A multilayer cortical model to study seizure propagation across microdomains (Basu et al. 2015)

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Accession:206238
A realistic neural network was used to simulate a region of neocortex to obtain extracellular LFPs from ‘virtual micro-electrodes’ and produce test data for comparison with multisite microelectrode recordings. A model was implemented in the GENESIS neurosimulator. A simulated region of cortex was represented by layers 2/3, 5/6 (interneurons and pyramidal cells) and layer 4 stelate cells, spaced at 25 µm in each horizontal direction. Pyramidal cells received AMPA and NMDA inputs from neighboring cells at the basal and apical dendrites. The LFP data was generated by simulating 16-site electrode array with the help of ‘efield’ objects arranged at the predetermined positions with respect to the surface of the simulated network. The LFP for the model is derived from a weighted average of the current sources summed over all cellular compartments. Cell models were taken from from Traub et al. (2005) J Neurophysiol 93(4):2194-232.
References:
1 . Basu I, Kudela P, Korzeniewska A, Franaszczuk PJ, Anderson WS (2015) A study of the dynamics of seizure propagation across micro domains in the vicinity of the seizure onset zone. J Neural Eng 12:046016 [PubMed]
2 . Basu I, Kudela P, Anderson WS (2014) Determination of seizure propagation across microdomains using spectral measures of causality. Conf Proc IEEE Eng Med Biol Soc 2014:6349-52 [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 U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Thalamus reticular nucleus GABA cell; Neocortex spiking low threshold (LTS) neuron; Neocortex spiking regular (RS) neuron; Neocortex layer 2-3 interneuron; Neocortex layer 5 interneuron;
Channel(s): I Na,p; I Na,t; I K; I A; I M; I h; I K,Ca; I A, slow; I L high threshold; I T low threshold; I Calcium;
Gap Junctions: Gap junctions;
Receptor(s): AMPA; GabaA; NMDA;
Gene(s):
Transmitter(s): Glutamate; Gaba; Amino Acids;
Simulation Environment: GENESIS;
Model Concept(s): Activity Patterns; Epilepsy;
Implementer(s): Anderson, WS ; Kudela, Pawel ;
Search NeuronDB for information about:  Thalamus reticular nucleus GABA cell; Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow; Amino Acids; Gaba; Glutamate;
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BasuEtAl2015
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ModelDescription.pdf
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P6RSd_P6RSc.g
P6RSd_P6RSd.g
P6RSd_P6RSd_Gap.g
P6RSd_raninput.g
P6RSd_ST4RS.g
P6RSd_synapsedefs.g
P6RSd_TCR.g
P6RSdcell3Dpk.p
P6RSdchanpk.g
P6RSdprotodefs.g
P6RSsyncond.g
pgenesis_command
protodefs.g
protospikeB23FS.g
protospikeB5FS.g
protospikeC23FS.g
protospikeC5FS.g
protospikeI23LTS.g
protospikeI5LTS.g
protospikenRT.g
protospikeP23FRBa.g
protospikeP23RSa.g
protospikeP23RSb.g
protospikeP23RSc.g
protospikeP23RSd.g
protospikeP5IBa.g
protospikeP5IBb.g
protospikeP5IBc.g
protospikeP5IBd.g
protospikeP5RSa.g
protospikeP6RSa.g
protospikeP6RSb.g
protospikeP6RSc.g
protospikeP6RSd.g
protospikeST4RS.g
protospikeTCR.g
randominputdefs.g
spikedefs.g
ST4RS.g
ST4RS_B23FS.g
ST4RS_B5FS.g
ST4RS_C23FS.g
ST4RS_C5FS.g
ST4RS_I23LTS.g
ST4RS_I5LTS.g
ST4RS_P23FRBa.g
ST4RS_P23RSa.g
ST4RS_P23RSb.g
ST4RS_P23RSc.g
ST4RS_P23RSd.g
ST4RS_P5IBa.g
ST4RS_P5IBb.g
ST4RS_P5IBc.g
ST4RS_P5IBd.g
ST4RS_P5RSa.g
ST4RS_P6RSa.g
ST4RS_P6RSb.g
ST4RS_P6RSc.g
ST4RS_P6RSd.g
ST4RS_raninput.g
ST4RS_ST4RS.g
ST4RS_ST4RS_Gap.g
ST4RS_synapsedefs.g
ST4RScell3Dpk.p
ST4RSchanpk.g
ST4RSprotodefs.g
ST4RSsyncond.g
synapticdelays.g *
synapticprobsTraub.g
synchansB23FS.g *
synchansB5FS.g *
synchansC23FS.g *
synchansC5FS.g *
synchansI23LTS.g *
synchansI5LTS.g *
synchansnRT.g *
synchansP23FRBa.g *
synchansP23RSa.g *
synchansP23RSb.g *
synchansP23RSc.g *
synchansP23RSd.g *
synchansP5IBa.g *
synchansP5IBb.g *
synchansP5IBc.g *
synchansP5IBd.g *
synchansP5RSa.g *
synchansP6RSa.g *
synchansP6RSb.g *
synchansP6RSc.g *
synchansP6RSd.g *
synchansSPIKEs.g *
synchansSPIKEs_base.g
synchansST4RS.g
synchansTCR.g *
syncond.g
syncond2.g
TCR.g
TCR_B23FS.g
TCR_B5FS.g
TCR_C23FS.g
TCR_C5FS.g
TCR_nRT.g
TCR_P23FRBa.g
TCR_P23RSa.g
TCR_P23RSb.g
TCR_P23RSc.g
TCR_P23RSd.g
TCR_P5IBa.g
TCR_P5IBb.g
TCR_P5IBc.g
TCR_P5IBd.g
TCR_P5RSa.g
TCR_P6RSa.g
TCR_P6RSb.g
TCR_P6RSc.g
TCR_P6RSd.g
TCR_raninput.g
TCR_ST4RS.g
TCR_synapsedefs.g
TCRcellpk.p
TCRchanpk.g
TCRprotodefs.g
TCRsyncond.g
                            
echo nRT Synapse Definitions...
echo

//P6RS - nRT AMPA synapses

str s

//Load synapse location array

str locations = "proxdendN distdendNlonga distdendNmida proxdendE distdendElonga distdendEmida proxdendS distdendSlonga distdendSmida proxdendW distdendWlonga distdendWmida"

foreach s ({arglist {locations}})

     ce /nRT/{s}

     make_Ex_ch21P6RSAMPA
     setfield /nRT/{s}/Ex_ch21P6RSAMPA gmax {CondmaxP6RSAMPA_nRT}
     addmsg /nRT/{s}/Ex_ch21P6RSAMPA /nRT/{s} CHANNEL Gk Ek
     addmsg /nRT/{s} /nRT/{s}/Ex_ch21P6RSAMPA VOLTAGE Vm

     ce /

end

//P6RS - nRT NMDA synapses

str locations = "proxdendN distdendNlonga distdendNmida proxdendE distdendElonga distdendEmida proxdendS distdendSlonga distdendSmida proxdendW distdendWlonga distdendWmida"

foreach s ({arglist {locations}})

     ce /nRT/{s}

     make_Ex_ch21P6RSNMDA
     setfield /nRT/{s}/Ex_ch21P6RSNMDA gmax {CondmaxP6RSNMDA_nRT}
     addmsg /nRT/{s}/Ex_ch21P6RSNMDA /nRT/{s} CHANNEL Gk Ek
     addmsg /nRT/{s} /nRT/{s}/Ex_ch21P6RSNMDA VOLTAGE Vm

     ce /

end

//TCR - nRT AMPA synapses

str locations = "proxdendN distdendNlonga distdendNmida proxdendE distdendElonga distdendEmida proxdendS distdendSlonga distdendSmida proxdendW distdendWlonga distdendWmida"

foreach s ({arglist {locations}})

     ce /nRT/{s}

     make_Ex_ch21TCRAMPA
     setfield /nRT/{s}/Ex_ch21TCRAMPA gmax {CondmaxTCRAMPA_nRT}
     addmsg /nRT/{s}/Ex_ch21TCRAMPA /nRT/{s} CHANNEL Gk Ek
     addmsg /nRT/{s} /nRT/{s}/Ex_ch21TCRAMPA VOLTAGE Vm

     ce /

end

//TCR - nRT NMDA synapses

str locations = "proxdendN distdendNlonga distdendNmida proxdendE distdendElonga distdendEmida proxdendS distdendSlonga distdendSmida proxdendW distdendWlonga distdendWmida"

foreach s ({arglist {locations}})

     ce /nRT/{s}

     make_Ex_ch21TCRNMDA
     setfield /nRT/{s}/Ex_ch21TCRNMDA gmax {CondmaxTCRNMDA_nRT}
     addmsg /nRT/{s}/Ex_ch21TCRNMDA /nRT/{s} CHANNEL Gk Ek
     addmsg /nRT/{s} /nRT/{s}/Ex_ch21TCRNMDA VOLTAGE Vm

     ce /

end

//nRT - nRT GABAa synapses

str locations = "distdendNlonga distdendNlongb distdendNlongc distdendNlongd distdendNlonge distdendNlongf distdendNlongg distdendNshorta distdendNshortb distdendNmida distdendNmidb distdendNmidc distdendElonga distdendElongb distdendElongc distdendElongd distdendElonge distdendElongf distdendElongg distdendEshorta distdendEshortb distdendEmida distdendEmidb distdendEmidc distdendSlonga distdendSlongb distdendSlongc distdendSlongd distdendSlonge distdendSlongf distdendSlongg distdendSshorta distdendSshortb distdendSmida distdendSmidb distdendSmidc distdendWlonga distdendWlongb distdendWlongc distdendWlongd distdendWlonge distdendWlongf distdendWlongg distdendWshorta distdendWshortb distdendWmida distdendWmidb distdendWmidc"

foreach s ({arglist {locations}})

     ce /nRT/{s}

     make_Inh_ch21nRTGABAa
     setfield /nRT/{s}/Inh_ch21nRTGABAa gmax {CondmaxnRTGABAa_nRT}
     addmsg /nRT/{s}/Inh_ch21nRTGABAa /nRT/{s} CHANNEL Gk Ek
     addmsg /nRT/{s} /nRT/{s}/Inh_ch21nRTGABAa VOLTAGE Vm

     ce /

end

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