Ca+/HCN channel-dependent persistent activity in multiscale model of neocortex (Neymotin et al 2016)

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Accession:185858
"Neuronal persistent activity has been primarily assessed in terms of electrical mechanisms, without attention to the complex array of molecular events that also control cell excitability. We developed a multiscale neocortical model proceeding from the molecular to the network level to assess the contributions of calcium regulation of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in providing additional and complementary support of continuing activation in the network. ..."
Reference:
1 . Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW (2016) Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex Neuroscience 316:344-366 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell; Synapse; Channel/Receptor; Molecular Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron; Neocortex layer 2-3 interneuron; Neocortex layer 5 interneuron; Neocortex layer 6a interneuron;
Channel(s): I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I CAN; I Calcium; I_AHP; I_KD; Ca pump;
Gap Junctions:
Receptor(s): mGluR1; GabaA; GabaB; AMPA; NMDA; mGluR; Glutamate; Gaba; IP3;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Ion Channel Kinetics; Oscillations; Spatio-temporal Activity Patterns; Signaling pathways; Working memory; Attractor Neural Network; Calcium dynamics; Laminar Connectivity; G-protein coupled; Rebound firing; Brain Rhythms; Dendritic Bistability; Reaction-diffusion; Beta oscillations; Persistent activity; Multiscale;
Implementer(s): Neymotin, Sam [samn at neurosim.downstate.edu]; McDougal, Robert [robert.mcdougal at yale.edu];
Search NeuronDB for information about:  Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; mGluR1; GabaA; GabaB; AMPA; NMDA; mGluR; Glutamate; Gaba; IP3; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I CAN; I Calcium; I_AHP; I_KD; Ca pump; Gaba; Glutamate;
  
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CaHDemo
readme.txt
cagk.mod
cal.mod *
calts.mod *
can.mod *
cat.mod *
gabab.mod
IC.mod *
icalts.mod *
Ih.mod
ihlts.mod *
IKM.mod *
kap.mod
kcalts.mod *
kdmc.mod
kdr.mod
kdrbwb.mod
km.mod *
mglur.mod *
misc.mod *
MyExp2SynBB.mod *
MyExp2SynNMDABB.mod
nafbwb.mod
nax.mod
stats.mod *
vecst.mod *
aux_fun.inc *
conf.py
declist.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
geom.py
ghk.inc *
grvec.hoc *
init.hoc
labels.hoc
labels.py *
local.hoc *
misc.h *
mpisim.py
netcfg.cfg
nqs.hoc
nqs.py
nrnoc.hoc *
onepyr.cfg
onepyr.py
pyinit.py *
python.hoc *
pywrap.hoc *
simctrl.hoc *
simdat.py
syncode.hoc *
xgetargs.hoc *
                            
// $Id: drline.hoc,v 1.41 2011/02/15 14:05:02 billl Exp $

print "Loading drline.hoc..."

// click and drag left button to draw lines on top of a figure interactively
// select graph to draw on with setdrl(Graph[])
// set color with clr, line width with lne
// select 'Draw curve' for continuous drawing
// select 'Arrow' to place an arrow pointing according to direction of drag

drlflush=1 //whether to flush line drawings each drline call

//* drline(x0,y0,x1,y1,OPT graph or color) 
proc drline () { local color,line
  if (numarg()==0) { print "drline(x0,y0,x1,y1[,g,col,line])"
    return }
  if (numarg()>4) { 
    if (argtype(5)==0) { color=$5 
                         if (numarg()>5) line=$6
    } else {             graphItem = $o5 
                         if (numarg()>5) color=$6
                         if (numarg()>6) line=$7      }}
  graphItem.beginline(color,line)
  graphItem.line($1,$2)
  graphItem.line($3,$4)
  if(drlflush) graphItem.flush()
}

//* set to drawlines on top of fig
proc setdrl () {
  g=$o1 // select this graph for further drawing
  xpanel("")
  $o1.menu_tool("Draw line","drl")
  $o1.menu_tool("Draw curve","drc")
  $o1.menu_tool("Label","drw")
  $o1.menu_tool("Arrow","dra")
  $o1.menu_tool("Circle","drci")
  $o1.menu_tool("Rectangle","drr")
  xvalue("Color","clr",1,"",1)
  xvalue("Line","lne",1,"",1)
  xbutton("Erase","g.erase_all()")
  xpanel()
  $o1.exec_menu("Draw line")
}

//* draw line interactively on top of fig
// interesting that this should work at all since x0,y0 local but still preserving their
// values across multiple calls
proc drl ()  { local x0,y0,type,x,y,keystate
  type=$1 x=$2 y=$3 keystate=$4
  if (type==2) {x0=x y0=y}
  if (type==3) drline(x0,y0,x,y,clr,lne)
}

//* draw circle interactively on top of fig
// drci(2,0,0,0) drci(3,1,0,0)
proc drci ()  { local a,x0,y0,type,x,y,keystate,ii,rad localobj xv,yv
  type=$1 x=$2 y=$3 keystate=$4
  if (type==2) {x0=x y0=y}
  if (type==3) { rad=sqrt((x-x0)^2+(y-y0)^2) 
    a=allocvecs(xv,yv) vrsz(360,xv,yv)
    print "Circle: ",x0,y0,rad
    yv.circ(xv,x0,y0,rad)
    yv.line(g,xv,clr,lne)
    dealloc(a)
  }
}

//* draw retangle interactively on top of fig
proc drr ()  { local x0,y0,type,x,y,keystate
  type=$1 x=$2 y=$3 keystate=$4
  if (type==2) {x0=x y0=y}
  if (type==3) { drline(x0,y0,x0,y,clr,lne)
    drline(x,y0,x,y,clr,lne) drline(x,y,x0,y,clr,lne) drline(x,y0,x0,y0,clr,lne) }
}

//* draw arrow interactively on top of fig
proc dra ()  { local xsz,ysz,type,x,y,keystate,rot
  type=$1 x=$2 y=$3 keystate=$4
  xsz=0.1*(g.size(2)-g.size(1)) // 10% of size
  ysz=0.1*(g.size(4)-g.size(3))
  if (type==2) {x0=x y0=y}
  if (type==3) {
    if (y==y0) {
      if (x>x0) rot=-90 else rot=90
    } else {
      rot=-atan((x-x0)/(y-y0))/2/PI*360
      if ((y-y0)<=0) rot+=180
    }
    g.glyph(arrow(),x,y,xsz,ysz,rot)
  }
}

//* draw curve interactively on top of fig
proc drc ()  { local x0,y0,type,x,y,keystate
  type=$1 x=$2 y=$3 keystate=$4
  if (type==2) { x0=x y0=y
  } else if (type==1) {
    drline(x0,y0,x,y,clr,lne)
    x0=x y0=y
  } else if (type==3) drline(x0,y0,x,y,clr,lne)
}

//* write label
proc drw ()  { local x0,y0,type,x,y,keystate
  type=$1 x=$2 y=$3 keystate=$4
  if (type==2) { 
   string_dialog("Label: ",tstr) 
   g.label(x,y,tstr,1,1,0.5,0.5,clr)
  }
}

obfunc arrow () { localobj o
  o=new Glyph()
  o.m(0,0)  o.l(0,2) o.s(1,4) // draw vertical line
  o.m(0,0)  o.l(0,-2) o.s(1,4) // draw vertical line
  o.m(0,-2) o.l(-2,0) o.s(1,4)
  o.m(0,-2) o.l(2,0) o.s(1,4)
  return o
}

//* hist(g,vec,min,max,bins)
{clr=1 hflg=1 ers=1 sym=1 pflg=0 lin=4 hbup=0} 
declared("hfunc")
// clr:color, hflg=1 draw lines; 2 draw boxes; 3 fill in; ers=erase; 
// pflg=1 normalize hist by size of $o2, so will be probability instead of count
// pflg=2 turn hist upside down
// pflg=3 operate on values with hfunc()
// style determined by hflg
// hflg==0 lines with dots
// hflg==0.x offset lines with dots
// hflg==1 outlines but not down to zero
// hflg==2 outlines with lines down to zero
// hflg==3 just dots
// hflg==3.x lines between dots
// hbup=1 // move baseline up by this amount
func hist () { local a,b,c,min,max,wid,bins,ii,jj,offset,x,y
  if (numarg()==0) { printf("hist(g,vec,min,max,bins)\n") return 0}
  if ($o2.size<2)  { printf("hist: $o2 too small\n",$o2) return -1}
  if ($o2.min==$o2.max)  { printf("hist: %s all one value: %g\n",$o2,$o2.min) return -1}
  if (numarg()==5) {min=$3 max=$4 bins=$5 
  } else if (numarg()==4) { min=0 max=$3 bins=$4 
  } else if (numarg()<=3) { 
    if ((min=0.95*$o2.min)<0) min=1.05*$o2.min
    if ((max=1.05*$o2.max)<0) max=0.95*$o2.max
    bins=100
    if (min>0) min*=0.9 else min*=1.1
    if (max>0) max*=1.1 else max*=0.9
    if (numarg()==3) bins=$3
  }
  wid=(max-min)/bins
  // print min,max,max-wid,wid
  a=b=c=allocvecs(3) b+=1 c+=2
  offset=0 x=-1
  if (ers) $o1.erase_all()
  mso[c].hist($o2,min,bins,wid) // c has values
  if(pflg==1) mso[c].div(mso[c].sum) // normalize to sum to 1
  if(pflg==2) mso[c].mul(-1)
  if(pflg==3) hfunc(mso[c])
  mso[a].resize(2*mso[c].size())
  mso[a].indgen(0.5) 
  mso[a].apply("int") 
  mso[b].index(mso[c], mso[a]) 
  mso[a].mul(wid) mso[a].add(min)
  mso[b].rotate(1)
  mso[b].x[0] = 0 
  mso[b].append(mso[b].x[mso[b].size-1],0)
  mso[b].add(hbup)
  mso[a].append(max,max)
  if (hflg==1 || hflg==2) { 
    mso[b].line($o1, mso[a],clr,lin)
    if (hflg==2) for vtr(&x,mso[a]) drline(x,0,x,mso[b].x[i1],$o1,clr,lin)
  } else if (int(hflg)==0 || hflg>=3) { 
    if (hflg%1!=0) offset=hflg*wid // use eg -0.5+ii/8 to move back to integer
    mso[a].indgen(min,max-wid,wid)
    mso[a].add(wid/2+offset)
    // print mso[a].min,mso[a].max
    // mso[c].mark($o1,mso[a],"O",6,clr,2) // this will place points where 0 count
    for jj=0,mso[a].size-1 if (mso[c].x[jj]!=0) {
      if (hflg!=3 && hflg%1!=0) drline(mso[a].x[jj],0,mso[a].x[jj],mso[c].x[jj],$o1,clr,lin)
      if (hflg==4) {
        if (x!=-1) drline(x,y,mso[a].x[jj],mso[c].x[jj],$o1,clr,lin)
        x=mso[a].x[jj] y=mso[c].x[jj]
      }
      $o1.mark(mso[a].x[jj],mso[c].x[jj],sg(sym).t,10,clr,2) // don't place points with 0 count
    }
  }
  $o1.flush()
  $o1.size(min,max,0,mso[b].max)
  dealloc(a)
  return 1
}

// barplot(g,yvec,xvec[,bar_width]) 
// barplot(g,yvec,xvec[,bar_width,color_vec]) -- for multicolored bars -- each point has a color
// barplot(g,yvec,xvec[,bar_width,color_vec,error_vec]) -- error_vec plots the error
scribble=0
func barplot () { local a,sz,wid,ii,jj,x,y,mulcol localobj go,vx,vy,v1,vcol
  if (numarg()==0) {
    printf("barplot(g,yvec,xvec[,bar_width]), scribble=1 to 'fill in'\n") 
    printf("set scribble=1 to fill in with single color (based on clr)\n")
    printf("barplot(g,yvec,xvec[,bar_width,color_vec]):multicolored bars-each point has a color\n")
    printf("barplot(g,yvec,xvec[,bar_width,color_vec,error_vec]):add +/- error to each bar\n")
    return 0}
  if ((sz=$o2.size)!=$o3.size)  { printf("barplot: x,y vectors differ in size\n") return -1}
  go=$o1 $o3.sort
  if (argtype(4)==0)  wid=$4 else wid=1
  if (argtype(5)==1)  {vcol=$o5 mulcol=-1
    if (sz!=vcol.size) { printf("barplot: color vec wrong size: %d %d\n",sz,vcol.size) return -1}  
  } else if (argtype(5)==0) mulcol=$5 else mulcol=0
  wid/=2
  // print min,max,max-wid,wid
  a=allocvecs(vx,vy,v1)
  if (ers) go.erase_all()
  for vtr2(&x,&y,$o3,$o2,&ii)  { 
    vx.append(x-wid,x-wid,x+wid,x+wid)
    vy.append(0,y,y,0)
  }
  if (mulcol) {
    for vtr2(&x,&y,$o3,$o2,&jj)  { 
      if (mulcol==-1) clr=vcol.x[jj] else clr=mulcol
      vrsz(0,vx,vy)
      vx.append(x-wid,x-wid)
      vy.append(0,y)
      for (ii=0;ii<2*wid;ii+=(wid/100)) { 
        vx.add(wid/100) 
        vy.line(go, vx, clr, 4)
      }
    }
    vy.line(go, vx, clr, 4)
  } else if (scribble) {
    vrsz(0,vx,vy)
    for vtr2(&x,&y,$o3,$o2,&ii)  { 
      vx.append(x-wid,x-wid,x-wid)
      vy.append(0,y,0)
    }
    for (ii=0;ii<2*wid;ii+=(wid/100)) { 
      vx.add(wid/100) 
      vy.line(go, vx, clr, 4)
    }
    vy.line(go, vx, clr, 4)
  } else vy.line(go, vx, clr, lne)
  if(numarg()>5) $o2.ploterr(go, $o3, $o6, 15, 1, 3)
  go.flush()
  go.size(vx.min-wid,vx.max+wid,0,vy.max)
  dealloc(a)
  return 1
}

proc smgs () { local a,b,c,min,max,wid,bins,ii,jj,offset,x,y localobj v1
  if ($o2.size<2)  { printf("smgs: $o2 too small\n",$o2) return -1}
  if ($o2.min==$o2.max)  { printf("smgs: %s all one value: %g\n",$o2,$o2.min) return -1}
  if (numarg()==5) {min=$3 max=$4 bins=$5 
  } else if (numarg()==4) { min=0 max=$3 bins=$4 
  } else if (numarg()<=3) { 
    if ((min=0.95*$o2.min)<0) min=1.05*$o2.min
    if ((max=1.05*$o2.max)<0) max=0.95*$o2.max
    bins=100
    if (min>0) min*=0.9 else min*=1.1
    if (max>0) min*=1.1 else max*=0.9
    if (numarg()==3) bins=$3
  }
  wid=(max-min)/bins
  // print min,max,max-wid,wid
  a=b=c=allocvecs(3,1e4) b+=1 c+=2
  offset=0 x=-1
  if (ers) $o1.erase_all()
  mso[a].indgen(min,max,wid)
  if (0) {
    mso[c].smgs($o2,min,max,wid,wid*wid/4) // c has values
    mso[c].line($o1, mso[a],clr,4)
  } else {
    v1=$o2.sumgauss(min,max,wid,wid/2) // c has values
    v1.line($o1, mso[a],clr,4)
  }
}

//* a few drawing utilities from sam (not too spectacular)
 
//** drawhticks(ticksz,minx,maxx,linewidth,$5-$numarg() == y position of horizontal ticks)
// draw horizontal ticks of a view box along left/right of box
proc drawhticks () { local ticksz,minx,maxx,lw,i
  ticksz=$1 minx=$2 maxx=$3 lw=$4
  for i=5,numarg() {
    drline(minx,$i,minx+ticksz,$i,g,1,lw)    drline(maxx,$i,maxx-ticksz,$i,g,1,lw)
  }
}

//** drawvticks(ticksz,miny,maxy,linewidth,$5-$numarg() == x position of vertical ticks)
// draw vertical ticks of a view box along top/bottom of box
proc drawvticks () { local ticksz,miny,maxy,lw,i
  ticksz=$1 miny=$2 maxy=$3 lw=$4
  for i=5,numarg() {
    drline($i,miny,$i,miny+ticksz,g,1,lw)    drline($i,maxy,$i,maxy-ticksz,g,1,lw)
  }
}

//** drawbox(minx,maxx,miny,maxy[,line,graph]) - draw box
proc drawbox () { local minx,maxx,miny,maxy,ln localobj myg
  minx=$1 maxx=$2 miny=$3 maxy=$4
  if(numarg()>4)ln=$5 else ln=3
  if(numarg()>5)myg=$o6 else myg=g
  drline(minx,miny,minx,maxy,myg,1,ln) //bottom
  drline(minx,miny,maxx,miny,myg,1,ln) //left
  drline(minx,maxy,maxx,maxy,myg,1,ln) //top
  drline(maxx,miny,maxx,maxy,myg,1,ln) //right
}

Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW (2016) Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex Neuroscience 316:344-366[PubMed]

References and models cited by this paper

References and models that cite this paper

Accili EA, Proenza C, Baruscotti M, DiFrancesco D (2002) From funny current to HCN channels: 20 years of excitation. News Physiol Sci 17:32-7 [PubMed]

Ames KC, Ryu SI, Shenoy KV (2014) Neural dynamics of reaching following incorrect or absent motor preparation. Neuron 81:438-51 [Journal] [PubMed]

Anderson CT, Sheets PL, Kiritani T, Shepherd GM (2010) Sublayer-specific microcircuits of corticospinal and corticostriatal neurons in motor cortex. Nat Neurosci 13:739-44 [PubMed]

Anwar H, Hong S, De Schutter E (2012) Controlling Ca(2+)-Activated K (+) Channels with Models of Ca (2+) Buffering in Purkinje Cells. Cerebellum 11:681-693 [Journal] [PubMed]

   Controlling KCa channels with different Ca2+ buffering models in Purkinje cell (Anwar et al. 2012) [Model]

Aponte Y, Lien CC, Reisinger E, Jonas P (2006) Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. J Physiol 574:229-43 [PubMed]

Arnsten AF, Jin LE (2012) Guanfacine for the treatment of cognitive disorders: a century of discoveries at Yale. Yale J Biol Med 85:45-58 [PubMed]

Arnsten AF, Paspalas CD, Gamo NJ, Yang Y, Wang M (2010) Dynamic Network Connectivity: A new form of neuroplasticity. Trends Cogn Sci 14:365-75 [PubMed]

Ashhad S, Johnston D, Narayanan R (2015) Activation of InsP3 receptors is sufficient for inducing graded intrinsic plasticity in rat hippocampal pyramidal neurons. J Neurophysiol 113:2002-13 [Journal] [PubMed]

Ashhad S, Narayanan R (2013) Quantitative interactions between the A-type K+ current and inositol trisphosphate receptors regulate intraneuronal Ca2+ waves and synaptic plasticity. J Physiol 591:1645-69 [Journal] [PubMed]

   Calcium waves and mGluR-dependent synaptic plasticity in CA1 pyr. neurons (Ashhad & Narayanan 2013) [Model]

Barbieri R, Wilson MA, Frank LM, Brown EN (2005) An analysis of hippocampal spatio-temporal representations using a Bayesian algorithm for neural spike train decoding. IEEE Trans Neural Syst Rehabil Eng 13:131-6 [Journal] [PubMed]

Bartos M, Vida I, Jonas P (2007) Synaptic mechanisms of synchronized gamma oscillations in inhibitory interneuron networks. Nat Rev Neurosci 8:45-56 [PubMed]

Bender RA, Brewster A, Santoro B, Ludwig A, Hofmann F, Biel M, Baram TZ (2001) Differential and age-dependent expression of hyperpolarization-activated, cyclic nucleotide-gated cation channel isoforms 1-4 suggests evolving roles in the developing rat hippocampus. Neuroscience 106:689-98 [PubMed]

Bernander O, Douglas RJ, Martin KA, Koch C (1991) Synaptic background activity influences spatiotemporal integration in single pyramidal cells. Proc Natl Acad Sci U S A 88:11569-73 [PubMed]

Berridge MJ (1998) Neuronal calcium signaling. Neuron 21:13-26 [PubMed]

Blackwell K (2013) Chapter 6: Calcium: the answer to life, the universe, and everything 20 Years of Computational Neuroscience, Bower J, ed. pp.141

Braver TS, Cohen JD, Nystrom LE, Jonides J, Smith EE, Noll DC (1997) A parametric study of prefrontal cortex involvement in human working memory. Neuroimage 5:49-62 [Journal] [PubMed]

Burdakov D (2005) Gain control by concerted changes in I(A) and I(H) conductances. Neural Comput 17:991-995 [PubMed]

Bygrave FL, Benedetti A (1996) What is the concentration of calcium ions in the endoplasmic reticulum? Cell Calcium 19:547-51 [PubMed]

Carcea I, Froemke RC (2013) Cortical plasticity, excitatory-inhibitory balance, and sensory perception. Prog Brain Res 207:65-90 [Journal] [PubMed]

Carnevale NT, Hines ML (2006) The NEURON Book

Castro-Alamancos MA (2013) The motor cortex: a network tuned to 7-14 Hz. Front Neural Circuits 7:21 [Journal] [PubMed]

Chadderdon GL, Mohan A, Suter BA, Neymotin SA, Kerr CC, Francis JT, Shepherd GM, Lytton WW (2014) Motor cortex microcircuit simulation based on brain activity mapping. Neural Comput 26:1239-62 [Journal] [PubMed]

   Motor cortex microcircuit simulation based on brain activity mapping (Chadderdon et al. 2014) [Model]

Chen S, Wang J, Siegelbaum SA (2001) Properties of hyperpolarization-activated pacemaker current defined by coassembly of HCN1 and HCN2 subunits and basal modulation by cyclic nucleotide. J Gen Physiol 117:491-504 [PubMed]

Chen X, Rochefort NL, Sakmann B, Konnerth A (2013) Reactivation of the same synapses during spontaneous up states and sensory stimuli. Cell Rep 4:31-9 [Journal] [PubMed]

Compte A, Brunel N, Goldman-Rakic PS, Wang XJ (2000) Synaptic mechanisms and network dynamics underlying spatial working memory in a cortical network model. Cereb Cortex 10:910-23 [PubMed]

Cossart R, Aronov D, Yuste R (2003) Attractor dynamics of network UP states in the neocortex. Nature 423:283-8 [PubMed]

   [30 reconstructed morphologies on NeuroMorpho.Org]

De Young GW, Keizer J (1992) A single-pool inositol 1,4,5-trisphosphate-receptor-based model for agonist-stimulated oscillations in Ca2+ concentration. Proc Natl Acad Sci U S A 89:9895-9 [PubMed]

Destexhe A, Bal T, McCormick DA, Sejnowski TJ (1996) Ionic mechanisms underlying synchronized oscillations and propagating waves in a model of ferret thalamic slices. J Neurophysiol 76:2049-70 [Journal] [PubMed]

   Thalamocortical and Thalamic Reticular Network (Destexhe et al 1996) [Model]

Destexhe A, Rudolph M, Pare D (2003) The high-conductance state of neocortical neurons in vivo. Nat Rev Neurosci 4:739-51 [PubMed]

Durstewitz D, Seamans JK, Sejnowski TJ (2000) Neurocomputational models of working memory. Nat Neurosci 3 Suppl:1184-91 [PubMed]

Dyhrfjeld-Johnsen J, Morgan RJ, Foldy C, Soltesz I (2008) Upregulated H-current in hyperexcitable CA1 dendrites after febrile seizures. Front Cell Neurosci 2:2 [Journal] [PubMed]

Dyhrfjeld-Johnsen J, Morgan RJ, Soltesz I (2009) Double Trouble? Potential for Hyperexcitability Following Both Channelopathic up- and Downregulation of I(h) in Epilepsy. Front Neurosci 3:25-33 [PubMed]

Egorov AV, Hamam BN, Fransen E, Hasselmo ME, Alonso AA (2002) Graded persistent activity in entorhinal cortex neurons. Nature 420:173-8 [PubMed]

Evans RC, Blackwell KT (2015) Calcium: amplitude, duration, or location? Biol Bull 228:75-83 [PubMed]

Fall CP, Lewis TJ, Rinzel J (2005) Background-activity-dependent properties of a network model for working memory that incorporates cellular bistability. Biol Cybern 93:109-18 [Journal] [PubMed]

Fall CP, Rinzel J (2006) An intracellular Ca2+ subsystem as a biologically plausible source of intrinsic conditional bistability in a network model of working memory J Comput Neurosci 20:97-107 [Journal] [PubMed]

Fall CP, Wagner JM, Loew LM, Nuccitelli R (2004) Cortically restricted production of IP3 leads to propagation of the fertilization Ca2+ wave along the cell surface in a model of the Xenopus egg. J Theor Biol 231:487-96

Fitzpatrick JS, Hagenston AM, Hertle DN, Gipson KE, Bertetto-D'Angelo L, Yeckel MF (2009) Inositol-1,4,5-trisphosphate receptor-mediated Ca2+ waves in pyramidal neuron dendrites propagate through hot spots and cold spots. J Physiol 587:1439-59 [Journal] [PubMed]

Fransen E, Tahvildari B, Egorov AV, Hasselmo ME, Alonso AA (2006) Mechanism of graded persistent cellular activity of entorhinal cortex layer v neurons. Neuron 49:735-46 [PubMed]

Fukushima M, Saunders RC, Leopold DA, Mishkin M, Averbeck BB (2012) Spontaneous high-gamma band activity reflects functional organization of auditory cortex in the awake macaque. Neuron 74:899-910 [Journal] [PubMed]

Ghitza O (2011) Linking speech perception and neurophysiology: speech decoding guided by cascaded oscillators locked to the input rhythm. Front Psychol 2:130 [Journal] [PubMed]

Giocomo LM, Hasselmo ME (2007) Neuromodulation by glutamate and acetylcholine can change circuit dynamics by regulating the relative influence of afferent input and excitatory feedback. Mol Neurobiol 36:184-200 [Journal] [PubMed]

Goldman-Rakic PS (1995) Cellular basis of working memory. Neuron 14:477-85 [PubMed]

Hagiwara N, Irisawa H (1989) Modulation by intracellular Ca2+ of the hyperpolarization-activated inward current in rabbit single sino-atrial node cells. J Physiol 409:121-41 [PubMed]

Harnett MT, Magee JC, Williams SR (2015) Distribution and function of HCN channels in the apical dendritic tuft of neocortical pyramidal neurons. J Neurosci 35:1024-37 [Journal] [PubMed]

Harnett MT, Xu NL, Magee JC, Williams SR (2013) Potassium channels control the interaction between active dendritic integration compartments in layer 5 cortical pyramidal neurons. Neuron 79:516-29 [Journal] [PubMed]

Hartsfield J () A quantitative study of neuronal calcium signaling Ph.D. diss., Baylor College of Medicine

Hasselmo ME, McGaughy J (2004) High acetylcholine levels set circuit dynamics for attention and encoding and low acetylcholine levels set dynamics for consolidation. Prog Brain Res 145:207-31 [PubMed]

Hay E, Hill S, Schurmann F, Markram H, Segev I (2011) Models of neocortical layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active properties. PLoS Comput Biol 7:e1002107 [Journal] [PubMed]

   [3 reconstructed morphologies on NeuroMorpho.Org]
   Cortical Layer 5b pyr. cell with [Na+]i mechanisms, from Hay et al 2011 (Zylbertal et al 2017) [Model]
   L5b PC model constrained for BAC firing and perisomatic current step firing (Hay et al., 2011) [Model]

Heys JG, Hasselmo ME (2012) Neuromodulation of I(h) in layer II medial entorhinal cortex stellate cells: a voltage-clamp study. J Neurosci 32:9066-72 [PubMed]

Hines ML, Carnevale NT (2000) Expanding NEURON's repertoire of mechanisms with NMODL. Neural Comput 12:995-1007 [PubMed]

Hong M, Ross WN (2007) Priming of intracellular calcium stores in rat CA1 pyramidal neurons. J Physiol 584:75-87 [PubMed]

Honnuraiah S, Narayanan R (2013) A calcium-dependent plasticity rule for HCN channels maintains activity homeostasis and stable synaptic learning. PLoS One 8:e55590 [Journal] [PubMed]

Hooks BM, Hires SA, Zhang YX, Huber D, Petreanu L, Svoboda K, Shepherd GM (2011) Laminar analysis of excitatory local circuits in vibrissal motor and sensory cortical areas. PLoS Biol 9:e1000572 [Journal] [PubMed]

   Laminar analysis of excitatory circuits in vibrissal motor and sensory cortex (Hooks et al. 2011) [Model]

Hooks BM, Mao T, Gutnisky DA, Yamawaki N, Svoboda K, Shepherd GM (2013) Organization of cortical and thalamic input to pyramidal neurons in mouse motor cortex. J Neurosci 33:748-60 [PubMed]

Hsieh CY, Cruikshank SJ, Metherate R (2000) Differential modulation of auditory thalamocortical and intracortical synaptic transmission by cholinergic agonist. Brain Res 880:51-64 [PubMed]

Hunter MD, Eickhoff SB, Miller TW, Farrow TF, Wilkinson ID, Woodruff PW (2006) Neural activity in speech-sensitive auditory cortex during silence. Proc Natl Acad Sci U S A 103:189-94 [Journal] [PubMed]

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

Kane MJ, Engle RW (2002) The role of prefrontal cortex in working-memory capacity, executive attention, and general fluid intelligence: an individual-differences perspective. Psychon Bull Rev 9:637-71 [PubMed]

Kay AR, Wong RK (1987) Calcium current activation kinetics in isolated pyramidal neurones of the Ca1 region of the mature guinea-pig hippocampus. J Physiol 392:603-16 [PubMed]

Kelemen E, Fenton AA (2010) Dynamic grouping of hippocampal neural activity during cognitive control of two spatial frames. PLoS Biol 8:e1000403 [PubMed]

Kiritani T, Wickersham IR, Seung HS, Shepherd GM (2012) Hierarchical connectivity and connection-specific dynamics in the corticospinal-corticostriatal microcircuit in mouse motor cortex. J Neurosci 32:4992-5001 [PubMed]

Kocsis B, Li S (2004) In vivo contribution of h-channels in the septal pacemaker to theta rhythm generation. Eur J Neurosci 20:2149-58 [PubMed]

Kole MH, Hallermann S, Stuart GJ (2006) Single Ih channels in pyramidal neuron dendrites: properties, distribution, and impact on action potential output. J Neurosci 26:1677-87 [Journal] [PubMed]

   [1 reconstructed morphology on NeuroMorpho.Org]
   Stochastic Ih and Na-channels in pyramidal neuron dendrites (Kole et al 2006) [Model]

Kumar S, Sedley W, Barnes GR, Teki S, Friston KJ, Griffiths TD (2014) A brain basis for musical hallucinations. Cortex 52:86-97 [Journal] [PubMed]

Larkum ME, Nevian T, Sandler M, Polsky A, Schiller J (2009) Synaptic integration in tuft dendrites of layer 5 pyramidal neurons: a new unifying principle. Science 325:756-60 [Journal] [PubMed]

   Synaptic integration in tuft dendrites of layer 5 pyramidal neurons (Larkum et al. 2009) [Model]

Li YX, Rinzel J (1994) Equations for InsP3 receptor-mediated [Ca2+]i oscillations derived from a detailed kinetic model: a Hodgkin-Huxley like formalism. J Theor Biol 166:461-73 [PubMed]

Lim S, Goldman MS (2013) Balanced cortical microcircuitry for maintaining information in working memory. Nat Neurosci 16:1306-14 [Journal] [PubMed]

   Model of working memory based on negative derivative feedback (Lim and Goldman, 2013) [Model]

Lim S, Goldman MS (2014) Balanced cortical microcircuitry for spatial working memory based on corrective feedback control. J Neurosci 34:6790-806 [Journal] [PubMed]

Lisman JE, Fellous JM, Wang XJ (1998) A role for NMDA-receptor channels in working memory. Nat Neurosci 1:273-5 [PubMed]

Loewenstein Y, Sompolinsky H (2003) Temporal integration by calcium dynamics in a model neuron. Nat Neurosci 6:961-7 [PubMed]

Lytton WW, Neymotin SA, Kerr CC (2014) Multiscale modeling for clinical translation in neuropsychiatric disease J Comput Surg 1:7

Lytton WW, Sejnowski TJ (1991) Simulations of cortical pyramidal neurons synchronized by inhibitory interneurons. J Neurophysiol 66:1059-79 [Journal] [PubMed]

Major G, Tank D (2004) Persistent neural activity: prevalence and mechanisms. Curr Opin Neurobiol 14:675-84 [PubMed]

Marder E, Abbott LF, Turrigiano GG, Liu Z, Golowasch J (1996) Memory from the dynamics of intrinsic membrane currents. Proc Natl Acad Sci U S A 93:13481-6 [PubMed]

Markram H, Lubke J, Frotscher M, Roth A, Sakmann B (1997) Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex. J Physiol 500 ( Pt 2):409-40 [PubMed]

McCormick DA, Huguenard JR (1992) A model of the electrophysiological properties of thalamocortical relay neurons. J Neurophysiol 68:1384-400 [Journal] [PubMed]

McCormick DA, Wang Z, Huguenard J (1993) Neurotransmitter control of neocortical neuronal activity and excitability. Cereb Cortex 3:387-98 [PubMed]

McDougal RA, Hines ML, Lytton WW (2013) Water-tight membranes from neuronal morphology files Journal of Neuroscience Methods 220(2):167-78 [Journal] [PubMed]

   Constructed Tessellated Neuronal Geometries (CTNG) (McDougal et al. 2013) [Model]

McDougal RA, Hines ML, Lytton WW (2013) Reaction-diffusion in the NEURON simulator. Front Neuroinform 7:28 [Journal] [PubMed]

   Reaction-diffusion in the NEURON simulator (McDougal et al 2013) [Model]

Migliore M, Messineo L, Ferrante M (2004) Dendritic Ih selectively blocks temporal summation of unsynchronized distal inputs in CA1 pyramidal neurons. J Comput Neurosci 16:5-13 [Journal] [PubMed]

   CA1 pyramidal neuron: effects of Ih on distal inputs (Migliore et al 2004) [Model]

Migliore M, Migliore R (2012) Know your current I: interaction with a shunting current explains the puzzling effects of its pharmacological or pathological modulations PLoS One 7(5):e36867 [Journal] [PubMed]

   CA1 pyramidal neuron: Ih current (Migliore et al. 2012) [Model]

Monyer H, Markram H (2004) Interneuron Diversity series: Molecular and genetic tools to study GABAergic interneuron diversity and function. Trends Neurosci 27:90-7 [Journal] [PubMed]

Nelson AB, Krispel CM, Sekirnjak C, du Lac S (2003) Long-lasting increases in intrinsic excitability triggered by inhibition. Neuron 40:609-20 [PubMed]

Nevian T, Larkum ME, Polsky A, Schiller J (2007) Properties of basal dendrites of layer 5 pyramidal neurons: a direct patch-clamp recording study. Nat Neurosci 10:206-14 [Journal] [PubMed]

   Dendritic Na+ spike initiation and backpropagation of APs in active dendrites (Nevian et al. 2007) [Model]

Neymotin S,McDougal R,Hines M,Lytton W (2014) Calcium regulation of HCN supports persistent activity associated with working memory: a multiscale model of prefrontal cortex. BMC Neuroscience 15:108

Neymotin S,Taxin Z,Mohan A,Lipton P (2013) Brain ischemia and stroke Encyclopedia of Computational Neuroscience, Jaeger D:Jang R, ed.

Neymotin SA, Hilscher MM, Moulin TC, Skolnick Y, Lazarewicz MT, Lytton WW (2013) Ih Tunes Theta/Gamma Oscillations and Cross-Frequency Coupling In an In Silico CA3 Model PLoS ONE 8(10):e76285 [Journal] [PubMed]

   Ih tunes oscillations in an In Silico CA3 model (Neymotin et al. 2013) [Model]

Neymotin SA, Jacobs KM, Fenton AA, Lytton WW (2011) Synaptic information transfer in computer models of neocortical columns. J Comput Neurosci. 30(1):69-84 [Journal] [PubMed]

   Synaptic information transfer in computer models of neocortical columns (Neymotin et al. 2010) [Model]

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]

Neymotin SA, Lee H, Fenton AA, Lytton WW (2010) Interictal EEG discoordination in a rat seizure model. J Clin Neurophysiol 27:438-44 [PubMed]

Neymotin SA, Lee H, Park E, Fenton AA, Lytton WW (2011) Emergence of physiological oscillation frequencies in a computer model of neocortex. Front Comput Neurosci 5:19-75 [Journal] [PubMed]

   Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011) [Model]

Neymotin SA, McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW (2015) Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model Neural Computation 27(4):898-924 [Journal] [PubMed]

   Neuronal dendrite calcium wave model (Neymotin et al, 2015) [Model]

Oikonomou KD, Singh MB, Sterjanaj EV, Antic SD (2014) Spiny neurons of amygdala, striatum, and cortex use dendritic plateau potentials to detect network UP states. Front Cell Neurosci 8:292 [Journal] [PubMed]

Papoutsi A, Sidiropoulou K, Cutsuridis V, Poirazi P (2013) Induction and modulation of persistent activity in a layer V PFC microcircuit model. Front Neural Circuits 7:161 [Journal] [PubMed]

   L5 PFC microcircuit used to study persistent activity (Papoutsi et al. 2014, 2013) [Model]

Papoutsi A, Sidiropoulou K, Poirazi P (2014) Dendritic nonlinearities reduce network size requirements and mediate ON and OFF states of persistent activity in a PFC microcircuit model PLoS Computational Biology 10(7):e1003764 [Journal] [PubMed]

   L5 PFC microcircuit used to study persistent activity (Papoutsi et al. 2014, 2013) [Model]

Peercy BE (2008) Initiation and propagation of a neuronal intracellular calcium wave. J Comput Neurosci 25:334-48 [PubMed]

Perez-Garci E, Gassmann M, Bettler B, Larkum ME (2006) The GABAB1b isoform mediates long-lasting inhibition of dendritic Ca2+ spikes in layer 5 somatosensory pyramidal neurons. Neuron 50:603-16 [PubMed]

Petersen CC, Crochet S (2013) Synaptic computation and sensory processing in neocortical layer 2/3. Neuron 78:28-48 [Journal] [PubMed]

Poolos NP, Migliore M, Johnston D (2002) Pharmacological upregulation of h-channels reduces the excitability of pyramidal neuron dendrites. Nat Neurosci 5:767-74 [PubMed]

   CA1 pyramidal neuron: effects of Lamotrigine on dendritic excitability (Poolos et al 2002) [Model]

Poskanzer KE, Yuste R (2011) Astrocytic regulation of cortical UP states. Proc Natl Acad Sci U S A 108:18453-8 [Journal] [PubMed]

Quian Quiroga R, Panzeri S (2009) Extracting information from neuronal populations: information theory and decoding approaches. Nat Rev Neurosci 10:173-85 [PubMed]

Rall W, Shepherd GM (1968) Theoretical reconstruction of field potentials and dendrodendritic synaptic interactions in olfactory bulb. J Neurophysiol 31:884-915 [Journal] [PubMed]

   Theoretical reconstrucion of field potentials and dendrodendritic synaptic...(Rall & Shepherd 1968) [Model]

Ramakrishnan N, Bhalla US (2008) Memory switches in chemical reaction space. PLoS Comput Biol 4:e1000122 [Journal] [PubMed]

Robinson RB, Siegelbaum SA (2003) Hyperpolarization-activated cation currents: from molecules to physiological function. Annu Rev Physiol 65:453-80 [PubMed]

Ross WN, Nakamura T, Watanabe S, Larkum M, Lasser-Ross N (2005) Synaptically activated ca2+ release from internal stores in CNS neurons. Cell Mol Neurobiol 25:283-95 [PubMed]

Safiulina VF, Caiati MD, Sivakumaran S, Bisson G, Migliore M, Cherubini E (2010) Control of GABA release at mossy fiber-CA3 connections in the developing hippocampus Front Synaptic Neurosci 2:1 [Journal] [PubMed]

   CA3 pyramidal neuron (Safiulina et al. 2010) [Model]

Santoro B, Baram TZ (2003) The multiple personalities of h-channels. Trends Neurosci 26:550-4 [PubMed]

Sawaguchi T, Goldman-Rakic PS (1991) D1 dopamine receptors in prefrontal cortex: involvement in working memory. Science 251:947-50 [PubMed]

Schroeder CE, Lakatos P (2012) The signs of silence. Neuron 74:770-2 [Journal] [PubMed]

Schwaller B (2010) Cytosolic Ca2+ buffers. Cold Spring Harb Perspect Biol 2:a004051 [Journal] [PubMed]

Schwindt PC, Spain WJ, Crill WE (1992) Effects of intracellular calcium chelation on voltage-dependent and calcium-dependent currents in cat neocortical neurons. Neuroscience 47:571-8 [PubMed]

Seidenstein A,Barone F,Lytton W (2015) Computer modeling of ischemic stroke Scholarpedia 10:32015

Sejnowski TJ, Koch C, Churchland PS (1988) Computational neuroscience. Science 241:1299-306 [PubMed]

Sheets PL, Suter BA, Kiritani T, Chan CS, Surmeier DJ, Shepherd GM (2011) Corticospinal-specific HCN expression in mouse motor cortex: I(h)-dependent synaptic integration as a candidate microcircuit mechanism involved in motor control. J Neurophysiol 106:2216-31 [Journal] [PubMed]

Shemer I, Brinne B, Tegner J, Grillner S (2008) Electrotonic signals along intracellular membranes may interconnect dendritic spines and nucleus. PLoS Comput Biol 4:e1000036 [PubMed]

Shipp S (2005) The importance of being agranular: a comparative account of visual and motor cortex. Philos Trans R Soc Lond B Biol Sci 360:797-814 [PubMed]

Sidiropoulou K, Lu FM, Fowler MA, Xiao R, Phillips C, Ozkan ED, Zhu MX, White FJ, Cooper DC (2009) Dopamine modulates an mGluR5-mediated depolarization underlying prefrontal persistent activity. Nat Neurosci 12:190-9 [PubMed]

Sidiropoulou K, Poirazi P (2012) Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons Plos Computational Biology 8(4):e1002489 [Journal] [PubMed]

   Layer V PFC pyramidal neuron used to study persistent activity (Sidiropoulou & Poirazi 2012) [Model]

Song W, Kerr CC, Lytton WW, Francis JT (2013) Cortical plasticity induced by spike-triggered microstimulation in primate somatosensory cortex. PLoS One 8:e57453-18 [PubMed]

Spruston N, Schiller Y, Stuart G, Sakmann B (1995) Activity-dependent action potential invasion and calcium influx into hippocampal CA1 dendrites. Science 268:297-300 [PubMed]

Stacey WC, Lazarewicz MT, Litt B (2009) Synaptic noise and physiological coupling generate high-frequency oscillations in a hippocampal computational model. J Neurophysiol 102:2342-57 [Journal] [PubMed]

   High frequency oscillations in a hippocampal computational model (Stacey et al. 2009) [Model]

Suter BA, Migliore M, Shepherd GM (2013) Intrinsic electrophysiology of mouse corticospinal neurons: a class-specific triad of spike-related properties. Cereb Cortex 23:1965-77 [PubMed]

Suter BA, Shepherd GM (2015) Reciprocal interareal connections to corticospinal neurons in mouse M1 and S2. J Neurosci 35:2959-74 [Journal] [PubMed]

   [28 reconstructed morphologies on NeuroMorpho.Org]

Suter BA, Yamawaki N, Borges K, Li X, Kiritani T, Hooks BM, Shepherd GM (2014) Neurophotonics applications to motor cortex research. Neurophotonics [Journal] [PubMed]

Taxin ZH, Neymotin SA, Mohan A, Lipton P, Lytton WW (2014) Modeling molecular pathways of neuronal ischemia. Prog Mol Biol Transl Sci 123:249-75 [Journal] [PubMed]

Taylor CW, Tovey SC (2010) IP(3) receptors: toward understanding their activation. Cold Spring Harb Perspect Biol 2:a004010 [Journal] [PubMed]

Thuault SJ, Malleret G, Constantinople CM, Nicholls R, Chen I, Zhu J, Panteleyev A, Vronskaya (2013) Prefrontal cortex HCN1 channels enable intrinsic persistent neural firing and executive memory function. J Neurosci 33:13583-99 [Journal] [PubMed]

Tiganj Z, Hasselmo ME, Howard MW (2015) A simple biophysically plausible model for long time constants in single neurons. Hippocampus 25:27-37 [Journal] [PubMed]

Tonnesen J, Sorensen AT, Deisseroth K, Lundberg C, Kokaia M (2009) Optogenetic control of epileptiform activity. Proc Natl Acad Sci U S A 106:12162-7 [PubMed]

Tsuno Y, Schultheiss NW, Hasselmo ME (2013) In vivo cholinergic modulation of the cellular properties of medial entorhinal cortex neurons. J Physiol 591:2611-27 [PubMed]

Tu H, Wang Z, Bezprozvanny I (2005) Modulation of mammalian inositol 1,4,5-trisphosphate receptor isoforms by calcium: a role of calcium sensor region. Biophys J 88:1056-69 [Journal] [PubMed]

Tu H, Wang Z, Nosyreva E, De Smedt H, Bezprozvanny I (2005) Functional characterization of mammalian inositol 1,4,5-trisphosphate receptor isoforms. Biophys J 88:1046-55 [Journal] [PubMed]

Wagner J, Fall CP, Hong F, Sims CE, Allbritton NL, Fontanilla RA, Moraru II, Loew LM, Nuccite (2004) A wave of IP3 production accompanies the fertilization Ca2+ wave in the egg of the frog, Xenopus laevis: theoretical and experimental support. Cell Calcium 35:433-47 [Journal] [PubMed]

Wang H, Stradtman GG, Wang XJ, Gao WJ (2008) A specialized NMDA receptor function in layer 5 recurrent microcircuitry of the adult rat prefrontal cortex. Proc Natl Acad Sci U S A 105:16791-6 [PubMed]

Wang J, Chen S, Nolan MF, Siegelbaum SA (2002) Activity-Dependent Regulation of HCN Pacemaker Channels by Cyclic AMP: Signaling through Dynamic Allosteric Coupling Neuron 36:451-61 [Journal] [PubMed]

   Activity dependent regulation of pacemaker channels by cAMP (Wang et al 2002) [Model]

Wang M, Ramos BP, Paspalas CD, Shu Y, Simen A, Duque A, Vijayraghavan S, Brennan A, Dudley A, (2007) Alpha2A-adrenoceptors strengthen working memory networks by inhibiting cAMP-HCN channel signaling in prefrontal cortex. Cell 129:397-410 [PubMed]

Wang XJ (1999) Synaptic basis of cortical persistent activity: the importance of NMDA receptors to working memory. J Neurosci 19:9587-603 [PubMed]

Wang XJ (2001) Synaptic reverberation underlying mnemonic persistent activity. Trends Neurosci 24:455-63 [PubMed]

Wang XJ (2002) Pacemaker neurons for the theta rhythm and their synchronization in the septohippocampal reciprocal loop. J Neurophysiol 87:889-900 [PubMed]

Wang XJ, Buzsaki G (1996) Gamma oscillation by synaptic inhibition in a hippocampal interneuronal network model. J Neurosci 16:6402-13 [Journal] [PubMed]

   Gamma oscillations in hippocampal interneuron networks (Wang, Buzsaki 1996) [Model]

Weiler N, Wood L, Yu J, Solla SA, Shepherd GM (2008) Top-down laminar organization of the excitatory network in motor cortex. Nat Neurosci 11:360-6 [Journal] [PubMed]

   Laminar connectivity matrix simulation (Weiler et al 2008) [Model]

White JA, Banks MI, Pearce RA, Kopell NJ (2000) Networks of interneurons with fast and slow gamma-aminobutyric acid type A (GABAA) kinetics provide substrate for mixed gamma-theta rhythm. Proc Natl Acad Sci U S A 97:8128-33 [PubMed]

Winograd M, Destexhe A, Sanchez-Vives MV (2008) Hyperpolarization-activated graded persistent activity in the prefrontal cortex. Proc Natl Acad Sci U S A 105:7298-303 [Journal] [PubMed]

   Hodgkin-Huxley model of persistent activity in prefrontal cortex neurons (Winograd et al. 2008) [Model]
   Hodgkin-Huxley model of persistent activity in PFC neurons (Winograd et al. 2008) (NEURON python) [Model]

Yamawaki N, Shepherd GM (2015) Synaptic circuit organization of motor corticothalamic neurons. J Neurosci 35:2293-307 [Journal] [PubMed]

Zemankovics R, Kali S, Paulsen O, Freund TF, Hajos N (2010) Differences in subthreshold resonance of hippocampal pyramidal cells and interneurons: the role of h-current and passive membrane characteristics. J Physiol 588:2109-32 [PubMed]

Zhou WL, Short SM, Rich MT, Oikonomou KD, Singh MB, Sterjanaj EV, Antic SD (2015) Branch specific and spike-order specific action potential invasion in basal, oblique, and apical dendrites of cortical pyramidal neurons. Neurophotonics 2:021006 [Journal] [PubMed]

Dura-Bernal S, Neymotin SA, Kerr CC, Sivagnanam S, Majumdar A, Francis JT, Lytton WW (2017) Evolutionary algorithm optimization of biological learning parameters in a biomimetic neuroprosthesis. IBM Journal of Research and Development (Computational Neuroscience special issue) 61(2/3):6:1-6:14 [Journal]

   Motor system model with reinforcement learning drives virtual arm (Dura-Bernal et al 2017) [Model]

McDougal RA, Bulanova AS, Lytton WW (2016) Reproducibility in computational neuroscience models and simulations IEEE Trans Biomed Eng 63(10):2021-2035 [Journal] [PubMed]

Neymotin SA, Dura-Bernal S, Lakatos P, Sanger TD, Lytton WW (2016) Multitarget Multiscale Simulation for Pharmacological Treatment of Dystonia in Motor Cortex. Front Pharmacol 7:157 [Journal] [PubMed]

   Multitarget pharmacology for Dystonia in M1 (Neymotin et al 2016) [Model]

Neymotin SA, Suter BA, Dura-Bernal S, Shepherd GM, Migliore M, Lytton WW (2017) Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. J Neurophysiol 117(1):148-162 [Journal] [PubMed]

   Computer models of corticospinal neurons replicate in vitro dynamics (Neymotin et al. 2017) [Model]

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