a few fixes

Makefile

@@ -6,7 +6,7 @@ TEXFILE=$(TEXBASE).tex
 PDFFILE=$(TEXBASE).pdf
 TXTFILE=$(TEXBASE).txt
 
-REVISION=493ed7b1e730a76adb6522831a34873d6fb525b5
+REVISION=3bcfb4a830f0d49e2db20a3e3abeaa7c8f2a119f
 
 PDFFIGURES=$(shell sed -n -e '/^[^%].*includegraphics/{s/^.*includegraphics.*{\(.*\)}/\1.pdf/;p}' $(TEXFILE))
 

manuscript.tex

@@ -160,7 +160,7 @@ Nils A. Koch\textsuperscript{1,2}, Lukas Sonnenberg\textsuperscript{1,2}, Ulrike
 \section*{Abstract (250 Words Maximum - Currently )}
 %\textit{It should provide a concise summary of the objectives, methodology (including the species and sex studied), key results, and major conclusions of the study.}
 
-Ion channels determine neuronal excitability and disruption in ion channel properties caused by mutations can result in neurological disorders called channelopathies. Often, mutations within one gene are associated with a specific channelepothy and the effects of these mutations  on channel function, i.e. the gating current of the affected ion channel, are generally determined using heterologous expression systems. Nevertheless, the impact of such mutations on neuronal firing is essential not only for determining brain function, but also for selecting personalized treatment options for the affected patient. The effect of ion channel mutations on firing in different cell types has been mostly neglect and it is unclear whether the effect of a given mutation on firing can simply be inferred from the effects identified at the current level. Here we use a diverse collection of computational neuronal models to determine that ion channel mutation effects at the current level cannot be indiscriminantly used to infer firing effects without consideration of cell-type. In particular, systematic simulation and evaluation of the effects of changes in ion current properties on firing properties in different neuronal types as well as for mutations in the \textit{KCNA1} gene encoding the \Kv potassium channel subtype associated with episodic ataxia type~1 (EA1) was performed. The effects of changes in ion current properties generally and due to mutations in the \Kv channel subtype on the firing of a neuron depends on the ionic current environment, or the neuronal cell type, in which such a change occurs in. Thus, while characterization of ion channel mutations as loss or gain of function is useful at the level of the ionic current, this characterization should not be extended to the level of neuronal excitability as the effects of ion channel mutations on the firing of a cell is dependent on the cell type and the composition of different ion channels and subunits therein. For increased efficiency and efficacy of personalized medicine approaches in channelopathies, the effects of ion channel mutations must be examined in the context of the appropriate cell types in which these mutations occur.
+Neuronal excitability is shaped by kinetics of ion channels and disruption in ion channel properties caused by mutations can result in neurological disorders called channelopathies. Often, mutations within one gene are associated with a specific channelopathy. The effects of these mutations  on channel function, i.e. the ionic current conducted by the affected ion channels, are generally characterized using heterologous expression systems. Nevertheless, the impact of such mutations on neuronal firing is essential not only for determining brain function, but also for selecting personalized treatment options for the affected patient. The effect of ion channel mutations on firing in different cell types has been mostly neglect and it is unclear whether the effect of a given mutation on firing can simply be inferred from the effects identified at the current level. Here we use a diverse collection of computational neuronal models to determine that ion channel mutation effects at the current level cannot be indiscriminantly used to infer firing effects without consideration of cell-type. In particular, systematic simulation and evaluation of the effects of changes in ion current properties on firing properties in different neuronal types as well as for mutations in the \textit{KCNA1} gene encoding the \Kv potassium channel subtype associated with episodic ataxia type~1 (EA1) was performed. The effects of changes in ion current properties generally and due to mutations in the \Kv channel subtype on the firing of a neuron depends on the ionic current environment, or the neuronal cell type, in which such a change occurs in. Thus, while characterization of ion channel mutations as loss or gain of function is useful at the level of the ionic current, this characterization should not be extended to the level of neuronal excitability as the effects of ion channel mutations on the firing of a cell is dependent on the cell type and the composition of different ion channels and subunits therein. For increased efficiency and efficacy of personalized medicine approaches in channelopathies, the effects of ion channel mutations must be examined in the context of the appropriate cell types in which these mutations occur.
 %Using a diverse collection of computational neuronal models, the effects of changes in ion current properties on firing properties of different neuronal types were simulated systematically and for mutations in the \textit{KCNA1} gene encoding the \Kv potassium channel subtype associated with episodic ataxia type~1 (EA1). The effects of changes in ion current properties or changes due to mutations in the \Kv channel subtype on the firing of a neuron depends on the ionic current environment, or the neuronal cell type, in which such a change occurs in. Characterization of ion channel mutations as loss or gain of function is useful at the level of the ionic current. However, the effects of mutations causing channelopathies on the firing of a cell is dependent on the cell type and thus on the composition of different ion channels and subunits. To further the efficacy of personalized medicine in channelopathies, the effects of ion channel mutations must be examined in the context of the appropriate cell types in which these mutations occur.
 \par\null
 
@@ -170,7 +170,6 @@ Ion channels determine neuronal excitability and disruption in ion channel prope
 Ion channels determine neuronal excitability and mutations that alter ion channel properties result in neurological disorders called channelopathies. Although the genetic nature of such mutations as well as their effects on the biophysical properties of an ion channel are routinely assessed experimentally, determination of the role in altering neuronal firing is more difficult. In particular, cell-type dependency of ion channel mutations on firing has been observed experimentally, and should be accounted for. In this context, computational modelling bridges this gap and demonstrates that the cell type in which a mutation occurs is an important determinant in the effects of neuronal firing. As a result, classification of ion channel mutations as loss or gain of function is useful to describe the ionic current but should not be blindly extend to classification at the level of neuronal firing.
 \par\null
 
-
 \section*{Introduction (750 Words Maximum  - Currently )} 
 %\textit{The Introduction should briefly indicate the objectives of the study and provide enough background information to clarify why the study was undertaken and what hypotheses were tested.}
 
@@ -184,11 +183,11 @@ In recent years, next generation sequencing has led to an increasing number of c
 
 % Ion channel mutations are the most common cause of such channelopathies  and are often associated with hereditary clinical disorders including ataxias, epilepsies, pain disorders, dyskinesias, intellectual disabilities, myotonias, and periodic paralyses \citep{bernard_channelopathies_2008, carbone_ion_2020}.
 
-The effects of mutations in ion channel genes on ionic current kinetics are frequently assessed using heterologous expression systems which do not express endogenous currents  \citep{Balestrini1044, Noebels2017, Dunlop2008}, and are frequently classified as either a loss of function (LOF) or a gain of function (GOF) with respect to changes in gating of the altered ion channels \citep{Musto2020, Kullmann2002, Waxman2011, Kim2021}. This classification of the effects on ionic currents is often directly used to predict the effects on neuronal firing \citep{Niday2018, Wei2017, Wolff2017}, which in turn is important for understanding the pathophysiology of these disorders and for identification of potential therapeutic targets \citep{Orsini2018, Yang2018, Colasante2020, Yu2006}. Genotype-phenotype relationships are complex and the understanding of the relationships between these is still evolving \citep{Wolff2017, johannesen_genotype-phenotype_2021}. Experimentally, the effects of channelopathies on neuronal firing can be assessed using primary neuronal cultures  \citep{Scalmani2006, Smith2018, Liu2019}  or \textit{in vitro} recordings from slices of transgenic mouse lines \citep{Mantegazza2019, Xie2010,Lory2020, Habib2015,  Hedrich2019}.
+The effects of mutations in ion channel genes on ionic current kinetics are frequently assessed using heterologous expression systems which do not express endogenous currents  \citep{Balestrini1044, Noebels2017, Dunlop2008}. Ion channel variants are frequently classified as either a loss of function (LOF) or a gain of function (GOF) with respect to changes in gating of the altered ion channels \citep{Musto2020, Kullmann2002, Waxman2011, Kim2021}. This classification of the effects on ionic currents is often directly used to predict the effects on neuronal firing \citep{Niday2018, Wei2017, Wolff2017}, which in turn is important for understanding the pathophysiology of these disorders and for identification of potential therapeutic targets \citep{Orsini2018, Yang2018, Colasante2020, Yu2006}. Genotype-phenotype relationships are complex and the understanding of the relationships between these is still evolving \citep{Wolff2017, johannesen_genotype-phenotype_2021}. Experimentally, the effects of channelopathies on neuronal firing can be assessed using primary neuronal cultures  \citep{Scalmani2006, Smith2018, Liu2019}  or \textit{in vitro} recordings from slices of transgenic mouse lines \citep{Mantegazza2019, Xie2010,Lory2020, Habib2015,  Hedrich2019}.
 
 However, the effect of a given channelopathy on the firing behavior of different neuronal types across the brain is often unclear and not feasible to experimentally obtain. Different neuron types differ in their composition of ionic currents \citep{yao2021taxonomy, Cadwell2016, BICCN2021, Scala2021} and therefore likely respond differently to changes in the properties of a single ionic current. The expression level of an affected gene can correlate with firing behavior in the simplest case \citep{Layer2021}. However, if gating kinetics are affected this can have complex consequences on the firing behavior of a specific cell type and the network activity within the brain.
 
-For instance, altering relative amplitudes of ionic currents can dramatically influence the firing behavior and dynamics of neurons \citep{rutecki_neuronal_1992, pospischil_minimal_2008,Kispersky2012, golowasch_failure_2002, barreiro_-current_2012, Noebels2017, Layer2021}, however other properties of ionic currents impact neuronal firing as well. Cell-type specific effects one firing can occur for instance increases inhibitory interneuron but not pyramidal neuron firing with R1648H mutation in \textit{SCN1A} \citep{Hedrich14874}. In extreme cases, a mutation can have opposite effects on different neuron types. For example, the R1627H  \textit{SCN8A} mutation is associated which increased firing in interneurons, but decreases pyramidal neuron excitability \citep{makinson_scn1a_2016}.
+For instance, altering relative amplitudes of ionic currents can dramatically influence the firing behavior and dynamics of neurons \citep{rutecki_neuronal_1992, pospischil_minimal_2008,Kispersky2012, golowasch_failure_2002, barreiro_-current_2012, Noebels2017, Layer2021}, however other properties of ionic currents impact neuronal firing as well. Cell-type specific effects one firing are possible. For instance, the R1648H mutation in \textit{SCN1A} increases firing in inhibitory interneurons but not pyramidal neurons \citep{Hedrich14874}. In extreme cases, a mutation can have opposite effects on different neuron types. For example, the R1627H  \textit{SCN8A} mutation is associated which increased firing in interneurons, but decreases pyramidal neuron excitability \citep{makinson_scn1a_2016}.
 
 Despite this evidence of cell-type specific effects of ion channel mutations on firing, the dependence of firing outcomes of ion channel mutations is generally not known. Cell-type specificity is likely vital for successful precision medicine treatment approaches. For example, Dravet syndrome was identified as the consquence of LOF mutations in \textit{SCN1A} \citep{Claes2001,Fujiwara2003,Ohmori2002}, however limited succes in treatment of Dravet syndrome persisted \citep{Claes2001,Oguni2001}. Once it became evident that only inhibitory interneurons and not pyramidal neurons had altered excitability as a result of LOF \textit{SCN1A} mutations alternative approaches, based on this understanding such as gene therapy, began to show promise \citep{Colasante2020, Yu2006}. Due to the high clinical relevance of understanding cell-type dependent effects of channelopathies, we use computationaly modelling approaches to assess the impacts of altered ionic current properties on firing behavior, bridging the gap between changes in the biophysical properties induced by mutations, firing and clinical symptoms. Conductance-based neuronal models enable insight into the effects of ion channel mutations with specific effects of the resulting ionic current as well as enabling \textit{in silico} assessment of the relative effects of changes in biophysical properties of ionic currents on neuronal firing. Furthermore, modelling approaches enable predictions of the effects of specific mutation and drug induced biophysical property changes \citep{Layer2021,Liu2019,johannesen_genotype-phenotype_2021, lauxmann_therapeutic_2021}.