Basket cell extrasynaptic inhibition modulates network oscillations (Proddutur et al., 2013)

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Accession:155601
Among the rhythmic firing patterns observed in brain, gamma oscillations, which are involved in memory formation and retrieval, are generated by networks of fast-spiking basket cells (FS-BCs) with robust interconnectivity through fast GABA synapses. Recently, we identified presence of extrasynaptic tonic GABA currents in FS-BCs and showed that experimentally-induced seizures enhance extrasynaptic tonic GABA currents and render GABA reversal potential (EGABA) depolarizing (Yu et al., 2013). Extrasynaptic GABA currents are mediated by extra- and peri-synaptically located GABAARs and can contribute to synaptic decay kinetics. Additionally, shunting rather than hyperpolarizing EGABA has been shown to increase the frequency and reduce coherence of network oscillations. Using homogeneous networks of biophysically-based, multi-compartmental model FS-BCs, we examined how the presence of extrasynaptic GABA currents and the experimentally identified seizure-induced alterations in GABA currents and EGABA modify the frequency and coherence of network firing.
Reference:
1 . Proddutur A, Yu J, Elgammal FS, Santhakumar V (2013) Seizure-induced alterations in fast-spiking basket cell GABA currents modulate frequency and coherence of gamma oscillation in network simulations. Chaos 23:046109 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Dentate gyrus basket cell;
Channel(s):
Gap Junctions: Gap junctions;
Receptor(s): GabaA;
Gene(s):
Transmitter(s): Gaba;
Simulation Environment: NEURON;
Model Concept(s): Oscillations;
Implementer(s):
Search NeuronDB for information about:  GabaA; Gaba;
/
ProdduturEtAl2013
readme.html
bgka.mod *
CaBK.mod *
ccanl.mod *
gap.mod
Gfluct2.mod *
gskch.mod *
hyperde3.mod *
ichan2.mod *
izap.mod
LcaMig.mod *
markov.mod *
nca.mod *
tca.mod *
tonic.mod *
IClamp 50% gaps 30 SYNAPSES tonicspill -74mV_0.6nA.hoc
PPSTIM 50% gaps 30 SYNAPSES tonicspill -74mV.hoc
screenshot1.png
                            
load_file("nrngui.hoc")
load_file("stdlib.hoc")
secondorder=2 
tstep=0
period=2
dt=0.1
tstop=2000
nbcell = 200
npp=200
TC=0.4
objref Bcell[nbcell]

	begintemplate BasketCell
ndend1=4
ndend2=4
ndend3=4
ndend4=4

public  pre_list, connect_pre, subsets, is_connected, is_art, stim
public soma, bcdend1, bcdend2, bcdend3, bcdend4
public all, adend, bdend, cdend, ddend
create soma, bcdend1[ndend1], bcdend2[ndend2], bcdend3[ndend3], bcdend4[ndend4]

objref syn, pre_list, stim


objref syn
proc init() {
	pre_list = new List()
	subsets()
	temp()
	synapse()
	}

objref all, adend, bdend, cdend, ddend

proc subsets() { local i

	objref all, adend, bdend, cdend, ddend
	all = new SectionList()

     		soma all.append()
		bcdend1[0] all.append()
		bcdend2[0] all.append()
		bcdend3[0] all.append()
		bcdend4[0] all.append()

		bcdend1[1] all.append()
		bcdend2[1] all.append()
		bcdend3[1] all.append()
		bcdend4[1] all.append()

		bcdend1[2] all.append()
		bcdend2[2] all.append()
		bcdend3[2] all.append()
		bcdend4[2] all.append()

		bcdend1[3] all.append()
		bcdend2[3] all.append()
		bcdend3[3] all.append()
		bcdend4[3] all.append()


	adend  = new SectionList()
		for i=0,3{
		bcdend1 [i] adend.append()}

	bdend  = new SectionList()
		for i=0,3{
		bcdend2 [i] adend.append()}

	cdend  = new SectionList()
		for i=0,3{
		bcdend3 [i] adend.append()}

	ddend  = new SectionList()
		for i=0,3{
		bcdend4 [i] adend.append()}

}

proc temp() {
	soma {nseg=1 L=20 diam=15} // changed L & diam
	bcdend1 [0] {nseg=1 L=75 diam=4}	
	bcdend2 [0] {nseg=1 L=75 diam=3}
	bcdend3 [0] {nseg=1 L=75 diam=2}
 	bcdend4 [0] {nseg=1 L=75 diam=1}

	bcdend1 [1] {nseg=1 L=75 diam=4}
	bcdend2 [1] {nseg=1 L=75 diam=3}
	bcdend3 [1] {nseg=1 L=75 diam=2}
	bcdend4 [1] {nseg=1 L=75 diam=1}
 		 
	bcdend1 [2] {nseg=1 L=50 diam=4} 	
	bcdend2 [2] {nseg=1 L=50 diam=3}
	bcdend3 [2] {nseg=1 L=50 diam=2}
	bcdend4 [2] {nseg=1 L=50 diam=1} 
	
	bcdend1 [3] {nseg=1 L=50 diam=4}
	bcdend2 [3] {nseg=1 L=50 diam=3}
	bcdend3 [3] {nseg=1 L=50 diam=2}
	bcdend4 [3] {nseg=1 L=50 diam=1} 	


	forsec all {
		insert ccanl
	catau_ccanl = 10
	caiinf_ccanl = 5.e-6
		insert borgka
	gkabar_borgka=0.00015
		insert nca  // HAV-N- Ca channel
	gncabar_nca=0.0008   //check to modify- original 0.004
		insert lca 
	glcabar_lca=0.005
		insert gskch
	gskbar_gskch=0.000002
		insert cagk
	gkbar_cagk=0.0002
	insert tonic
    	g_tonic =  0.000008    //0.001
   	e_tonic = -74
	}

	soma {insert ichan2  //ildikos ichan
	gnatbar_ichan2=0.12  //original 0.030 to .055 
	gkfbar_ichan2=0.013  //original 0.015
	gl_ichan2 = 0.00014
	cm=1.4
	} 

	forsec adend {insert ichan2
	gnatbar_ichan2=0.12  //original 0.015
	gkfbar_ichan2=0.013
	gl_ichan2 = 0.00012
	cm=1.4
	}		
	forsec bdend {insert ichan2
	gnatbar_ichan2=0.0
	gkfbar_ichan2=0.00
	gl_ichan2 = 0.00012
	cm=1.4}
		
	forsec cdend {insert ichan2
	gnatbar_ichan2=0.0
	gkfbar_ichan2=0.00
	gl_ichan2 = 0.00012
	cm=1.4}

	forsec ddend {insert ichan2
	gnatbar_ichan2=0.0
	gkfbar_ichan2=0.00
	gl_ichan2 = 0.00012
	cm=1.4}

	connect bcdend1[0](0), soma(1)
	connect bcdend1[1](0), soma(1)
	connect bcdend1[2](0), soma(0)
	connect bcdend1[3](0), soma(0)
	
	connect bcdend2[0](0), bcdend1[0](1)
	connect bcdend2[1](0), bcdend1[1](1)
	connect bcdend2[2](0), bcdend1[2](1)
	connect bcdend2[3](0), bcdend1[3](1)
	
	connect bcdend3[0](0), bcdend2[0](1)
	connect bcdend3[1](0), bcdend2[1](1)
	connect bcdend3[2](0), bcdend2[2](1)
	connect bcdend3[3](0), bcdend2[3](1)

	connect bcdend4[0](0), bcdend3[0](1)
	connect bcdend4[1](0), bcdend3[1](1)
	connect bcdend4[2](0), bcdend3[2](1)
	connect bcdend4[3](0), bcdend3[3](1)


		forsec all {Ra=100}
	forsec all {enat = 55 ekf = -90  ek=-90  elca=130	esk=-90
		 el_ichan2 =-75
		cao_ccanl=2 }  // make catau slower70e-3 	cao=2 cai=50.e-6 


	}

	objref syn  
	proc synapse() {
	bcdend4 [0] syn = new Exp2Syn(0.5)	
	syn.tau1 = 2	syn.tau2 = 6.3	syn.e = 0    //2 and 6.3         
	pre_list.append(syn)
	
	bcdend2 [1] syn = new Exp2Syn(0.5)	//BC(GABA) syn to apical IML dend Bartos
	syn.tau1 = 0.16		syn.tau2 = 1.8	syn.e = -74    //0.16 and 1.8
	pre_list.append(syn)
//******************************Tonic GABA synapses**************

	bcdend3[0] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum  2
	syn.tau1 = 7	syn.tau2 = 200	syn.e = -74
	pre_list.append(syn)
	
	bcdend3[1] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum	3
	syn.tau1 = 7	syn.tau2 = 200	syn.e = -74
	pre_list.append(syn)
	
	bcdend3[2] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum	4
	syn.tau1 = 7	syn.tau2 = 200	syn.e = -74
	pre_list.append(syn)
	
	bcdend3[3] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum	5
	syn.tau1 = 7	syn.tau2 = 200	syn.e = -74
	pre_list.append(syn)
	
	bcdend2[0] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum	6
	syn.tau1 = 7	syn.tau2 = 200	syn.e = -74
	pre_list.append(syn)
	
	bcdend1[2] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum	7
	syn.tau1 = 7	syn.tau2 = 200	syn.e = -74
	pre_list.append(syn)
	
	bcdend2[2] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum	8
	syn.tau1 = 7	syn.tau2 = 200	syn.e = -74
	pre_list.append(syn)
	
	bcdend2[3] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum	9
	syn.tau1 = 7	syn.tau2 = 200	syn.e = -74
	pre_list.append(syn)

	}

	proc connect_pre() {  // $o1 target point process, $o2 returned NetCon
	soma $o2 = new NetCon (&v(1), $o1) 
	}

		func is_art()  { return 0 }
	endtemplate BasketCell
//**********************************************************************************

objref PPSt[npp]

	begintemplate PPstim

	public pp, connect_pre, is_art, acell
	create acell
	objref pp

	proc init() {
		actemp() 		
	}
		proc actemp() {
				acell pp = new NetStim(.5)
				pp.interval =5 
				pp.number = 100
				pp.start = 0
				pp.noise=0.5
				}

	func is_art() {return 1}
	proc connect_pre() {acell $o2 = new NetCon(pp, $o1)}

endtemplate PPstim

//********************************************************************

// NETWORK SPECIFICATION INTERFACE

	for i=0, nbcell-1 {Bcell[i] = new BasketCell(i)} 
	for i =0, npp-1 {PPSt[i] = new PPstim(i)}

//*********************************************************************


objref nclist, netcon, cells, net_c, net_bc
{  cells = new List()
nclist = new List()
}
 func cell_append() {cells.append($o1) 
	return cells.count -1}

func nc_append() {

	if ($3 >= 0 )	{
		cells.object($1).connect_pre(cells.object($2).pre_list.object($3),netcon)
		netcon.weight = $4	netcon.delay = $5		netcon.threshold = $6
	} 
	nclist.append(netcon)
	return nclist.count-1
		}
func is_connected() {local i, c
	c=0
	for i=0, nclist.count-1 {
	net_c= nclist.object(i)
	if (($o1 == net_c.postcell())  && ($o2 == net_c.precell())) {c=1}
}
return c
}
objref vbc2bc
	{
	vbc2bc = new Vector(nbcell, 0)
	}

//initiating randm number generator

objref rdsyna, rdbc2bc, rdgap, rddend
ropen("/proc/uptime")		// get a seed  that is changing based on the processing time
	 {			
 	rseed = fscan()		// so simulation will not start with the same seed
	ropen()		
	}
//rseed=12345

rdgap = new Random(rseed)                            
proc new_rdgap() {rdgap.discunif(-20,20)}    // use for gap junc
new_rdgap()
rddend = new Random(rseed)                            
proc new_rddend() {rddend.discunif(0,3)}    
new_rddend()
rdbc2bc = new Random(rseed)			// use for syn.connections 
proc new_rdbc2bc() {rdbc2bc.discunif(-15, 15)}
new_rdbc2bc()
rdsyna = new Random(rseed)		// initialize random distr.
proc new_rdsyna() {rdsyna.discunif(1, 1)}
new_rdsyna()

//	NETWORK INITIATION
	for i = 0, nbcell-1 {cell_append(Bcell[i])} 
	for i = 0, npp-1 {cell_append(PPSt[i])}



//*********************************************************************************
//**************Preforant Path  synaptic connections ******************************
proc initPP() { local i
	for i=0, 199{
	nc_append(i+nbcell,i, 0, 2e-2, 3, 1)  //0.5e-3 each cell is receiving independent single PP input
		     }
			    }
//**********************************************************************************


objref randomVector
randomVector = new Vector(nbcell)


proc initBcell() { local i,j

for  i=0, nbcell-1 {

	randomVector.resize(nbcell)
	for k = 0, randomVector.size-1 {randomVector.x[k]=0}
	while (randomVector.sum < 30) {
	Gauz3  = rdbc2bc.repick()
	dist = abs(Gauz3)
	axdel = dist/5*0.2
	if (Gauz3==0){Gauz3  = rdbc2bc.repick()}
	if (i+Gauz3==i){Gauz3  = rdbc2bc.repick()}
	if (Gauz3==0){Gauz3  = rdbc2bc.repick()}
	if (i+Gauz3==i){Gauz3  = rdbc2bc.repick()}
	if (i+Gauz3 > nbcell-1) {npost = i+Gauz3-nbcell }
	if (i+Gauz3 < 0) {npost = i+Gauz3+nbcell} 
	if ((i+Gauz3 >-1) && (i+Gauz3 < nbcell)) {npost = i+Gauz3}
	if ((randomVector.x[npost] == 0) && (vbc2bc.x[npost] < 31)) {
	   randomVector.x[npost] += 1
	   vbc2bc.x[npost] += 1
	}
	dbr = rdsyna.repick()
	}
	for k = 0, randomVector.size-1 {
	    if (randomVector.x[k] == 1) {
	    	nc_append(i, k, dbr, 7.6e-3, 0.8+axdel, 0)  
		u=k
		v=u+1
		w=u-1
		r=0.4*TC
		if (v > 199) {v = v-1}
		if (w < 0) {w = w+1}
		nc_append(i, v, 8, r*0.0125e-3, 8, 10)
		nc_append(i, v, 9, r*0.0125e-3, 8, 10)
		nc_append(i, u, 8, TC*0.0125e-3, 8, 10)
		nc_append(i, u, 9, TC*0.0125e-3, 8, 10)
		nc_append(i, w, 8, r*0.0125e-3, 8, 10)
		nc_append(i, w, 9, r*0.0125e-3, 8, 10)

	    }
	}
   }
}


objref gaps[20000]
for i=0,19999{
gaps[i] = new Gap(0.5)
gaps[i].r = 100000}


n=0
for i=0,199{
d = rddend.repick() 
pre=i    //for bcells
for j=1,50{
post = j+i
n +=2 
if (post == pre){post =pre-post}   
if (post>199) {post = post-200}                                                                                   	  
Bcell[pre].bcdend3[d] gaps[n-2].loc(0.5)
Bcell[post].bcdend3[d] gaps[n-1].loc(0.5)                                                      
setpointer gaps[n-2].vgap, Bcell[post].bcdend3[d].v(0.5)
setpointer gaps[n-1].vgap, Bcell[pre].bcdend3[d].v(0.5)
}
}
//*******************************************************************************************************
//*********************************Print out Net cons***************************************************
strdef strvar
objref nfile
nfile = new File()

proc saveNet(){ local i
nfile.wopen("N_connect_50GJ_30syn_74mV tonicspill.txt")
	nfile.printf("Precell \tps.tcell \t Synapse \n")
	for i=0, nclist.count-1 {
	nfile.printf("%s\t%s\t%s\n", nclist.object[i].precell, nclist.object[i].postcell, nclist.object[i].syn)}
nfile.printf("TO BC\tBC")
for i= 0, nbcell-1 {nfile.printf("%d\t \n",  vbc2bc.x[i])}
//print "BCout"
nfile.close("N_connect_50GJ_30syn_74mV tonicspill.txt")
}

//**************************************************************************

objref  VmT
objref VmMat[nbcell]
VmT = new Vector()
for i=0, nbcell-1 {
	VmMat[i] = new Vector()
	}

proc VecMx() { local i
	VmT.append(t)
	for i=0, nbcell-1 {
		VmMat[i].append( cells.object[i].soma.v(0.5))
		}
	}
objref Spike[nbcell]
for i=0, nbcell-1 {
	Spike[i] = new Vector()
	}
strdef Spkstr
objref dfile
dfile = new File()

proc SpkMx() { local i, j
	k = 0
     	for i=0, nbcell-1 {
		Spike[i].spikebin(VmMat[i], 0)
		}
dfile.wopen("Spike50gaps_30syn_74mV tonicspill.txt")

	while(k <  VmT.size) {
	for j = 0, nbcell-1 {
	if(Spike[j].x[k] != 0) {
	dfile.printf("%f\t%d\n", VmT.x[k], j)}
	}
	k +=1 }
dfile.close("Spike50gaps_30syn_74mV tonicspill.txt")
	}



strdef strmat
objref efile
efile = new File()

	efile.wopen("Mempot50gaps_30syn_74mV tonicspill.txt")
	efile.printf("t\t")
for i = 0, 199 {
	efile.printf("%s\t", Bcell[i])}
	efile.printf("\n")
efile.close("Mempot50gaps_30syn_74mV tonicspill.txt")

proc sMatrix(){ local  i
	efile.aopen("Mempot50gaps_30syn_74mV tonicspill.txt")
	efile.printf("%f\t", t)
	for i = 0, 199 {
	efile.printf("%f\t", Bcell[i].soma.v(0.5))}
	efile.printf("\n")
	efile.close("Mempot50gaps_30syn_74mV tonicspill.txt")

}


strdef strmat
objref gfile
gfile = new File()

gfile.wopen("gapctesthz_50GJ_30syn_74mV tonicspill.txt")
	gfile.printf("t\t")
for i = 50, 100 {
	gfile.printf("%s\t", Gap[i])}
	gfile.printf("\n")
gfile.close("gapctesthz_50GJ_30syn_74mV tonicspill.txt")

proc gMatrix(){ local  i
	gfile.aopen("gapctesthz_50GJ_30syn_74mV tonicspill.txt")
	gfile.printf("%f\t", t)
	for i=50, 100 {
	gfile.printf("%f\t", Gap[i].i)}
	gfile.printf("\n")
	gfile.close("gapctesthz_50GJ_30syn_74mV tonicspill.txt")
	}

objref r_plt
proc initrPlt() {
	r_plt = new Graph(0)
	r_plt.size(0, tstop,0, cells.count-npp)
	r_plt.label(0.95, 0.02, "ms")
	r_plt.label(0.01, 0.82, "neu")
	r_plt.view(0,0, tstop, cells.count,320,20,300,230)
}
 initrPlt()

proc plotAP() { local i, a
	a=1
 	r_plt.erase()
	while(j < cells.count-npp-1) {
	for i = 0, VmT.size-1 {
	if (Spike[j].x[i] == 1) {
	r_plt.mark(VmT.x[i], j, "T", 5, a, 1)}}
	j+=1}
	r_plt.flush()
	}


proc init() { local dtsav, temp, secsav
finitialize(v_init)
t = -1000
dtsav = dt
secondorder =0
dt= 10
	// if cvode is on, turn it off to do large fixed step
temp= cvode.active()
if (temp!=0) {cvode.active(0)}
while(t<-100) { fadvance() print t}
	//restore cvode if reqd
if (temp!=0) {cvode.active(1)}
dt = dtsav
secondorder =2
t = 0
if (cvode.active()){
cvode.re_init()
}else{
fcurrent()
}
//frecord_init()
}
proc continuerun() {local rt
	eventcount =0
	eventslow =1
	stoprun =0
	if (using_cvode_) {
	cvode.event($1)
	}
	while(t < $1 && stoprun == 0) {
	step()
	sMatrix()
	gMatrix()
	VecMx()
	rt = stopsw()
	if (rt > realtime) {
		realtime = rt
		if (!stdrun_quiet) fastflushPlot()
		doNotify()
		if (realtime == 2 && eventcount > 50) {
			eventslow = int(eventcount/50)+1
		}
		eventcount = 0
	}else{
		eventcount = eventcount +1
		if ((eventcount%eventslow) == 0) {
			doEvents()
		}
	}
	}
	flushPlot()
}

objectvar save_window_, rvp_
objectvar scene_vector_[4]
objectvar ocbox_, ocbox_list_, scene_, scene_list_
{ocbox_list_ = new List()  scene_list_ = new List()}

{
xpanel("RunControl", 0)
v_init = -60
xvalue("Init","v_init", 1,"stdinit()", 1, 1 )
xbutton("Init & Run","run()")
xbutton("Stop","stoprun=1")
runStopAt = 5
xvalue("Continue til","runStopAt", 1,"{continuerun(runStopAt) stoprun=1}", 1, 1 )
runStopIn = 1
xvalue("Continue for","runStopIn", 1,"{continuerun(t + runStopIn) stoprun=1}", 1, 1 )
xbutton("Single Step","steprun()")
t = 0
xvalue("t","t", 2 )
tstop = 1000	//1500
xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
dt = 0.1
xvalue("dt","dt", 1,"setdt()", 0, 1 )
steps_per_ms = 10	//40
xvalue("Points plotted/ms","steps_per_ms", 1,"setdt()", 0, 1 )
xpanel(544,121)
}
{
save_window_ = new Graph(0)
save_window_.size(0,tstop,-80,40)
scene_vector_[2] = save_window_
{save_window_.view(0, -80, tstop, 120, 290, 470, 579.84, 208)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addexpr("Bcell[1].soma.v(0.5)",1,1)
save_window_.addexpr("Bcell[10].soma.v(0.5)",2,1)
save_window_.addexpr("Bcell[20].soma.v(0.5)",3,1)
save_window_.addexpr("Bcell[30].soma.v(0.5)",4,1)
save_window_.addexpr("Bcell[40].soma.v(0.5)",5,1)
save_window_.addexpr("Bcell[50].soma.v(0.5)",6,1)
save_window_.addexpr("Bcell[60].soma.v(0.5)",7,1)
save_window_.addexpr("Bcell[70].soma.v(0.5)",8,1)
save_window_.addexpr("Bcell[80].soma.v(0.5)",9,1)
save_window_.addexpr("Bcell[90].soma.v(0.5)",2,1)
save_window_.addexpr("Bcell[100].soma.v(0.5)",3,1)
save_window_.addexpr("Bcell[120].soma.v(0.5)",4,1)
save_window_.addexpr("Bcell[140].soma.v(0.5)",5,1)
save_window_.addexpr("Bcell[160].soma.v(0.5)",6,1)
save_window_.addexpr("Bcell[180].soma.v(0.5)",7,1)
save_window_.addexpr("Bcell[199].soma.v(0.5)",8,1)
}
save_window_ = new Graph(0)
save_window_.size(0,1000,-2,2)
scene_vector_[3] = save_window_
{save_window_.view(0, -2, tstop, 120, 290, 470, 579.84, 208)}
graphList[1].append(save_window_)
save_window_.save_name("graphList[1].")
save_window_.addexpr("Gap[10].i",2,1)

save_window_ = new Graph(0)
save_window_.size(0,1000,-2,2)
scene_vector_[3] = save_window_
{save_window_.view(0, -2, tstop, 120, 290, 470, 579.84, 208)}
graphList[1].append(save_window_)
save_window_.save_name("graphList[1].")
save_window_.addexpr("Bcell[10].bcdend4[0].igaba_tonic",2,1)
save_window_.addexpr("Bcell[10].soma.igaba_tonic",3,1)


proc rrun(){
initBcell()
initPP()
saveNet()
run()
SpkMx()
}
rrun()
plotAP()
objectvar scene_vector_[1]
{doNotify()}

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