Hotspots of dendritic spine turnover facilitates new spines and NN sparsity (Frank et al 2018)

 Download zip file 
Help downloading and running models
Accession:227087
Model for the following publication: Adam C. Frank, Shan Huang, Miou Zhou, Amos Gdalyahu, George Kastellakis, Panayiota Poirazi, Tawnie K. Silva, Ximiao Wen, Joshua T. Trachtenberg, and Alcino J. Silva Hotspots of Dendritic Spine Turnover Facilitate Learning-related Clustered Spine Addition and Network Sparsity
Reference:
1 . Frank AC, Huang S, Zhou M, Gdalyahu A, Kastellakis G, Silva TK, Lu E, Wen X, Poirazi P, Trachtenberg JT, Silva AJ (2018) Hotspots of dendritic spine turnover facilitate clustered spine addition and learning and memory. Nat Commun 9:422 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Connectionist Network;
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron with dendritic subunits;
Channel(s):
Gap Junctions:
Receptor(s): NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program; MATLAB;
Model Concept(s): Active Dendrites; Synaptic Plasticity;
Implementer(s): Kastellakis, George [gkastel at gmail.com];
Search NeuronDB for information about:  NMDA;
/
tomodel
data
distributionPlot
exportfig
fig
figs
mtrand
README
.exrc *
an_m_to.m
an_to.m
barwitherr.m *
btagstats.m *
CImg.h *
constructs. *
constructs.cpp *
constructs.h
csvgraph.m
defaults.m
dir2.m *
gconstructs.cpp *
getspikedata.m *
getsynstate.m *
getsynstate2.m *
graphs.m *
hist_percents.m *
hist_with_errs.m *
interact.m *
kurtos.m *
lamodel
lamodel.cpp
LICENSE *
make_graphs.m *
Makefile *
matlab.mat *
mtrand.cpp *
mtrand.h *
multistats.m *
nextplot.m *
pairstrong.m *
repeated.m *
rotateXLabels.m *
run_to.sh
S2sparse.m *
savefig.m *
scratch.m *
sensitivity.m *
stats.m *
stats.py *
stderr.m *
strong2.m *
strongstrong.m *
submit_lamodel.sh *
three.m *
to.cpp
trevrolls.m *
vis.py *
weastrong.m *
wxglmodel *
wxglmodel.cpp *
wxglmodel.h *
wxmodel.cpp *
wxmodel.h *
                            
close all
clear all
set(0,'DefaultAxesFontSize', 18)
set(0,'DefaultTextFontSize', 18)

nruns = 10
itvls = [60, 120, 180, 240]
pops = zeros(2, length(itvls), nruns);

conds = {'w1c','w2c','w1n', 'w2n', 'w1cL','w2cL'}

for cond = 1:length(conds)

    scond = conds{cond}
    for run = 1:10  
        for d = 1:length(itvls)
            itvl = itvls(d)
            fn=sprintf('N100.B40.I10.i6.P2.p1.T%d.S%d.%s', itvl, 1980+run-1,scond)

            stimduration = 2000;

            ar = sscanf(fn, 'N%d.B40.I10.i6.P%d.p1.T%d.S%d.w%d');

            nneurons = ar(1);
            npatterns = ar(2);
            interval = ar(3);
            seed = ar(4);
            weakmem = ar(5);
            npyrs = nneurons*0.8;

            ff = sprintf('./data/%s/spikes.dat', fn);
            f = fopen(ff);
            t = fgets(f);
            raster = zeros(nneurons, stimduration*npatterns*2);
            nid = 1;
            while (ischar(t))
               times = str2num(t);
               raster(nid, times) = 1;
               t = fgets(f);
               nid=nid+1;
            end
            fclose(f)

            %figure()
            %imagesc(raster)

            trainingspikes = zeros(npyrs, npatterns);
            recallspikes = zeros(npyrs, npatterns);

            for n=1:npyrs
                for j=1:npatterns
                    tstart = (j-1)*stimduration;
                    tend = tstart + stimduration;
                    trainingspikes(n,j) = sum(raster(n, tstart+1:tend));

                    tstart = npatterns*stimduration + (j-1)*stimduration;
                    tend = tstart + stimduration;
                    recallspikes(n,j) = sum(raster(n, tstart+1:tend));
                end
            end

            pop = sum(recallspikes > 30)/npyrs;

            ff = sprintf('./data/%s/synstate.dat', fn);
            ss = load(ff);
            for n=1:npatterns
                sb = ss(find(ss(:,5)==n & ss(:,7) > 1.4) , 2); % branch ids array
                sun = unique(sb);
                zz = [];
                for k=1:length(sun)
                    zz(end+1) = length(find(sb(:) == sun(k)));
                end
            end


            pops(:, d, run) = pop';

        end
    end

    figure()
    %title('Strong before weak')
    pops = pops*100.0
    mpop = mean(pops, 3)
    stdpop = std(pops, 0, 3)
    errorbar(mpop', stdpop')
    ylim([0,40])
    xlabel('Interval between memories (minutes)')
    ylabel('% of recruited pyramidal neurons')
    if (mod(cond ,2)==0)
        legend('Strong memory', 'Weak memory');
    else
        legend('Weak memory', 'Strong memory');
    end
    set(gca, 'XTick',[1:length(itvls)]);
    set(gca, 'XTickLabel',itvls);
    saveas(gcf, sprintf('./figs/BTAG_%s.eps', scond), 'epsc')


end