing rates.
American Journal of Physiology , cellMLA Quantitative Analysis of Cardiac Myocyte Relaxation: A Simulation Study
Steven Niederer, Peter Hunter, Nicholas Smith, 2006 Biophysical Journal, 90 1697-1722 PubMed ID: 16339881
A biophysical data driven model of length, velocity and calcium dependent tension development in rat cardiac muscle at room temperature.
Science Direct , cellML