Neural model of frog ventilatory rhythmogenesis (Horcholle-Bossavit and Quenet 2009)

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Accession:123987
"In the adult frog respiratory system, periods of rhythmic movements of the buccal floor are interspersed by lung ventilation episodes. The ventilatory activity results from the interaction of two hypothesized oscillators in the brainstem. Here, we model these oscillators with two coupled neural networks, whose co-activation results in the emergence of new dynamics. .. The biological interest of this formal model is illustrated by the persistence of the relevant dynamical features when perturbations are introduced in the model, i.e. dynamic noises and architecture modifications. The implementation of the networks with clock-driven continuous time neurones provides simulations with physiological time scales."
Reference:
1 . Horcholle-Bossavit G, Quenet B (2009) Neural model of frog ventilatory rhythmogenesis. Biosystems 97:35-43 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: MATLAB;
Model Concept(s): Temporal Pattern Generation; Oscillations; Synchronization;
Implementer(s):
%Biosystems. 2009 Jul;97(1):35-43.
%Horcholle-Bossavit G, Quenet B.
%Neural model of frog ventilatory rhythmogenesis.
%Fig.3

clear all
global beta gamma cumul maxAc Em0 Ac Eml1 delta

format long
matdep =[ 0  0  -1   
          1  0  -1   
          0  1  0 ];                      
Rdep=[1 0 0 ]; 
matL=[0 -1 0 ; 0 -1 0; 0 0 0];
X=5;
Y=1;
mattoub=boucladj(matdep,Rdep', X, [4,2],1, [2,5], -1);  
Spre=mattoub(:,1:end-1);
Rpre=mattoub(:,end);
Spara=bouclpara(Spre,Rpre, Y); 
R=Spara(:,end);
S=Spara(:,1:end-1);
R=R';
vectv=zeros(size(S,1),1);
vectv([1:Y*(1+X*2)])=1;
vecth=zeros(1, size(S,2));
inhibsl=[];
for y=1:Y
    inhibsl=[inhibsl, [0:X-1]*2+3+(y-1)*((X*2)+1)];
end
inhibsl;
vecth(inhibsl)=-1;
excitateurs=[1,[1:X]*2];
for y=2:Y
    excitateursy=[1+(y-1)*((X*2)+1),[1:X]*2+(y-1)*((X*2)+1)];
    excitateurs=[excitateurs;excitateursy];
end
excitateurs;

S=completelop(matL,vectv,vecth,S,1);
R=[0 1 0,R];
inhibsl=inhibsl+3;
excitateurs=excitateurs+3;
excitateurs=excitateurs(:,2:end);
excitateurs=reshape(excitateurs',1,size(excitateurs,1)*size(excitateurs,2));
v=1:Y;
for i=1:X
    for j=1:Y
        for k=1:Y
            S(excitateurs((k-1)*X+i),inhibsl((j-1)*X+i))=-1;
        end
    end
end
groupex=find(sum(S)>=0);
groupin=find(sum(S)<0); 
Ne=length(groupex);     Ni=length(groupin);
retards=ones(Ne+Ni);
th=[0.5*ones(Ne,1); 	0.5*ones(Ni,1)];

modul=1;        
epsilon=0;              
beta=1.05 ;             
gamma=0.00;            
maxAc=6;
delta=0;
Em0=0.1;
            

vseuiL=[1;zeros(Ne+Ni-1,1)];    
seedscalevol=3760;
randn('seed',seedscalevol)     
rand('seed',seedscalevol)

Tsim=150;
Init=zeros(Ne+Ni,1);
type=(sign(sum(S)))';
nirings=[zeros(sum(Init),1),find(Init==1),type((Init==1))];
hstock=zeros(Ne+Ni,Tsim);
hstock(:,1)=Init;
matact=zeros(Ne+Ni,Tsim);
matact(:,1)=Init;
Ac=0;
Eml1=0;
retL=1; 


Tomax=max(max(retards));
cumul=0;

for t=1:Tsim
    feu=[];
    matfiltre=zeros(Ne+Ni);
    h=R';
    if ~isempty(nirings)
       for ret=1:max(max(retards))
           fincre=zeros(Ne+Ni);                          
           inter=find(nirings(:,1)==t-ret);               
           feu=[feu; ret+0*inter,inter];                
           finter=[[nirings(inter,2)]', Ne+Ni+1];      
           fincre(1:Ne+Ni,finter)=1;                       
           fincre=fincre(:,1:Ne+Ni);                       
           matinter=(retards==ret);                        
           matfiltre=matfiltre+((matinter==fincre)&(matinter>0));   
       end
       tfire=nirings(feu(:,2),1);                          
       firedt=nirings(feu(:,2),2);                         
       st=sort(firedt); 
    
       if ~isempty(st)                                     
           dst=diff(st);                                   
           y=st(dst>0);
           firedtone=[y;st(end)];                         
           Sfiltre=S.*matfiltre;                           
           h=h+sum(Sfiltre(:,firedtone),2);  
       end
       inter1=find(nirings(:,1)==t-retL);   
       finter1=[nirings(inter1,2)];
       finter2=[nirings(inter1,1)];
       lfire=(sum(finter1==1)>0);   
       modulation(lfire);
       
    end
    randh=randn(Ne+Ni,1);
    hent=h+Eml1(end)*(modul==1)*vseuiL+epsilon*randh-th;                                                            
    hstock(:,t+1)=hent;
    n=(hent>0);                                               
    fired=find(n>0);
    matact(:,t+1)=n;
    if ~isempty(fired);
        nirings=[nirings; t+0*fired,fired,type(fired)]; 
    end
    
end

actot=sum(matact(groupex,:));
actotin=sum(matact(groupin,:));


   % Create figure
figure1 = figure('PaperType','a4letter','PaperSize',[20.98 29.68],...
    'Color',[1 1 1]);

% Create textbox
annotation(figure1,'textbox','String',{'A'},'FontSize',16,...
    'FontName','Arial',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.003 0.97 0.004 0.001]);

% Create textbox
annotation(figure1,'textbox','String',{'a'},'FontSize',16,...
    'FontName','Arial',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.03 0.85 0.004 0.001]);

% Create textbox
annotation(figure1,'textbox','String',{'B'},'FontSize',16,...
    'FontName','Arial',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.003 0.65 0.004 0.001]);

% Create textbox
annotation(figure1,'textbox','String',{'C'},'FontSize',16,...
    'FontName','Arial',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.003 0.4 0.004 0.001]);

% Create textbox
annotation(figure1,'textbox','String',{'D'},'FontSize',16,...
    'FontName','Arial',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.005 0.22 0.004 0.001]);


% Create textbox
annotation(figure1,'textbox','String',{'b'},'FontSize',16,...
    'FontName','Arial',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.39 0.85 0.004 0.001]);

% Create textbox
annotation(figure1,'textbox','String',{'c'},'FontSize',16,...
    'FontName','Arial',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.52 0.85 0.004 0.001]); 
if exist('model1onechain5loop3N&R.jpg')
subplot('Position',[0.58 0.70 0.38 0.25]);
    fig1=imread('model1onechain5loop3N&R.jpg');
    imagesc(fig1);
    axis off;
end  

subplot('Position',[0.12 0.72 0.25 0.25]);

imagesc(S)
notremap=[0 0 0;1 1 1;0.5 0.5 0.5];
colormap(flipud(notremap))
set(gcf,'Color',[1 1 1])
set(gca,'FontName','arial','FontWeight','bold','FontSize',9)

box on

subplot('Position',[0.48 0.72 0.02 0.25]);
imagesc(R',[-1 1])
set(gcf,'Color',[1 1 1])
set(gca,'XTick',[])
set(gca,'FontName','arial','FontWeight','bold','FontSize',9)

box on

subplot('Position',[0.08 0.45 0.85 0.2]);
plot(nirings(find(nirings(:,3)>=0),1), nirings(find(nirings(:,3)>=0),2),'diamond','MarkerEdgeColor',[0 0 0],'MarkerFaceColor',[0 0 0], 'MarkerSize', 1.5 )
hold on
plot(nirings(find(nirings(:,3)<0),1), nirings(find(nirings(:,3)<0),2),'o','MarkerEdgeColor',[0.5 0.5 0.5],'MarkerFaceColor',[0.5 0.5 0.5], 'MarkerSize', 1)
set(gca,'XLim', [0 Tsim],'YLim',[0 Ne+Ni+1]);
set(gca,'YDir','reverse')
set(gca,'XTick',[0: Tsim/3: Tsim])
set(gca,'XTick',[])
set(gca,'FontName','arial','FontWeight','bold','FontSize',9)
text(4,0,['neurone activities'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','bold','FontSize',9,'FontAngle','normal','Color',[0 0 0])

box off
line([82 90],[15,15],'LineWidth',4,'Color',[0 0 0], 'LineStyle','-')
text(84,17,['Tp'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','bold','FontSize',9,'FontAngle','italic','Color',[0 0 0])

subplot('Position',[0.08 0.25 0.85 0.15])
plot([0:Tsim],actot,'k');
set(gca,'XLim', [0 Tsim],'YLim',[min(actot)  max(actot)+1]);
set(gca,'XTick',[0: Tsim/3: Tsim])
set(gca,'XTick',[])
set(gca,'FontName','arial','FontWeight','bold','FontSize',9)
text(4,max(actot)+1,['number of active excitatory neurones'],...
    'VerticalAlignment','middle',...
   'HorizontalAlignment','left',...
   'FontName','arial','FontWeight','bold','FontSize',9,'FontAngle','normal','Color',[0 0 0])
text(30,max(actot)-2,['OS'],...
    'VerticalAlignment','middle',...
   'HorizontalAlignment','left',...
   'FontName','arial','FontWeight','bold','FontSize',9,'FontAngle','italic','Color',[0 0 0])
box off

subplot('Position',[0.08 0.08 0.85 0.12]);
plot(Eml1,'k')
set(gca,'XLim', [0 Tsim],'YLim',[min(Eml1)  max(Eml1)]);
set(gca,'YTick',[0: max(Eml1)/2:max(Eml1)])
set(gca,'YTick',[])
set(gca,'XTick',[0: Tsim/3: Tsim])
set(gca,'XTickLabel',[0 5 10 15])
set(gca,'FontName','arial','FontWeight','bold','FontSize',9)
xlabel('time (s)');
set(gca,'FontName','arial','FontWeight','bold','FontSize',9)
text(4,max(Eml1),['Em'],'FontWeight','bold','FontSize',9,'FontAngle','italic')
text(11,max(Eml1)-0.5,['l1'],'FontWeight','bold','FontSize',8,'FontAngle','normal')
box off
set(gcf,'Color',[1 1 1],'position',[100 100 520 420]);