Ajuha 2017, Bickenback 2013, Fehlings 2017 - background on SCI
Witiw 2015 - phases of SCI pathology
Rowald 2022 - activity-dependent stimulation restores function by activating specific circuits
	- Superior results with dorsal root targeting
	- Computational modelling -> design
Kathe 2022 - mechanism of functional restoration with SCS
Arber 2017 - brain connects to cord to control movement
Courtine 2019, Courtine 2008 - SCI does not damage all pathways, but disrupts
Anderson 2004, Fawcett 2007 - limited recovery after initial stages
Courtine 2008, Courtine 2009, Takeoka 2014, Friedli 2015, Murray 2010 - reorganisation of circuits after SCI for recovery
- recovery even after significant lesions
Gerasimenko 2015 - tSCS for SCI; alters excitability of circuits
Wenger 2016 - spatiotemporally patterned stimulation, modelling for design
Moraud 2016, Capogrosso 2013 - mechanisms of neuromodulation for SCI (root-mediated)
Capogrosso 2016 - dorsal roots as mechanism
Gaunt 2006 - intraspinal stimulation activates roots before spinal cord neurons
Capogrosso 2013 - model of EES for SCI; shows mediated by roots
Capgrosso 2018 - targeting specific roots along with gait cycle
Molnar 2014 - mechanism of SCS for pain (dorsal columns)
Kathe 2022 - mechanism of EES for rehab: reorganisation of SC circuits

List of citations for each chapter

Chapter 1: DONE
- SCI produces functional loss - Ahuja 2017, Bickenback 2013, Fehlings 2017
- Morbidity of SCI - Ahuja 2017, Bickenback 2013, Fehlings 2017
- Prognosis of SCI (acute improvement) - Witiw 2015, Fawcett 2007
- Poor recovery after acute phase - Fawcett 2007, Anderson 2004
- SCI epidemiology - Ahuja 2017, Bickenback 2013
- SCI UK epidemiology - Lee013
- Complications of SCI - Ahuja 2017
- Epidural SCS after SCI - Harkema2011, Vogt2018, Wagner2018, Lorach2023, Rowald 2022, Kathe 2022
- Autonomic function with epidural stim - Squair 2022
- Epidural arrays activate spinal reflexes - Moraud 2016, Capogrosso 2013
- H reflex - Troni 1996
- Posterior root-muscle reflexes - mechanism papers. Dimitrijevic 1980
- Stimulation alters excitability - Angeli 2014
- Stimulation produced locomotor activity - Minassian 2007, Minassian 2004, Wegner 2016, van den Brand 2012, Gill 2018, Grahn 2017
- Stimulation for rehab - Harkema2011, Vogt2018, Wagner2018, Lorach2023, Rowald 2022, Kathe 2022
- Mechanism for repair: residual pathways - Courtine 2019, Courtine 2008, Kathe 2022
	Courtine 2008, Courtine 2009, Takeoka 2014, Friedli 2015, Murrary 2010 - reorganisation of pathways
- Maintenance of effect with stim off - Wagner 2018, Lorach 2023, Pena Pino 2020
- Spatiotemporal patterning of stimulation - Wagner2018, Wegner 2016
- Modelling of epidural stimulation for SCI - Capogrosso 2013, Capogrosso 2016, Rowald 2022
- Autonomic function and epidural stim - Squair 2022
- tSCS producing PRMRs - Krenn 2013, Minassian2007
- Rostrocaudal selectivity of tSCS - Sayenko 2015, Maertens de Noordhout 1988, Krenn 2013
- tSCS producing stepping movements - Sayenko 2015, Hofstoetter 2013
- tSCS in SCI - systematic review - MegiaGarcia2020
- tSCS in SCI - examples - Al'joboori 2020, Gerasimenko 2015, Sayenko 2019
- tSCS in SCI - example electrode montages - Sayenko2019, Gad2017, Gad2018a
- tSCS in SCI - lateral selectivity - Calvert 2019
- tSCS in SCI - rostrocaudal selectivity - Sayenko 2015, Maertens de Noordhout 1988, Krenn 2013, Sayenko 2015a
- tSCS computational models - Danner2011
- Modelling detailed anatomy - Lempka2020, Gunalan2017
- Modelling with post-procedure imaging - Lempka2020, Gunalan2017, ?LeadDBS
- Biophysical models for stimulation: example applications - Capogrosso2016, Holsheimer1998
- Simple trajectories - Kuhn 2008, Danner 2011, Ladenbauer 2010, Rattay 2000
- Hand-drawn trajectories - Capogrosso2016

Chapter 2: DONE
- Electrical neuromodulation
- Laws of electromagnetism - Maxwell 1865, Griffiths 2017
- FEM book - Langtangen 2019
- Electrode-tissue interface - Keogh 2020, Cogan 2008
- Capacitive and Faradaic reactions - Keogh 2020, Cogan 2008, Merrill 2005
- Double layer - Helmholtz 1879
- Electrode tissue interface models - Heuschkel 2001
- Capacitor - resistor model - Merrill 2005
- More complex models - Chapman 1913, Gouy 1910, Stern 1924, Franks 2005, Fricke 1932, Warburg 1989
- Robin condition - Joucla 2012
- Simple bounary conditions - Butson 2006, McIntyre 2001, McIntyre 2004, Rattay 2001, Miocinovic 2006
- Models of neurons - Koch 2003
- Cable models - Hodgkin 1946, Holmes 1992, Rall 1977
- HH dynamics - Hodgkin1952
- Myelinated axon models - McNeal1976
- MRG model - McIntyre2002
- Use of MRG model for stimulation - duffley2019, butson 2007, butson 2005
- VTA measures - Butson2007
- E-field based metrics, Duffley2019, Horn 2019
- Other e-field models - Duffley2019, astrom 2015
- Activating function - Rattay 1986, Rattay1989
- Numerical optimisation methods - Nocedal 2006


Chapter 3: DONE
- Models of stimulation for novel devices - Capogrosso2016, Wagner2018, Holsheimer 1998, Noailly 2014
- Optimisation of stimulation for therapies - Gunalan2017, Lempka2020
- Multicompartment model with HH dynamics - Hodgkin1952
- Activating function - Rattay1986, Rattay1989
- VTA - Butson2007
- Dielectric properties database - Hasgall2018
- COMSOL - COMSOL
- MRG model - McIntyre2002
- NEURON - Carnevale2006
- Comparison of VTA methods - Duffley2019

Chapter 4: DONE
- SCS for pain - Kumar2007
- SCS for rehab - Harkema2011, Vogt2018, Wagner2018
- Complications of SCS - Turner2004, Mekhail2011
- tSCS after SCI example - Sayenko2019
- tSCS after SCI lower limbs - Gad2017
- tSCS after SCI upper limbs - Gad2018a
- tSCS after SCI urinary tract - Gad2018
- tSCS after SCI spasticity - Hofstoetter2020
- Systematic review of tSCS after SCI - MegiaGarcia2020
- Interferential stimulation - Grossman2017
- COMSOL - COMSOL
- Simplified model of tSCS - Danner2011
- Individual anatomy in models - Lempka2020
- Individual anatomy in DBS models - Gunalan2017
- Spatiotemporally patterned stim for rehab - Wagner2018
- 3D Slicer - Kikinis2014
- CGAL - cgal
- iso2mesh - Fang2009
- Dielectric database - Hasgall2018
- Activating function - Rattay1986
- tSCS for rehab - Sayenko2019, Gad2017, Gad2018a

Chapter 5: DONE
- Electrical neuromodulation
- Voltage-sensitive ion channels - ?ephys text
- Modelling for SCS - Lempka2020
- Modelling for DBS - Gunalan2017
- Modelling for PNS - FitzGerald 2016?
- Modelling for design of new therapies - Capogrosso2016, Rowald 2022, Wagner 2018, Wegner 2016
- Laws of electromagnetics - Maxwell 1865
- Neural membrane time constant - Abbott 2001
- FEM method - Langtangen 2019
- COMSOL - COMSOL
- Python - van Rossum 2009
- FENICS - Scroggs 2022
- COMSOL- COMSOL

Chapter 6: DONE
- Electrical neuromodulation
- Side effects of neuromodulation due to activation
- Simplified metrics, e.g. quadratic decay - astrom2015, duffley2019
- FEM models for neuromodulation - Lempka2020, Gunalan2017, Capogrosso2016
- Modelling of tDCS - Saturnino 2019, Huang 2018
- Modelling of DBS - Gunalan2017
- Modelling of SCS - Lempka2020
- Anatomy in models - Lempka2020, Gunalan2017
- Norm of e-field as metric - Horn 2019, Duffley 2019
- VTA - Butson2007
- Activating function - Rattay1986, Rattay1989
- Biophysics for modelling stimulation - Capogrosso2016, Lempka2020, Gunalan2017
- HH models - Hodgkin1952
- Cable model - Hodgkin 1946, Holmes 1992, Rall 1977
- Neuron models for stimulation - mcneal1976, duffley2019, butson 2007, butson 2005
- MRG model - McIntyre2002
- MRG validation - McIntyre2002
- MRG for stimulation - duffley2019, butson 2007, butson 2005
- Coupled models for neuromodulation - Capogrosso2016, Gunalan2017, Lempka2020
- Idealised geometries - Gunalan2017, Danner2011
- Hand-drawn trajectories - Capogrosso2016
- Orientation-dependent response - Slopsema 2018, Anderson 2019
- Anatomy in models - Lempka2020, Gunalan2017
- Numerical optimisation - Nocedal 2006
- NEURON - Carnevale2006
- MRG - McIntyre2002
- Python - van Rossum 2009
- Anatomy in models - Lempka2020, Gunalan2017
- Simplified metrics - Duffley2019
- Validation of cable models for stimulation - Capogrosso2016, Wegner 2016, Rowald 2022
- Simplified geometries - DDanner 2011, Ladenbauer 2010, Rattay 2000
- Hand-drawn trajectories - Capogrosso2016
- Tractography - Catani 2008
- Modelling for developing new interventions - Capogrosso2016, Wagner2018, Holsheimer1998

Chapter 7: DONE
- SCS for walking after SCI - Wagner2018, Harkema2011, Vogt2018
- SCS for pain - Kumar2007
- Risk of SCS - Turner2004, Mekhail2011
- Maintenance of effect with stim off - Wagner 2018, Lorach 2023
- tSCS for SCI - MegiaGarcia2020, Sayenko2019, Gad2017, Gad2018a
- Ongoing trials of tSCS for SCI - Bye 2021
- Dielectric properties - Hasgall2018
- MRG model - McIntyre2002
- HH dynamics - Hodgkin1952
- NEURON - Carnevale2006
- SCS for rehab - Wagner2018, Harkema2011, Vogt2018
- tSCS for rehab - MegiaGarcia2020
- Mechanism of epidural stim for rehab - residual pathways - Courtine 2019, Courtine 2008, Kathe 2022
	Courtine 2008, Courtine 2009, Takeoka 2014, Friedli 2015, Murrary 2010
- Root entry zone mediated activation - Capogrosso 2013, Capogrosso 2016, Rowald 2022
- Spatially patterned stimulation - Wagner2018, Wegner 2016, Rowald 2022

Chapter 8: DONE
- Ongoing trials of tSCS for SCI - Bye 2021
- Mechanism of epidural SCS for rehab - root mediated vs. via reorganisation?
- Interferential stimulation - Grossman2017
- tSCS in SCI - lateral selectivity - Calvert 2019
- tSCS in SCI - rostrocaudal selectivity - Sayenko 2015, Maertens de Noordhout 1988, Krenn 2013, Sayenko 2015a
- Spatiotemporally patterned stimulation - Wagner2018, Wegner 2016, Rowald 2022
- Modelling for new therapies and optimisation - Capogrosso2016, Wagner2018, Holsheimer1998

Appendix A: DONE
- Finite element method - Langtangen 2019

Appendix B: DONE
- Neuromodulation for pain - Kumar2007
- Neuromodulation for movement disorders - Okun 2012, Deuschl 2006
- Neuromodulation for rehabilitation - Wagner2018, Harkema2011, Vogt2018
- Electrical neuromodulation
- Modelling for novel treatments and individual optimisation - Capogrosso2016, Lempka2020, Gunalan2017
- Anatomy in models - Lempka 2020, Gunalan2017
- Simplified metrics e.g. E-field
- Activating function - Rattay1986, Rattay1989
- Biophysical models - Hodgkin1952
- Python - van Rossum 2009
- Numpy - Harris 2020
- Matplotlib - Hunter 2007
- FENICS - Scroggs 2022
- NEURON - Carnevale2006
- scikit-learn - Pedregosa 2011

Appendix C: DONE
- Electrical neuromodulation
- Neuromodulation for pathologies - Kumar2007, Wagner2018
- Burst stimulation - de Ridder 2010
- Burst in tSCS - Gerasimenko 2015, Gad 2021
- Effects of burst on comfort - Gerasimenko 2015
- Burst - de Ridder 2010
- High frequency SCS - Kapural 2015
