From 9363a6bc6b67291b236a5aea4b8e58711537a7b9 Mon Sep 17 00:00:00 2001 From: Michael Clerx Date: Wed, 7 Aug 2024 00:24:19 +0100 Subject: [PATCH] Updating model tree --- c/tree.md | 91 ++++++++++++++++++++++++++++--------------------------- 1 file changed, 47 insertions(+), 44 deletions(-) diff --git a/c/tree.md b/c/tree.md index 4adbbfe..82092f1 100644 --- a/c/tree.md +++ b/c/tree.md @@ -38,7 +38,6 @@ Some papers with model lists or model comparison: - [Wilders (2007) Computer modelling of the sinoatrial node](https://doi.org/10.1007/s11517-006-0127-0) - [Ricci, Bartolucci, Severi (2022) The virtual sinoatrial node: What did computational models tell us about cardiac pacemaking?](https://doi.org/10.1016/j.pbiomolbio.2022.10.008) - Some reductions and propagation models: - Fitzugh 1961 reduces HH to a "Bonhoeffer-Van der Pol" model - Nagumo 1962 makes Fitzhugh 1961 suitable for propagation @@ -71,6 +70,10 @@ Some CaRU stochastic/spatial models: - Tanskanen 2005 builds on Greenstein 2002 - Greenstein 2006 builds on Greenstein 2002 - Flaim et al 2006 modified Greenstein 2006 +- Stern 2014 built a sparking SAN model based on Maltsev 2009 +- Voigt 2014 built a CaRU model based on Voigt 2013 +- Sutanto 2018 adapted the Voigt 2014 model +- Maltsev 2022 build on Stern 2014 A number of software packages are referenced, because they contain models. Some experimented with re-use of model code, making the models difficult to extract. @@ -664,7 +667,7 @@ Modifications: - Rescaled IKs ## 2008 Himeno GS -Base: [Kuzumoto 2007](#2007-kuzumoto-gv), [Sarai 2003](#2003-sarai-ms) +Base: [Sarai 2003](#2003-sarai-ms), [Kuzumoto 2007](#2007-kuzumoto-gv) | [Original simBio code](http://www.sim-bio.org/model) | [Paper](https://doi.org/10.2170/physiolsci.RP015207) Himeno, Sarai, Matsuoka, Noma (2008) Ionic mechanisms underlying the positive chronotropy induced by beta1-adrenergic stimulation in guinea pig sinoatrial node cells @@ -720,7 +723,7 @@ Base: [Lindblad 1996](#1996-lindblad-ra) | [Paper](https://doi.org/10.1016/j.bpj.2008.09.057) Aslanidi, Boyett et al., Zhang (2009) Mechanisms of transition from normal to reentrant electrical activity in a model of rabbit atrial tissue; interaction of tissue heterogeneity and anisotropy ## 2009b Aslanidi CP -Base: [Benson 2008](2008-benson-cv) +Base: [Benson 2008](#2008-benson-cv) | [Paper](https://doi.org/10.1016/j.bpj.2009.03.061) Aslanidi, Stewart, Boyett, Zhang (2009) Optimal Velocity and Safety of Discontinuous Conduction through the Heterogeneous Purkinje-Ventricular Junction ## 2009 Decker CV @@ -788,7 +791,7 @@ Base: [Kurata 2002](#2002-kurata-rs) | [Paper](https://doi.org/10.1016/j.yjmcc.2010.03.015) Imtiaz, von der Weid, Laver, van Helden (2010) SR Ca store refill; a key factor in cardiac pacemaking ## 2010 Korhonen Md -Base: [Korhonen 2008](2008-korhonen-md) +Base: [Korhonen 2008](#2008-korhonen-md) | [Paper](https://doi.org/10.1113/jphysiol.2009.185173) Korhonen, Rapila et al., Tavi (2010) Local Ca releases enable rapid heart rates in developing cardiomyocytes ## 2010 Li MV @@ -839,7 +842,7 @@ Modifications: | [Paper](https://doi.org/10.1016/j.yjmcc.2011.02.007) Heijman, Volders, Westra, Rudy (2011) Local control of beta-adrenergic stimulation; effects on ventricular myocyte electrophysiology and Ca transient ## 2011 Kharche MS -Base: Many +Base: [Zhang 2000](#2000-zhang-rs), [Kurata 2002](#2002-kurata-rs) | [Paper](https://doi.org/10.1152/ajpheart.00143.2010) Kharche, Yu, Lei, Zhang (2011) A mathematical model of action potentials of mouse sinoatrial node cells with molecular bases ## 2011 Koivumaki HA @@ -871,7 +874,7 @@ Bits: - INaK from Smith 2004, with reparametrisation ## 2011 Tao LS -Base: [Kurata 2002](#2002-kurata-rs) +Base: [Zhang 2000](#2000-zhang-rs), [Kurata 2002](#2002-kurata-rs) | [Paper](https://doi.org/10.1016/j.bpj.2011.05.069) Tao, Paterson, Smith (2011) A model of cellular cardiac-neural coupling that captures the sympathetic control of sinoatrial node excitability in normotensive and hypertensive rats ## 2012 Christel MS @@ -921,11 +924,12 @@ Base: [Courtemanche 1998](#1998-courtemanche-ha) ## 2013 Paci Hi **Included** | Base: [Paci 2012](#2012-paci-he) -| [Paper]() +| [Paper](https://doi.org/10.1007/s10439-013-0833-3) Paci, Hyttinen, Aalto-Setala, Severi (2013) Computational Models of Ventricular and Atrial-Like Human Induced Pluripotent Stem Cell Derived Cardiomyocytes ## 2013 Voigt-Heijman HA **Included** | Base: [Grandi 2011](#2011-grandi-pandit-voigt-ha) +| Authors provided mmt code | [Paper](https://doi.org/10.1016/j.yjmcc.2013.03.011) Voigt, Heijman et al., Dobrev (2013) Impaired Na-dependent regulation of acetylcholine-activated inward-rectifier K current modulates AP rate dependence in cAF Modifications: @@ -934,11 +938,11 @@ Modifications: - Modified IK1 (changed gK1 and a) ## 2013a Yaniv RS -Base: +Base: [Yaniv 2012](#2012-yaniv-rs) | [Paper](https://doi.org/10.1016/j.yjmcc.2013.04.026) Yaniv, Sirenko et al., Lakatta (2013) New evidence for coupled clock regulation of the normal automaticity of sinoatrial nodal pacemaker cells; bradycardic effects of ivabradine are linked to suppression of intracellular Ca cycling ## 2013b Yaniv RS -Base: +Base: [Maltsev 2009](#2009-maltsev-rs) | [Paper](https://doi.org/10.1016/j.bpj.2013.08.024) Yaniv, Stern, Lakatta, Maltsev (2013) Mechanisms of beat-to-beat regulation of cardiac pacemaker cell function by Ca cycling dynamics ## 2014 Asakura HV @@ -969,10 +973,6 @@ Base: [Soltis 2010](#2010-soltis-rv) | [Original matlab code](https://github.com/drgrandilab/Morotti-et-al-2014-Mouse-Ventricular-Model) | [Paper](https://doi.org/10.1113/jphysiol.2013.266676) Morotti, Edwards et al., Grandi (2014) A novel computational model of mouse myocyte electrophysiology to assess the synergy between Na+ loading and CaMKII -## 2014 Stern RS -Base: -| [Paper](https://doi.org/10.1085/jgp.201311123) Stern, Maltseva et al., Maltsev (2014) Hierarchical clustering of ryanodine receptors enables emergence of a calcium clock in sinoatrial node cells - ## 2014 Yang MV Base: [Yang 2012 mouse](#2012-yang-mv) | [Original matlab code](https://github.com/saucermanlab/model-archive) @@ -997,30 +997,36 @@ Bits: - Currents, Ca-handling, Na-handling: Shannon 2004 - CaMKII, PKA: Soltis 2010 -## 2015 Schmidt -Base: -| [Paper]() +## 2015 Paci Hi +Base: [Paci 2013](#2013-paci-hi) +| [Paper](https://doi.org/10.1111/bph.13282) Paci, Hyttinen, Rodriguez, Severi (2015) Human induced pluripotent stem cell-derived versus adult cardiomyocytes; an in silico electrophysiological study on ionic current block effects + +## 2015 Schmidt HA +Base: [Voigt-Heijman 2013](#2013-voigt-heijman-ha) +| [Paper](https://doi.org/10.1161/CIRCULATIONAHA.114.012657) + +Modifications: +- Added K2p3.1 current ## 2015 Yaniv RS -Base: +Base: Probably [Yaniv 2013a](#2013a-yaniv-rs) | [Paper](https://doi.org/10.1016/j.yjmcc.2015.07.024) Yaniv, Ganesan et al., Lakatta (2015) Real-time relationship between PKA biochemical signal network dynamics and increased action potential firing rate in heart pacemaker cells ## 2016 Behar RS -Base: +Base: [Yaniv 2015](#2015-yaniv-rs) | [Paper](https://doi.org/10.3389/fphys.2016.00419) Behar, Ganesan, Zhang, Yaniv (2016) The autonomic nervous system regulates the heart rate through cAMP-PKA dependent and independent coupled-clock pacemaker cell mechanisms -## 2016 Gattoni -Base: Pandit 2001 -| [Paper]() +## 2016 Gattoni LV +Base: [Pandit 2001](#2001-pandit-lv) +| [Paper]() Gattoni, Roe et al., Smith (2016) The calcium-frequency response in the rat ventricular myocyte; an experimental and modelling study -## 2016 Gray RV -**Included** -| Base: New -| [Paper](https://doi.org/10.1371/journal.pcbi.1005087) Gray, Pathmanathan (2016) A Parsimonious Model of the Rabbit Action Potential Elucidates the Minimal Physiological Requirements for Alternans and Spiral Wave Breakup +Modifications: +- Hinch 2004 Ca dynamics +- Lewalle et al. 2014 INaK model (despite Smith as co-author?) -## 2016 Majumder RA -Base: -| [Paper]() +## 2016 Majumder RAd +Base: [Korhonen 2009](#2009-korhonen-ld) +| [Paper](https://doi.org/10.1371/journal.pcbi.1004946) Majumder et al., Pijnappels, Panfilov (2016) A Mathematical Model of Neonatal Rat Atrial Monolayers with Constitutively Active Acetylcholine-Mediated K Current ## 2016 Morotti HA Base: [Grandi 2011](#2011-grandi-pandit-voigt-ha) @@ -1042,12 +1048,12 @@ Modifications: - Modified INa steady states ## 2016 Pohl HS -Base: +Base: [Dokos 1996a](#1996a-dokos-rs) | [Paper](https://doi.org/10.1088/2057-1976/2/3/035006) Pohl, Wachter, Hatam, Leonhardt (2016) A computational model of a human single sinoatrial node cell ## 2016 Varela CA -Base: -| [Paper]() +Base: [Ramirez 2000](#2000-ramirez-ca) +| [Paper](https://doi.org/10.1371/journal.pcbi.1005245) Varela, Colman, Hancox, Aslanidi (2016) Atrial Heterogeneity Generates Re-entrant Substrate during Atrial Fibrillation and Anti-arrhythmic Drug Action ## 2017 Aguilar HA Base: [Courtemanche 1998](#1998-courtemanche-ha) @@ -1115,6 +1121,10 @@ Modifications: Bits: - Calcium subspaces based on Koivumaki 2011 +## 2017 Paci Hi +Base: [Paci 2015](#2015-paci-hi) +| [Paper](https://doi.org/10.1016/j.hrthm.2017.07.026) Paci, Passini et al., Rodriguez (2017) Phenotypic Variability in LQT3 Human induced pluripotent stem cell-derived cardiomyocytes and their response to antiarrhythmic pharmacologic therapy; an in silico approach + ## 2017 Surdo MV Base: [Morotti 2014](#2014-morotti-mv) | [Original matlab code](https://github.com/drgrandilab/Surdo-et-al-2017-Mouse-Ventricular-Model-with-Myofilament-Contraction) @@ -1129,24 +1139,20 @@ Base: [Ten Tusscher 2006](#2006-ten-tusscher-hv) | [Paper](https://doi.org/10.1038/s41598-018-33958-y) Bai, Gladding et al., Zhao (2018) Ionic and cellular mechanisms underlying TBX5-PITX2 insufficiency-induced atrial fibrillation; Insights from mathematical models of human atrial cells ## 2018 Colman HA -Base: This model has 4 variants +Base: [Courtemanche 1998](#1998-courtemanche-ha), [Nygren 1998](#1998-nygren-ha), [Chang 2014](#2014-chang-ha) | [Original code](https://github.com/michaelcolman/hAM_WL) | [Paper](https://doi.org/10.3389/fphys.2018.01211) Colman, Saxena, Kettlewell, Workman (2018) Description of the Human Atrial Action Potential Derived From a Single, Congruent Data Source; Novel Computational Models for Integrated Experimental-Numerical Study of Atrial Arrhythmia Mechanisms ## 2018 Koivumaki Hi -Base: Korhonen 2010, Paci 2015 +Base: [Korhonen 2010](#2010-korhonen-md), [Paci 2015](#2015-paci-hi) | [Paper]() Koivumaki, Naumenko et al., Tavi (2018) Structural Immaturity of Human iPSC-Derived Cardiomyocytes; In Silico Investigation of Effects on Function and Disease Modeling ## 2018 Paci Hi **Included** -| Base: [Paci 2013](#2013-paci-hi) +| Base: [Paci 2017](#2017-paci-hi) | [Paper](https://doi.org/10.3389/fphys.2018.00709) Paci, Polonen et al., Hyttinen (2018) Automatic optimization of an in silico model of human iPSC derived cardiomyocytes recapitulating calcium handling abnormalities -## 2018 Sutanto HA -Base: -| [Paper]() - ## Loewe 2019 HS Base: [Fabbri 2017](#2017-fabbri-hs) | [Official CellML](https://models.physiomeproject.org/workspace/58f) @@ -1242,8 +1248,9 @@ Base: [Yang 2012](#2012-yang-hv) | [Paper](https://doi.org/10.1002/cpt.2240) Fogli Iseppe, Ni et al., Grandi (2021) Sex-specific classification of drug-induced Torsade de Pointes susceptibility using cardiac simulations and machine learning ## 2021 Gaur PV -Base: -[Paper](https://doi.org/10.1371/journal.pcbi.1009137) Gaur, Qi et al., Vigmond (2021) A computational model of pig ventricular cardiomyocyte electrophysiology and calcium handling; Translation from pig to human electrophysiology +Base: [O'Hara 2011](#2011-ohara-hv), but many new parts +| Official openCARP, Myokit, and CellML code is provided in the supplement +| [Paper](https://doi.org/10.1371/journal.pcbi.1009137) Gaur, Qi et al., Vigmond (2021) A computational model of pig ventricular cardiomyocyte electrophysiology and calcium handling; Translation from pig to human electrophysiology ## 2021 Hoekstra HS Base: [Fabbri 2017](#2017-fabbri-hs) @@ -1280,10 +1287,6 @@ Base: [Koivumaki 2011](#2011-koivumaki-ha), Regazzoni 2020 Known as: MBS2023 -## 2022 Maltsev RS -Base: -| [Paper](https://doi.org/10.1085/jgp.202113061) Maltsev, Stern, Maltsev (2022) Disorder in Ca release unit locations confers robustness but cuts flexibility of heart pacemaking - ## 2022 Moise RS Base: [Severi 2012](#2012-severi-rs) | [Original matlab code](https://github.com/SHWeinberg/SAN_FeedbackModel)