Electrostimulation to reduce synaptic scaling driven progression of Alzheimers (Rowan et al. 2014)

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Accession:154096
"... As cells die and synapses lose their drive, remaining cells suffer an initial decrease in activity. Neuronal homeostatic synaptic scaling then provides a feedback mechanism to restore activity. ... The scaling mechanism increases the firing rates of remaining cells in the network to compensate for decreases in network activity. However, this effect can itself become a pathology, ... Here, we present a mechanistic explanation of how directed brain stimulation might be expected to slow AD progression based on computational simulations in a 470-neuron biomimetic model of a neocortical column. ... "
Reference:
1 . Rowan MS, Neymotin SA, Lytton WW (2014) Electrostimulation to reduce synaptic scaling driven progression of Alzheimer's disease. Front Comput Neurosci 8:39 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex V1 L6 pyramidal corticothalamic cell; Neocortex V1 L2/6 pyramidal intratelencephalic cell; Neocortex V1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON; Python;
Model Concept(s): Long-term Synaptic Plasticity; Aging/Alzheimer`s; Deep brain stimulation; Homeostasis;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu]; Rowan, Mark [m.s.rowan at cs.bham.ac.uk];
Search NeuronDB for information about:  Neocortex V1 L6 pyramidal corticothalamic cell; Neocortex V1 L2/6 pyramidal intratelencephalic cell; Neocortex V1 interneuron basket PV cell; GabaA; AMPA; NMDA; Gaba; Glutamate;
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RowanEtAl2014
batchscripts
mod
README
alz.hoc
alzinfo.m
autotune.hoc *
basestdp.hoc *
batch.hoc *
batch2.hoc *
batchcommon
checkirreg.hoc *
clusterrun.sh
col.dot *
col.hoc *
comppowspec.hoc *
condisconcellfig.hoc *
condisconpowfig.hoc *
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
e2hubsdisconpow.hoc *
e2incconpow.hoc *
filtutils.hoc *
flexinput.hoc
geom.hoc *
graphplug.hoc *
grvec.hoc *
infot.hoc *
init.hoc *
labels.hoc *
load.hoc *
local.hoc *
makepopspikenq.hoc *
matfftpowplug.hoc *
matpmtmplug.hoc *
matpmtmsubpopplug.hoc *
matspecplug.hoc *
mosinit.hoc
network.hoc *
nload.hoc *
nqpplug.hoc *
nqs.hoc *
nqsnet.hoc *
nrnoc.hoc *
params.hoc
plot.py
plotavg.py
plotbatch.sh
plotbatchcluster.sh
plotdeletions.py
plotntes.py
powchgtest.hoc *
pyhoc.py
python.hoc *
pywrap.hoc *
ratlfp.dat *
redE2.hoc *
run.hoc
runsim.sh
setup.hoc *
shufmua.hoc *
sim.hoc
simctrl.hoc *
spkts.hoc *
stats.hoc *
syncode.hoc *
vsampenplug.hoc *
writedata.hoc
xgetargs.hoc *
                            
// $Id: shufmua.hoc,v 1.16 2012/01/11 19:39:35 samn Exp $ 

ncells = 300
nsec = 30
binsz = 5
refrac = 2.5
jitterdt = 0
declare("reg",0)
declare("noisespks", 0)

objref vs[ncells],vh[ncells],vmua,rdm,vy,vx
vmua=new Vector()
rdm=new Random()
vy=new Vector()
vx=new Vector()

sz =  (1e3/binsz) * nsec
rate  = 1 // rate in Hz

sampr = 1e3 / binsz

objref nqp[300]

SPECTY=0
PRESM=0

//* checkrefrac(vector,refrac)
proc checkrefrac () { local i localobj v1
  v1=$o1
  for i=1,v1.size-1 {
    if(v1.x(i)-v1.x(i-1)<$2) v1.x(i) = v1.x(i) + $2
  }
}

//* myshuf(vec,nshuffles,rdm)
proc myshuf () { local idx,i,j,k,n localobj v1,rdm,vm,vr,vr2
  v1=$o1 n=$2 rdm=$o3
  vm=new Vector(v1.size)
  vm.resize(0)
  for i=0,v1.size-1 if(v1.x(i)>0) vm.append(i)
  vr=new Vector(n)
  vr2=new Vector(n)
  rdm.discunif(0,vm.size-1)
  vr.setrand(rdm)
  rdm.discunif(0,v1.size-1)
  vr2.setrand(rdm)
  for i=0,n-1 {
    idx = vm.x(vr.x(i))
    j = vr2.x(i)
    k = v1.x(idx)
    v1.x(idx) = v1.x(j)
    v1.x(j) = k
  }
}

//* applyjitter(vec,rdm,dt)
proc applyjitter () { local i,jdt localobj v1,rdm,vj
  v1=$o1 rdm=$o2 jdt=$3
  vj=new Vector(v1.size)
  rdm.uniform(-jdt,jdt)
  vj.setrand(rdm)
  v1.add(vj)
  for i=0,v1.size-1 if(v1.x(i)<0) v1.x(i)=0// make sure no neg #s
  v1.sort()
}

//* addnoise(numspikes,rdm)
proc addnoise () { local i,ns localobj vec
  ns=$1 rdm.uniform(0,nsec*1e3)
  vec=new Vector(ns)
  for i=0,ncells-1 {
    vec.setrand(rdm)
    vs[i].append(vec)
    vs[i].sort()
  }
}

//* initcells
proc initcells () { local tt,isi,i,nshuf localobj vr
  nspks =  rate * nsec
  rdm.ACG(1234*nshuf)  
  for i=0,ncells-1 if(vs[i]==nil) vs[i]=new Vector() else vs[i].resize(0)
  if(reg) {
    isi = 1e3 / rate
    tt = isi
    for i=0,nspks-1 {
      vs[0].append(tt)
      tt += isi
    }
  } else {
    vs[0].resize(nspks)
    rdm.uniform(0,nsec*1e3)
    vs[0].setrand(rdm)
    vs[0].sort()
  }
  checkrefrac(vs[0],refrac)
  for i=1,ncells-1 {
    vs[i].copy(vs[0])
    applyjitter(vs[i],rdm,jitterdt)
    checkrefrac(vs[i],refrac)
  }
  if(noisespks) addnoise(noisespks,rdm)
}

//* histcells - make spike counts per time for each cell
proc histcells () { local i
  for i=0,ncells-1 {
    if(vh[i]==nil) vh[i]=new Vector() 
    vh[i].hist(vs[i],0,sz,binsz)
  }
}

//* shufhist(nshuf)
proc shufhist () { local i,nshuf
  nshuf=$1
  for i=1,ncells-1 {
    vh[i].copy(vh[0])
    myshuf(vh[i],nshuf,rdm)
    if(refrac) checkrefrac(vh[i],refrac)
  }
}

//* mkmua
proc mkmua () { local i
  vmua.resize(vh[0].size())
  vmua.fill(0)
  for i=0,ncells-1 vmua.add(vh[i])
  vmua.sub(vmua.mean())
}

//* plotrast
proc plotrast () { local i
  vrsz(0,vx,vy)
  for i=0,ncells-1 {
    for j=0,vs[i].size-1 {
      vx.append(vs[i].x(j))
      vy.append(i)
    }
  }
  vy.mark(g,vx,"O",2,1)
  g.exec_menu("View = plot")
}

//* setjitter(jitterdt)
proc setjitter () {
  jitterdt = $1
  initcells()
  histcells()
  mkmua()
}

//* jittertest(maxjitter,jitterinc)
proc jittertest () { local i
  for(jitterdt=0;jitterdt<=$1;jitterdt+=$2) {
    print "jitterdt is " , jitterdt
    setjitter(jitterdt)
    {nqsdel(nqp[i]) nqp[i]=getspecnq(vmua,sampr,SPECTY,PRESM)}
    // nqp.gr("pow","f",0,1,1)
    i += 1
  }
}

proc nqpg () {
  nqp[$1].gr("pow","f",0,1,1)
  g.exec_menu("View = plot")
}

//* main

setjitter(0)
gg()

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