CA3 Network Model of Epileptic Activity (Sanjay et. al, 2015)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:186768
This computational study investigates how a CA3 neuronal network consisting of pyramidal cells, basket cells and OLM interneurons becomes epileptic when dendritic inhibition to pyramidal cells is impaired due to the dysfunction of OLM interneurons. After standardizing the baseline activity (theta-modulated gamma oscillations), systematic changes are made in the connectivities between the neurons, as a result of step-wise impairment of dendritic inhibition.
Reference:
1 . Sanjay M, Neymotin SA, Krothapalli SB (2015) Impaired dendritic inhibition leads to epileptic activity in a computer model of CA3. Hippocampus 25:1336-50 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Extracellular;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA3 pyramidal cell; Hippocampus CA3 basket cell; Hippocampus CA3 stratum oriens lacunosum-moleculare interneuron;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s): HCN1; HCN2;
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Activity Patterns; Oscillations; Pathophysiology; Epilepsy; Brain Rhythms;
Implementer(s): Neymotin, Sam [samn at neurosim.downstate.edu]; Sanjay, M [msanjaycmc at gmail.com];
Search NeuronDB for information about:  Hippocampus CA3 pyramidal cell; Hippocampus CA3 basket cell; GabaA; AMPA; NMDA;
/
SanjayEtAl2015
readme.html
CA1ih.mod *
CA1ika.mod *
CA1ikdr.mod *
CA1ina.mod *
caolmw.mod *
capr.mod *
icaolmw.mod *
icapr.mod *
iholmkop.mod *
iholmw.mod *
ihpyrkop.mod *
kahppr.mod *
kaolmkop.mod *
kapyrkop.mod *
kcaolmw.mod *
kcpr.mod *
kdrbwb.mod *
kdrolmkop.mod *
kdrpr.mod *
kdrpyrkop.mod *
misc.mod *
MyExp2Syn.mod *
MyExp2SynAlpha.mod *
MyExp2SynBB.mod *
MyExp2SynNMDA.mod *
MyExp2SynNMDABB.mod *
nafbwb.mod *
nafolmkop.mod *
nafpr.mod *
nafpyrkop.mod *
stats.mod
vecst.mod *
wrap.mod *
aux_fun.inc *
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
Epileptic Activity.png
geom.hoc *
geom.py *
grvec.hoc *
init.hoc *
labels.hoc *
local.hoc *
misc.h *
mosinit.py
network.py *
networkmsj.py
nqs.hoc *
nqs_utils.hoc *
nrnoc.hoc *
params.py
pyinit.py *
run.py
simctrl.hoc *
stats.hoc *
syncode.hoc *
xgetargs.hoc *
xtmp
                            
// $Id: decnqs.hoc,v 1.38 2011/03/01 19:06:15 billl Exp $

load_file("nqs.hoc")
objref nq[10],pq[10]

//** prl2nqs(NQS[,min,max,nointerp]) -- transfer printlist to NQS
proc rename () {}
// eg proc rename () { sprint($s1,"P%d",objnum($s1)) }
obfunc prl2nqs () { local tstep localobj st,oq
  st=new String2()
  oq=new NQS()
  if (numarg()>=1) min=$1 else min=0
  if (numarg()>=2) max=$2 else max=printlist.count-1
  if (numarg()>=3) interp=$3 else interp=0 // no interp when looking at spk times
  if (interp) oq.resize(max-min+2)
  if (interp) {
    tstep=0.1 // 0.1 ms step size for interpolation
    oq.s[0].s="time"
    oq.v[0].indgen(0,printlist.object(0).tvec.max,tstep)
    for ii=min,max {
      XO=printlist.object(ii)
      oq.s[ii+1-min].s = XO.var
      rename(oq.s[ii+1-min].s)
      oq.v[ii+1-min].resize(oq.v.size)
      oq.v[ii+1-min].interpolate(oq.v[0],XO.tvec,XO.vec)
    }
  } else {
    for ii=min,max {
      XO=printlist.object(ii)
      st.s=XO.name
      sprint(st.t,"%s-time",XO.name)
      rename(st.s) rename(st.t)
      oq.resize(st.s,st.t)
      oq.setcols(XO.vec,XO.tvec)
    }
  }
  return oq
}

//** pvp2nqs(NQS) -- transfer grvec data file to NQS
obfunc pvp2nqs () { local min,max,interp,gvnum,ii,jj,n localobj oq,po,st,xo
  interp=min=max=gvnum=0
  if (argtype(1)==2) { po=gvnew($s1) gvnum=panobjl.count()-1 }
  if (argtype(1)==0) gvnum=$1
  if (numarg()>=2) min=$2
  if (numarg()>=3) max=$3
  if (numarg()>=4) interp=$4 // no interp when looking at spk times
  if (po==nil) po=panobjl.o(gvnum)
  oq=new NQS() st=new String2()
  if (gvnum>0) {
    if (max==0) max=po.llist.count()-1
    for ii=min,max {
      xo=po.llist.object(ii)
      po.tmpfile.seek(xo.loc)
      if (xo.num==-2) {
        sprint(st.s,"%s-time",xo.name)
        jj=oq.resize(st.s)-1
        oq.v[jj].vread(po.tmpfile)
      }
      jj=oq.resize(xo.name)-1
      oq.v[jj].vread(po.tmpfile)
    }
  } else { // from printlist
    if (max==0) max=printlist.count()-1
    for ii=min,max {
      xo=printlist.o(ii)
      jj=oq.resize(xo.name)-1
      oq.v[jj].copy(xo.vec)
      if (xo.pstep==0) {
        sprint(st.s,"%s-time",xo.name)
        jj=oq.resize(st.s)-1
        oq.v[jj].copy(xo.tvec)
      }
    }
  }
  return oq
}

//** veclist2nqs(nqs[,STR1,STR2,...])
proc veclist2nqs () { local flag,i
  if (numarg()==0) {printf("veclist2nqs(nqs[,STR1,STR2,...])\n") return}
  $o1.resize(veclist.count)
  if (numarg()==1+$o1.m) flag=1 else flag=0
  for ltr(XO,veclist) {
    $o1.v[i1].copy(XO)
    if (flag) {i=i1+2 $o1.s[i1].s=$si} else {sprint(tstr,"v%d",i1) $o1.s[i1].s=tstr}
  }
  $o1.cpout()
}

// fudup(vec[,nq,#CUTS,LOGCUT,MIN]) -- use updown() to find spikes
// LOC(0) PEAK(1) WIDTH(2) BASE(3) HEIGHT(4) START(5) SLICES(6) SHARP(7) INDEX(8) FILE(9) NESTED(10)
// other options
pos_fudup=1 // set to 1 to move whole curve up above 0
maxp_fudup=0.95 // draw top sample at 95% of max 
minp_fudup=0.05 // draw bottom sample at 5% of max
over_fudup=1    // turn over and try again if nothing found
allover_fudup=0 // turn over and add these locs (not debugged)
verbose_fudup=0 // give messages, can also turn on DEBUG_VECST for messages from updown()
obfunc fudup () { local a,i,ii,npts,logflag,min,x,sz localobj bq,cq,v1,v2,v3,bb,tl,v5,eq
  if (verbose_fudup) printf("MAXTIME appears to be %g (dt=%g)\n",$o1.size*dt,dt)
  logflag=0  npts=10 // n sample locations by default
  bq=new NQS("LOC","PEAK","WIDTH","BASE","HEIGHT","START","SLICES","SHARP","INDEX","FILE","NESTED") 
  i=2
  if (argtype(i)==1) {i+=1 if ($o2==nil) {cq=new NQS() $o2=cq} else cq=$o2} else cq=new NQS()
  if (cq.m!=11) { cq.resize(0) 
  cq.resize("LOC","PEAK","WIDTH","BASE","HEIGHT","START","SLICES","SHARP","INDEX","FILE","NESTED")}
  if (argtype(i)==0){ npts=$i i+=1
    if (argtype(i)==0){ logflag=$i i+=1
      if (argtype(i)==1) { v5=$oi i+=1
        if (npts!=v5.size) printf("Correcting npts from %d to %d\n",npts,npts=v5.size)
        if (v5.ismono(1)) v5.reverse
        if (! v5.ismono(-1)) {printf("fudup: final arg (%s) must be monotonic\n",v5) return}
      }
    }
  }
  bq.listvecs(bb)
  bq.pad(5000)
  eq=new NQS(-2,npts) a=allocvecs(v1,v2,v3)
  tl=eq.vl
  eq.clear(2e4) vrsz(2e4,v1,v2,v3)
  v1.copy($o1)
  if (pos_fudup) {
    min=v1.min
    v1.sub(min) // make it uniformly positive
  } else min=0
  if (numarg()>4) v2.copy(v5) else {
    v2.indgen(2,2+npts-1,1)   // sampling at npts points, start at 2 to avoid log(1)=0
    if (logflag) v2.log() // log sampling
    v2.scale(-maxp_fudup*v1.max,-minp_fudup*v1.max) v2.mul(-1)
  }
  v1.updown(v2,tl,bb)
  if (pos_fudup) { bq.v[1].add(min) bq.v[3].add(min) }
  cq.append(bq)
  sz=bq.size(1)
  if (allover_fudup) { // do it upside down as well
    v1.mul(-1) // v2 will be upside-down
    if (pos_fudup) {min=v1.min v1.sub(min)}
    if (0) {  // can't see a rationale to recalc sampling points
      v2.indgen(2,2+npts-1,1)   // sampling at npts points
      if (logflag) v2.log() // log sampling
      v2.scale(-0.95*v1.max,-0.05*v1.max) v2.mul(-1)
    }
    v1.updown(v2,tl,bb)
    bq.v[8].add(sz) bq.v[4].mul(-1) // turn HEIGHT upside down
    cq.append(bq)
  } else if (over_fudup && sz==0) { // turn it over an try again
    print "fudup() checking upside-down"
    v1.mul(-1) // v2 will be upside-down
    v1.updown(v2,tl,bb)
  } 
  for case(&x,0,2,5) cq.v[x].mul(dt)
  nqsdel(bq,eq)
  dealloc(a)
  return cq
}

//** listsort(LIST[,START,REV]) sorts list of strings numerically
// optional start gives a regexp to start at
proc listsort () { local x,rev localobj nq,st,xo
  if (numarg()==0) { 
    print "listsort(LIST[,RXP,REV]) numerically, optional RXP starts after there" return}
  if (numarg()==3) if ($3) rev=-1 else rev=0
  nq=new NQS("STR","NUM") nq.strdec("STR")
  st=new String()
  for ltr(xo,$o1) {
    if (numarg()>=2) sfunc.tail(xo.s,$s2,st.s) else st.s=xo.s
    if (sscanf(st.s,"%g",&x)!=1) print "listsort ERR: num not found in ",st.s
    nq.append(xo.s,x)
  } 
  nq.sort("NUM",rev)
  $o1.remove_all
  for nq.qt(st.s,"STR") $o1.append(new String(st.s))
}

// stat(VEC) print stats for the vector
// stat(VEC1,VEC2) append stats of VEC1 on VEC2
// stat(VEC1,NQS) append stats of VEC1 on NQS (create if necessary)
proc stat () { local sz
  sz=$o1.size
  if (sz<=1) {printf("decnqs::stat() WARN: %s size %d\n",$o1,$o1.size) return}
  if (numarg()==1 && sz>1) {
    printf("Sz:%d\tmax=%g; min=%g; mean=%g; stdev=%g\n",$o1.size,$o1.max,$o1.min,$o1.mean,$o1.stdev)
  } else {
    if (!isassigned($o2)) { $o2=new NQS("SIZE","MAX","MIN","MEAN","STDEV")
    } else if (isobj($o2,"NQS")) { 
      if ($o2.m!=5) {$o2.resize(0) $o2.resize("SIZE","MAX","MIN","MEAN","STDEV")}
    } else if (isobj($o2,"Vector")) revec($o2)
    if (sz>2) {$o2.append($o1.size,$o1.max,$o1.min,$o1.mean,$o1.stdev) // .append for Vector or NQS
    } else   $o2.append($o1.size,$o1.max,$o1.min,$o1.min,0) // no sdev
  }
}

//* fil2nqs(FILE,NQS) reads lines of file and places all numbers in NQS
func fil2nqs () { local a,n localobj v1
  $o2.clear
  a=allocvecs(v1)
  tmpfile.ropen($s1)
  for (n=1;tmpfile.gets(tstr)!=-1;n+=1) {
    if (n%1e3==0) printf("%d ",n)
    parsenums(tstr,v1)
    if (v1.size!=$o2.m) {
      printf("Wrong size at line %d (%d)  ",n,v1.size)  vlk(v1)
      return
    }
    $o2.append(v1)
  }
  dealloc(a)
  return $o2.size(1)
}

//** plnqs(file,NQS) reads output of txt2num.pl
// format ascii 'rows cols' then binary contents
proc plnqs () { local a,rows,cols localobj v1,v2
  a=allocvecs(v1,v2)
  tmpfile.ropen($s1)
  tmpfile.gets(tstr)
  sscanf(tstr,"%d %d",&rows,&cols)
  printf("%s: %d rows x %d cols\n",$s1,rows,cols)
  v1.fread(tmpfile,rows*cols) // could now use .transpose
  v2.indgen(0,rows*cols,cols)
  $o2.resize(cols,rows)
  for ii=0,cols-1 {
    v2.add(ii)
    $o2.v[ii].index(v1,v2)
  }
  dealloc(a)
}
    
// DEST=maxem(SRC,MIN,WIDTH) -- keep looking for maxima till get down to min
obfunc maxem () { local a,min,wid,ii,ix,beg,end localobj v1,aq
  a=allocvecs(v1)
  aq=new NQS("max","loc") aq.clear(v1.size/2)
  v1.copy($o1)
  min=$2 wid=$3
  while(v1.max>min) {
   aq.append(v1.max,ix=v1.max_ind)
   beg=ix-wid if (beg<0) beg=0
   end=ix+wid if (end>=v1.size) end=v1.size-1
   for ii=beg,end v1.x[ii]=-1e9
  }
  dealloc(a)
  return aq
}

// nqo=percl(nq,"COLA", ..) generates NQS of percentile values (10..90) for these cols
// nqo=percl(nq,min,max,step,"COLA", ..) -- eg percl(nq,50,70,5,"COLA","COLB")
obfunc percl () {  local i,ii,a,p localobj v1,v2,v3,aq,xo
  a=allocvecs(v1,v2,v3)
  aq=new NQS(numarg())
  if (argtype(2)==0) {
    v3.indgen($2,$3,$4) 
    aq.resize(aq.size(1)-3)
    i=5 j=4 // start at arg i and aq col #j
  } else {
    v3.indgen(10,90,10)
    i=2 j=1
  }
  aq.setcol(0,"PERCL",v3)
  for (;i<=numarg();i+=1) {
    $o1.getcol($si,v1)
    v1.sort()
    v2.resize(0)
    for vtr(&ii,v3) {ii/=100 v2.append(v1.x[round(ii*v1.size)])}
    aq.setcol(i-j,$si,v2)
  }
  dealloc(a)
  return aq
}

// pqunq(NQS) returns columns of sorted nique values corresponding to the arg
// NB: does not produce a rectangular array
obfunc pqunq () { local a localobj v1,v2,aq
  aq=new NQS()
  a=allocvecs(v1,v2,1e5)
  aq.sethdrs($o1)
  aq.resize(-2) 
  for ii=0,aq.m-1 {
    $o1.getcol(ii,v1)
    v1.sort 
    v2.redundout(v1)
    aq.v[ii].copy(v2)
  }
  dealloc(a)
  return aq
}

//** aa=seqind(ind) -- find beginning and end of sequential indices with 
obfunc seqind () { local a,n,skip,ii,x,last localobj vi,oq
  vi=$o1
  if (numarg()>=2) skip=$2+1 else skip=1
  if (numarg()>=3) oq=$o3
  if (!isassigned(oq)) {oq=new NQS() if (numarg()>=3) $o3=oq}
  if (oq.m!=3) { oq.resize(0) oq.resize("beg","end","diff") }
  oq.clear()
  n=last=0
  for ii=1,vi.size(1)-1 {
    if (vi.x[ii]-vi.x[ii-1]>skip) {
      if (n>0) oq.append(vi.x[last],vi.x[ii-1],0)
      last=ii
      n=0
    } else n+=1
  }
  if (n>0) oq.append(vi.x[last],vi.x[ii-1],0)
  oq.pad()
  oq.calc("<diff>.copy(<end>.c.sub(<beg>))")
  return oq
}

//** list_transpose
proc list_transpose () { localobj aq,mat,xo,inlist,outlist
  aq=new NQS() inlist=$o1 outlist=$o2
  if (!isojt(outlist,inlist)) {outlist=new List() $o2=outlist}
  for ltr(xo,inlist) aq.resize("",xo)
  mat=aq.tomat(1) // transpose
  aq.frmat(mat)
  outlist.remove_all
  aq.listvecs(outlist)
  delnqs(aq)
}

//* Sam's additions -- moved from nqs_utils.hoc
//get row of Vectors
//$o1 = nqs
//$2 = row number
//$s3 - $snumarg() - name of cols to get values for
//returns list with associated Vectors
obfunc getobjrow(){ local i,rowid localobj nq,vt,ls
  nq=$o1 rowid=$2
  ls=new List()
  vt=new Vector()
  for(i=3;i<=numarg();i+=1){
    nq.get($si,rowid,vt)
    ls.append(vt)
  }
  return ls
}

//get column of objects as Vector using oform
//$o1 = nqs
//$s2 = col name
//$3=iff==1 return list of Vectors in column, else return vector of oform of each row in column
obfunc getobjcol(){ local idx,getl localobj nq,vt,vt2,ls
  nq=$o1
  if(numarg()>2) getl=$3 else getl=0
  if(getl){
    ls=new List()
    vt=new Vector()
    for idx=0,nq.size-1{
      nq.get($s2,idx,vt)
      ls.append(vt)
    }
    return ls
  } else {
    vt=new Vector(nq.size)
    vt.resize(0)
    vt2=new Vector()
    for idx=0,nq.size-1{
      nq.get($s2,idx,vt2)
      vt.append(oform(vt2))
    }
    return vt
  }
}

//get correlation between 2 columns of an NQS
//$o1=nqs
//$s2=column name
//$s3=column name
//$4=pearson correlation iff == 1 (default), otherwise spearman
func nqcor(){ local pc localobj nq1,v1,v2
  if(numarg()>3) pc=$4 else pc=1
  nq1=$o1
  v1=nq1.getcol($s2)  v2=nq1.getcol($s3)
  if (pc) return v1.pcorrel(v2) else return v1.scorrel(v2)
}

//func nqgrslice(){ local startidx,endidx localobj nq,vtmp
//  nq=$o1 startidx=$2 endidx=$3
//  vtmp=new Vector($3-$2+1)
//  gg(
//}

func MIN(){ if($1<$2)return $1 else return $2 }

//get correlation matrix/nqs of all columns to all columns
//$o1 = NQS
//$2 = num columns 0 - NQS.m
//$3 = start row/index
//$4 = end row/index
//$5 = index increment
//$6 = window size , iff <= 0, do full columns against each other
obfunc nqcolcor(){ local startidx,endidx,inct,wint,c1,c2,ncol localobj vhr,vhl,nqc,nqf
 if(numarg()<1){
   printf("nqcolcor usage: \n\t$o1 = NQS\
                           \n\t$2 = num columns 0 - NQS.m\
                           \n\t$3 = start row/index\
                           \n\t$4 = end row/index\
                           \n\t$5 = index increment\
                           \n\t$6 = window size , iff <= 0, do full columns against each other\n")
   return nil
 }
 nqf=$o1
 if(numarg()>1) ncol=$2 else ncol=nqf.m
 if(numarg()>2) startidx=$3 else startidx=0
 if(numarg()>3) endidx=$4 else endidx=nqf.size
 if(numarg()>4) inct=$5 else inct=50*2//50ms
 if(numarg()>5) wint=$6 else wint=100*2//50ms

 vhr=new Vector(wint) vhl=new Vector(wint)

 if(wint<=0){ //full column cross-correlation
   nqc=new NQS("ID0","ID1","cor") 
   for c1=0,ncol-1{
     for c2=c1+1,ncol-1{
       nqc.append(c1,c2,nqf.v[c1].pcorrel(nqf.v[c2]))
     }
   }
 } else { //cross correlation using slices of column
   nqc=new NQS("ID0","ID1","start","end","cor") 
   for c1=0,ncol-1{
     for c2=c1+1,ncol-1{
       for(startidx=0;startidx<endidx;startidx+=inct){
         vhl.copy(nqf.v[c1],startidx,MIN(startidx+wint,endidx-1))
         vhr.copy(nqf.v[c2],startidx,MIN(startidx+wint,endidx-1))
         nqc.append(c1,c2,startidx,startidx+wint,vhl.pcorrel(vhr))
       }
     }
   }
 }

 return nqc
}

 
//read wmf ascii file (just skips header and calls rdcol)
//$s1 = wmf file path
//$2 = # of columns
// obfunc rdwmf(){ local idx,jdx,hdrlines localobj nq,myf,myftmp,strf,str,strtmp,lcols
// myf=new File() myftmp=new File() strf=new StringFunctions() str=new String() lcols=new List()
// strtmp=new String() hdrlines=6
// myf.ropen($s1)
// if(!myf.is_open()){
//  printf("rdwmf ERRA: couldn't open wmf file %s for read\n",$s1)
//  return nil
// }
// for idx=0,hdrlines-1{
//  if(myf.gets(str.s)==-1){
//    printf("rdwmf ERRB: corrupt header\n")
//    return nil
//  } else if(idx==2){
//    jdx=strf.tail(str.s,"",strtmp.s)            
//  }
// }
// myf.close()
// return nq
// }

//draw regression line
//$o1 = nqs, $s2 = column 1, $s3 = column 2
// or
//$o1 = Vector 1 , $o2 = Vector 2
//returns vo
obfunc drawregline(){ local x0,y0,x1,y1,gvtmp,r localobj vo,nq,v1,v2,vx,vy,str
  vo=new Vector(5)
  if(numarg()==3){
    nq = $o1
    v1=new Vector()  v2=new Vector()
    nq.getcol($s2,v1)
    nq.getcol($s3,v2)
  } else {
    v1=$o1 v2=$o2
  }
  v1.vstats(v2,vo)
  x0 = v2.min
  y0 = x0*vo.x(0)+vo.x(1)
  x1 = v2.max
  y1 = x1*vo.x(0)+vo.x(1)
  vx=new Vector(2)
  vx.x(0)=x0
  vx.x(1)=x1
  vy=new Vector(2)
  vy.x(0)=y0
  vy.x(1)=y1
  gvtmp=gvmarkflag
  gvmarkflag=0
  gg(vy,vx)
  gvmarkflag=gvtmp
  str=new String()
  r=v1.pcorrel(v2)
  if(name_declared("rpval_stats")){
    sprint(str.s,"r = %.2f, p = %g, N = %d",r,rpval_stats(v1.size,r),v1.size)
    g.label(0,0,str.s)
  }
  return vo
}

// select from a vector handled as a matrix -- see matrix.mod
halfmat=0
obfunc mindsel () { local a,x,r,c localobj vm,vi,oq
  vm=$o1 
  a=allocvecs(vi)
  if (numarg()==4) vi.indvwhere(vm,$s2,$3,$4) else vi.indvwhere(vm,$s2,$3)
  oq=new NQS("row","col","val") 
  oq.clear(vi.size)
  for vtr(&x,vi) {
    r=int(x/COLS) c=x-r*COLS
    if (!halfmat || c>r) oq.append(r,c,vm.x[x])
  }
  dealloc(a)
  print oq.size(1)
  return oq
}

//* return row $2 of nqs $o1 
obfunc nqrow () { local row,col localobj vout,nq
  nq=$o1
  row=$2
  vout=new Vector(nq.m)
  for col=0,nq.m-1 vout.x(col)=nq.v[col].x(row)
  return vout
}

//* find row $o2 (vector) in $o1 (nqs) and return index
//  if not there return -1
func nqfindrow () { local idx,jdx,sz localobj nq,vf,vrow
  nq=$o1  vf=$o2
  sz=nq.size(-1)
  for idx=0,sz-1 {
    vrow = nqrow(nq,idx)
    if(vrow.eq(vf)) return idx
  }
  return -1
}

//* nquniq(NQS) -- return a new NQS with unique rows in $o1
obfunc nquniq () { local sz,idx,outrow,jdx localobj nqin,nqout,vrow
  nqin=$o1
  nqout=new NQS()
  for idx=0,nqin.m-1{
    nqout.resize(nqin.s[idx].s)
    nqout.v[nqout.m-1].resize(nqin.v[idx].size)
  }
  sz=nqin.size(-1)
  jdx=0
  outrow=0
  for idx=0,sz-1{
    vrow=nqrow(nqin,idx)
    if(nqfindrow(nqout,vrow)==-1){
      for jdx=0,nqin.m-1 nqout.v[jdx].x(outrow) = vrow.x(jdx)
      outrow += 1
    }
  }
  for idx=0,nqout.m-1 nqout.v[idx].resize(outrow)
  return nqout
}

Sanjay M, Neymotin SA, Krothapalli SB (2015) Impaired dendritic inhibition leads to epileptic activity in a computer model of CA3. Hippocampus 25:1336-50[PubMed]

References and models cited by this paper

References and models that cite this paper

Barbarosie M, Avoli M (1997) CA3-driven hippocampal-entorhinal loop controls rather than sustains in vitro limbic seizures. J Neurosci 17:9308-14 [PubMed]

Bihi RI, Jefferys JG, Vreugdenhil M (2005) The role of extracellular potassium in the epileptogenic transformation of recurrent GABAergic inhibition. Epilepsia 46 Suppl 5:64-71 [Journal] [PubMed]

Bikson M, Hahn PJ, Fox JE, Jefferys JG (2003) Depolarization block of neurons during maintenance of electrographic seizures. J Neurophysiol 90:2402-8 [PubMed]

Borhegyi Z, Varga V, Szilágyi N, Fabo D, Freund TF (2004) Phase segregation of medial septal GABAergic neurons during hippocampal theta activity. J Neurosci 24:8470-9 [PubMed]

Buhl EH, Halasy K, Somogyi P (1994) Diverse sources of hippocampal unitary inhibitory postsynaptic potentials and the number of synaptic release sites. Nature 368:823-8 [PubMed]

Carnevale NT, Hines ML (2006) The NEURON Book

Cobb SR, Halasy K, Vida I, Nyiri G, Tamas G, Buhl EH, Somogyi P (1997) Synaptic effects of identified interneurons innervating both interneurons and pyramidal cells in the rat hippocampus. Neuroscience 79:629-48 [PubMed]

Colgin LL, Moser EI (2010) Gamma oscillations in the hippocampus. Physiology (Bethesda) 25:319-29 [PubMed]

Cooke SF, Bliss TV (2006) Plasticity in the human central nervous system. Brain 129:1659-73 [PubMed]

Cossart R, Dinocourt C, Hirsch JC, Merchan-Perez A, De Felipe J, Ben-Ari Y, Esclapez M, Berna (2001) Dendritic but not somatic GABAergic inhibition is decreased in experimental epilepsy. Nat Neurosci 4:52-62 [PubMed]

Curley AA, Lewis DA (2012) Cortical basket cell dysfunction in schizophrenia. J Physiol 590:715-24 [Journal] [PubMed]

Cymerblit-Sabba A, Schiller Y (2012) Development of hypersynchrony in the cortical network during chemoconvulsant-induced epileptic seizures in vivo. J Neurophysiol 107:1718-30 [Journal] [PubMed]

Dinocourt C, Petanjek Z, Freund TF, Ben-Ari Y, Esclapez M (2003) Loss of interneurons innervating pyramidal cell dendrites and axon initial segments in the CA1 region of the hippocampus following pilocarpine-induced seizures. J Comp Neurol 459:407-25 [Journal] [PubMed]

Dragoi G, Carpi D, Recce M, Csicsvari J, Buzsáki G (1999) Interactions between hippocampus and medial septum during sharp waves and theta oscillation in the behaving rat. J Neurosci 19:6191-9 [PubMed]

Dudek FE,Stanley KJ (2007) How does the balance of excitation and inhibition shift during epileptogenesis? Epilepsy Curr 7:86-88

Dzhala VI, Staley KJ (2003) Transition from interictal to ictal activity in limbic networks in vitro. J Neurosci 23:7873-80 [PubMed]

El-Hassar L, Milh M, Wendling F, Ferrand N, Esclapez M, Bernard C (2007) Cell domain-dependent changes in the glutamatergic and GABAergic drives during epileptogenesis in the rat CA1 region. J Physiol 578:193-211 [PubMed]

Furman M (2013) Seizure initiation and propagation in the pilocarpine rat model of temporal lobe epilepsy. J Neurosci 33:16409-11 [Journal] [PubMed]

Gloveli T, Dugladze T, Rotstein HG, Traub RD, Monyer H, Heinemann U, Whittington MA, Kopell N (2005) Orthogonal arrangement of rhythm-generating microcircuits in the hippocampus. Proc Natl Acad Sci U S A 102:13295-300 [Journal] [PubMed]

   Gamma and theta rythms in biophysical models of hippocampus circuits (Kopell et al. 2011) [Model]

Hines ML, Davison AP, Muller E (2009) NEURON and Python Frontiers in Neuroinformatics 3:1 [Journal] [PubMed]

   NEURON + Python (Hines et al. 2009) [Model]

Jahr CE, Stevens CF (1990) Voltage dependence of NMDA-activated macroscopic conductances predicted by single-channel kinetics. J Neurosci 10:3178-82 [PubMed]

Jung S, Warner LN, Pitsch J, Becker AJ, Poolos NP (2011) Rapid loss of dendritic HCN channel expression in hippocampal pyramidal neurons following status epilepticus. J Neurosci 31:14291-5 [Journal] [PubMed]

Karlócai MR, Kohus Z, Káli S, Ulbert I, Szabó G, Máté Z, Freund TF, Gulyás AI (2014) Physiological sharp wave-ripples and interictal events in vitro: what's the difference? Brain 137:463-85 [Journal] [PubMed]

Kurz JE, Moore BJ, Henderson SC, Campbell JN, Churn SB (2008) A cellular mechanism for dendritic spine loss in the pilocarpine model of status epilepticus. Epilepsia 49:1696-710 [Journal] [PubMed]

Lazarewicz MT, Migliore M, Ascoli GA (2002) A new bursting model of CA3 pyramidal cell physiology suggests multiple locations for spike initiation. Biosystems 67:129-37 [Journal] [PubMed]

   CA3 pyramidal neuron (Lazarewicz et al 2002) [Model]

Leite JP, Neder L, Arisi GM, Carlotti CG, Assirati JA, Moreira JE (2005) Plasticity, synaptic strength, and epilepsy: what can we learn from ultrastructural data? Epilepsia 46 Suppl 5:134-41 [Journal] [PubMed]

Lytton WW (2008) Computer modelling of epilepsy. Nat Rev Neurosci 9:626-37 [Journal] [PubMed]

Lytton WW, Orman R, Stewart M (2005) Computer simulation of epilepsy: implications for seizure spread and behavioral dysfunction. Epilepsy Behav 7:336-44 [Journal] [PubMed]

Maglóczky Z, Freund TF (2005) Impaired and repaired inhibitory circuits in the epileptic human hippocampus. Trends Neurosci 28:334-40 [Journal] [PubMed]

Manganotti P, Miniussi C, Santorum E, Tinazzi M, Bonato C, Marzi CA, Fiaschi A, Dalla Bernard (1998) Influence of somatosensory input on paroxysmal activity in benign rolandic epilepsy with 'extreme somatosensory evoked potentials'. Brain 121 ( Pt 4):647-58 [PubMed]

McAllister AK (2000) Cellular and molecular mechanisms of dendrite growth. Cereb Cortex 10:963-73 [PubMed]

Middleton S, Jalics J, Kispersky T, Lebeau FE, Roopun AK, Kopell NJ, Whittington MA, Cunningh (2008) NMDA receptor-dependent switching between different gamma rhythm-generating microcircuits in entorhinal cortex. Proc Natl Acad Sci U S A 105:18572-7 [PubMed]

Navarro Mora G, Bramanti P, Osculati F, Chakir A, Nicolato E, Marzola P, Sbarbati A, Fabene P (2009) Does pilocarpine-induced epilepsy in adult rats require status epilepticus? PLoS One 4:e5759 [Journal] [PubMed]

Neymotin SA, Lazarewicz MT, Sherif M, Contreras D, Finkel LH, Lytton WW (2011) Ketamine disrupts theta modulation of gamma in a computer model of hippocampus Journal of Neuroscience 31(32):11733-11743 [Journal] [PubMed]

   Ketamine disrupts theta modulation of gamma in a computer model of hippocampus (Neymotin et al 2011) [Model]

Ren H, Shi YJ, Lu QC, Liang PJ, Zhang PM (2014) The role of the entorhinal cortex in epileptiform activities of the hippocampus. Theor Biol Med Model 11:14 [Journal] [PubMed]

Rutecki PA, Yang Y (1998) Ictal epileptiform activity in the CA3 region of hippocampal slices produced by pilocarpine. J Neurophysiol 79:3019-29 [PubMed]

Seddigh S, Thömke F, Vogt TH (1999) Complex partial seizures provoked by photic stimulation. J Neurol Neurosurg Psychiatry 66:801-2 [PubMed]

Sloviter RS, Zappone CA, Harvey BD, Bumanglag AV, Bender RA, Frotscher M (2003) "Dormant basket cell" hypothesis revisited: relative vulnerabilities of dentate gyrus mossy cells and inhibitory interneurons after hippocampal status epilepticus in the rat. J Comp Neurol 459:44-76

Stewart M, Fox SE (1990) Do septal neurons pace the hippocampal theta rhythm? Trends Neurosci 13:163-8 [PubMed]

Stoop R, Pralong E (2000) Functional connections and epileptic spread between hippocampus, entorhinal cortex and amygdala in a modified horizontal slice preparation of the rat brain. Eur J Neurosci 12:3651-63

Sylwestrak EL, Ghosh A (2012) Elfn1 regulates target-specific release probability at CA1-interneuron synapses. Science 338:536-40 [Journal] [PubMed]

Whittington MA, Traub RD, Jefferys JG (1995) Erosion of inhibition contributes to the progression of low magnesium bursts in rat hippocampal slices. J Physiol 486 ( Pt 3):723-34 [PubMed]

Witter MP (2007) Intrinsic and extrinsic wiring of CA3: indications for connectional heterogeneity. Learn Mem 14:705-13 [PubMed]

Wittner L, Eross L, Czirják S, Halász P, Freund TF, Maglóczky Z (2005) Surviving CA1 pyramidal cells receive intact perisomatic inhibitory input in the human epileptic hippocampus. Brain 128:138-52 [Journal] [PubMed]

Zhang W, Buckmaster PS (2009) Dysfunction of the dentate basket cell circuit in a rat model of temporal lobe epilepsy. J Neurosci 29:7846-56 [PubMed]

Ziburkus J, Cressman JR, Barreto E, Schiff SJ (2006) Interneuron and pyramidal cell interplay during in vitro seizure-like events. J Neurophysiol 95:3948-54 [PubMed]

(46 refs)