Respiratory control model with brainstem CPG and sensory feedback (Diekman, Thomas, and Wilson 2017)

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Accession:229640
This is a closed-loop respiratory control model incorporating a central pattern generator (CPG), the Butera-Rinzel-Smith (BRS) model, together with lung mechanics, oxygen handling, and chemosensory components. The closed-loop system exhibits bistability of bursting and tonic spiking. Bursting corresponds to coexistence of eupnea-like breathing, with normal minute ventilation and blood oxygen level. Tonic spiking corresponds to a tachypnea-like state, with pathologically reduced minute ventilation and critically low blood oxygen. In our paper, we use the closed-loop system to demonstrate robustness to changes in metabolic demand, spontaneous autoresuscitation in response to hypoxia, and the distinct mechanisms that underlie rhythmogenesis in the intact control circuit vs. the isolated, open-loop CPG.
Reference:
1 . Diekman CO, Thomas PJ, Wilson CG (2017) Eupnea, tachypnea, and autoresuscitation in a closed-loop respiratory control model. J Neurophysiol 118:2194-2215 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Brainstem;
Cell Type(s): Respiratory column neuron; PreBotzinger complex neuron;
Channel(s): I Na,p; I Na,t; I K;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: MATLAB; XPP;
Model Concept(s): Pacemaking mechanism; Respiratory control;
Implementer(s): Diekman, Casey O. [casey.o.diekman at njit.edu];
Search NeuronDB for information about:  I Na,p; I Na,t; I K;
function hh = rotateXLabels( ax, angle, varargin )
%rotateXLabels: rotate any xticklabels
%
%   hh = rotateXLabels(ax,angle) rotates all XLabels on axes AX by an angle
%   ANGLE (in degrees). Handles to the resulting text objects are returned
%   in HH.
%
%   hh = rotateXLabels(ax,angle,param,value,...) also allows one or more
%   optional parameters to be specified. Possible parameters are:
%     'MaxStringLength'   The maximum length of label to show (default inf)
%
%   Examples:
%   >> bar( hsv(5)+0.05 )
%   >> days = {'Monday','Tuesday','Wednesday','Thursday','Friday'};
%   >> set( gca(), 'XTickLabel', days )
%   >> rotateXLabels( gca(), 45 )
%
%   See also: GCA, BAR

%   Copyright 2006-2013 The MathWorks Ltd.

error( nargoutchk( 2, inf, nargin ) );
if ~isnumeric( angle ) || ~isscalar( angle )
    error( 'RotateXLabels:BadAngle', 'Parameter ANGLE must be a scalar angle in degrees' )
end
angle = mod( angle, 360 );

% From R2014b, rotating labels is built-in using 'XTickLabelRotation'
if ~verLessThan('matlab','8.4.0')
    set(ax, 'XTickLabelRotation', angle)
    if nargout > 1
        hh = [];
    end
    return;
end

[maxStringLength] = parseInputs( varargin{:} );

% Get the existing label texts and clear them
[vals, labels] = findAndClearExistingLabels( ax, maxStringLength );

% Create the new label texts
h = createNewLabels( ax, vals, labels, angle );

% Reposition the axes itself to leave space for the new labels
repositionAxes( ax );

% If an X-label is present, move it too
repositionXLabel( ax );

% Store angle
setappdata( ax, 'RotateXLabelsAngle', angle );

% Only send outputs if requested
if nargout
    hh = h;
end

%-------------------------------------------------------------------------%
    function [maxStringLength] = parseInputs( varargin )
        % Parse optional inputs
        maxStringLength = inf;
        if nargin > 0
            params = varargin(1:2:end);
            values = varargin(2:2:end);
            if numel( params ) ~= numel( values )
                error( 'RotateXLabels:BadSyntax', 'Optional arguments must be specified as parameter-value pairs.' );
            end
            if any( ~cellfun( 'isclass', params, 'char' ) )
                error( 'RotateXLabels:BadSyntax', 'Optional argument names must be specified as strings.' );
            end
            for pp=1:numel( params )
                switch upper( params{pp} )
                    case 'MAXSTRINGLENGTH'
                        maxStringLength = values{pp};
                        
                    otherwise
                        error( 'RotateXLabels:BadParam', 'Optional parameter ''%s'' not recognised.', params{pp} );
                end
            end
        end
    end % parseInputs
%-------------------------------------------------------------------------%
    function [vals,labels] = findAndClearExistingLabels( ax, maxStringLength )
        % Get the current tick positions so that we can place our new labels
        vals = get( ax, 'XTick' );
        
        % Now determine the labels. We look first at for previously rotated labels
        % since if there are some the actual labels will be empty.
        ex = findall( ax, 'Tag', 'RotatedXTickLabel' );
        if isempty( ex )
            % Store the positions and labels
            labels = get( ax, 'XTickLabel' );
            if isempty( labels )
                % No labels!
                return
            else
                if ~iscell(labels)
                    labels = cellstr(labels);
                end
            end
            % Clear existing labels so that xlabel is in the right position
            set( ax, 'XTickLabel', {}, 'XTickMode', 'Manual' );
            setappdata( ax, 'OriginalXTickLabels', labels );
        else
            % Labels have already been rotated, so capture them
            labels = getappdata( ax, 'OriginalXTickLabels' );
            set(ex, 'DeleteFcn', []);
            delete(ex);
        end
        % Limit the length, if requested
        if isfinite( maxStringLength )
            for ll=1:numel( labels )
                if length( labels{ll} ) > maxStringLength
                    labels{ll} = labels{ll}(1:maxStringLength);
                end
            end
        end
        
    end % findAndClearExistingLabels
%-------------------------------------------------------------------------%
    function restoreDefaultLabels( ax )
        % Restore the default axis behavior
        removeListeners( ax );
        
        % Try to restore the tick marks and labels
        set( ax, 'XTickMode', 'auto', 'XTickLabelMode', 'auto' );
        rmappdata( ax, 'OriginalXTickLabels' );
        
        % Try to restore the axes position
        if isappdata( ax, 'OriginalAxesPosition' )
            set( ax, 'Position', getappdata( ax, 'OriginalAxesPosition' ) );
            rmappdata( ax, 'OriginalAxesPosition' );
        end
    end
%-------------------------------------------------------------------------%
    function textLabels = createNewLabels( ax, vals, labels, angle )
        % Work out the ticklabel positions
        zlim = get(ax,'ZLim');
        z = zlim(1);
        
        % We want to work in normalised coords, but this doesn't print
        % correctly. Instead we have to work in data units even though it
        % makes positioning hard.
        y = getYPositionToUse( ax );
        
        % Now create new text objects in similar positions.
        textLabels = -1*ones( numel( vals ), 1 );
        for ll=1:numel(vals)
            textLabels(ll) = text( ...
                'Units', 'Data', ...
                'Position', [vals(ll), y, z], ...
                'String', labels{ll}, ...
                'Parent', ax, ...
                'Clipping', 'off', ...
                'Rotation', angle, ...
                'Tag', 'RotatedXTickLabel', ...
                'UserData', vals(ll));
        end
        % So that we can respond to CLA and CLOSE, attach a delete
        % callback. We only attach it to one label to save massive numbers
        % of callbacks during axes shut-down.
        set(textLabels(end), 'DeleteFcn', @onTextLabelDeleted);
        
        % Now copy font properties into the texts
        updateFont();
        % Update the alignment of the text
        updateAlignment();
        
    end % createNewLabels

%-------------------------------------------------------------------------%
    function repositionAxes( ax )
        % Reposition the axes so that there's room for the labels
        % Note that we only do this if the OuterPosition is the thing being
        % controlled
        if ~strcmpi( get( ax, 'ActivePositionProperty' ), 'OuterPosition' )
            return;
        end
        
        % Work out the maximum height required for the labels
        labelHeight = getLabelHeight(ax);
        
        % Remove listeners while we mess around with things, otherwise we'll
        % trigger redraws recursively
        removeListeners( ax );
        
        % Change to normalized units for the position calculation
        oldUnits = get( ax, 'Units' );
        set( ax, 'Units', 'Normalized' );
        
        % Not sure why, but the extent seems to be proportional to the height of the axes.
        % Correct that now.
        set( ax, 'ActivePositionProperty', 'Position' );
        pos = get( ax, 'Position' );
        axesHeight = pos(4);
        % Make sure we don't adjust away the axes entirely!
        heightAdjust = min( (axesHeight*0.9), labelHeight*axesHeight );
        
        % Move the axes
        if isappdata( ax, 'OriginalAxesPosition' )
            pos = getappdata( ax, 'OriginalAxesPosition' );
        else
            pos = get(ax,'Position');
            setappdata( ax, 'OriginalAxesPosition', pos );
        end
        if strcmpi( get( ax, 'XAxisLocation' ), 'Bottom' )
            % Move it up and reduce the height
            set( ax, 'Position', pos+[0 heightAdjust 0 -heightAdjust] )
        else
            % Just reduce the height
            set( ax, 'Position', pos+[0 0 0 -heightAdjust] )
        end
        set( ax, 'Units', oldUnits );
        set( ax, 'ActivePositionProperty', 'OuterPosition' );
        
        % Make sure we find out if axes properties are changed
        addListeners( ax );
        
    end % repositionAxes

%-------------------------------------------------------------------------%
    function repositionXLabel( ax )
        % Try to work out where to put the xlabel
        removeListeners( ax );
        labelHeight = getLabelHeight(ax);
        
        % Use the new max extent to move the xlabel. We may also need to
        % move the title
        xlab = get(ax,'XLabel');
        titleh = get( ax, 'Title' );
        set( [xlab,titleh], 'Units', 'Normalized' );
        if strcmpi( get( ax, 'XAxisLocation' ), 'Top' )
            titleExtent = get( xlab, 'Extent' );
            set( xlab, 'Position', [0.5 1+labelHeight-titleExtent(4) 0] );
            set( titleh, 'Position', [0.5 1+labelHeight 0] );
        else
            set( xlab, 'Position', [0.5 -labelHeight 0] );
            set( titleh, 'Position', [0.5 1 0] );
        end
        addListeners( ax );
    end % repositionXLabel

%-------------------------------------------------------------------------%
    function height = getLabelHeight(ax)
        height = 0;
        textLabels = findall( ax, 'Tag', 'RotatedXTickLabel' );
        if isempty(textLabels)
            return;
        end
        oldUnits = get( textLabels(1), 'Units' );
        set( textLabels, 'Units', 'Normalized' );
        for ll=1:numel(vals)
            ext = get( textLabels(ll), 'Extent' );
            if ext(4) > height
                height = ext(4);
            end
        end
        set( textLabels, 'Units', oldUnits );
    end % getLabelExtent

%-------------------------------------------------------------------------%
    function updateFont()
        % Update the rotated text fonts when the axes font changes
        properties = {
            'FontName'
            'FontSize'
            'FontAngle'
            'FontWeight'
            'FontUnits'
            };
        propertyValues = get( ax, properties );
        textLabels = findall( ax, 'Tag', 'RotatedXTickLabel' );
        set( textLabels, properties, propertyValues );
    end % updateFont

    function updateAlignment()
        textLabels = findall( ax, 'Tag', 'RotatedXTickLabel' );
        angle = get( textLabels(1), 'Rotation' );
        % Depending on the angle, we may need to change the alignment. We change
        % alignments within 5 degrees of each 90 degree orientation.
        if strcmpi( get( ax, 'XAxisLocation' ), 'Top' )
            if 0 <= angle && angle < 5
                set( textLabels, 'HorizontalAlignment', 'Center', 'VerticalAlignment', 'Bottom' );
            elseif 5 <= angle && angle < 85
                set( textLabels, 'HorizontalAlignment', 'Left', 'VerticalAlignment', 'Bottom' );
            elseif 85 <= angle && angle < 95
                set( textLabels, 'HorizontalAlignment', 'Left', 'VerticalAlignment', 'Middle' );
            elseif 95 <= angle && angle < 175
                set( textLabels, 'HorizontalAlignment', 'Left', 'VerticalAlignment', 'Top' );
            elseif 175 <= angle && angle < 185
                set( textLabels, 'HorizontalAlignment', 'Center', 'VerticalAlignment', 'Top' );
            elseif 185 <= angle && angle < 265
                set( textLabels, 'HorizontalAlignment', 'Right', 'VerticalAlignment', 'Top' );
            elseif 265 <= angle && angle < 275
                set( textLabels, 'HorizontalAlignment', 'Right', 'VerticalAlignment', 'Middle' );
            elseif 275 <= angle && angle < 355
                set( textLabels, 'HorizontalAlignment', 'Right', 'VerticalAlignment', 'Bottom' );
            else % 355-360
                set( textLabels, 'HorizontalAlignment', 'Center', 'VerticalAlignment', 'Bottom' );
            end
        else
            if 0 <= angle && angle < 5
                set( textLabels, 'HorizontalAlignment', 'Center', 'VerticalAlignment', 'Top' );
            elseif 5 <= angle && angle < 85
                set( textLabels, 'HorizontalAlignment', 'Right', 'VerticalAlignment', 'Top' );
            elseif 85 <= angle && angle < 95
                set( textLabels, 'HorizontalAlignment', 'Right', 'VerticalAlignment', 'Middle' );
            elseif 95 <= angle && angle < 175
                set( textLabels, 'HorizontalAlignment', 'Right', 'VerticalAlignment', 'Bottom' );
            elseif 175 <= angle && angle < 185
                set( textLabels, 'HorizontalAlignment', 'Center', 'VerticalAlignment', 'Bottom' );
            elseif 185 <= angle && angle < 265
                set( textLabels, 'HorizontalAlignment', 'Left', 'VerticalAlignment', 'Bottom' );
            elseif 265 <= angle && angle < 275
                set( textLabels, 'HorizontalAlignment', 'Left', 'VerticalAlignment', 'Middle' );
            elseif 275 <= angle && angle < 355
                set( textLabels, 'HorizontalAlignment', 'Left', 'VerticalAlignment', 'Top' );
            else % 355-360
                set( textLabels, 'HorizontalAlignment', 'Center', 'VerticalAlignment', 'Top' );
            end
        end
    end

%-------------------------------------------------------------------------%
    function onAxesFontChanged( ~, ~ )
        updateFont();
        repositionAxes( ax );
        repositionXLabel( ax );
    end % onAxesFontChanged

%-------------------------------------------------------------------------%
    function onAxesPositionChanged( ~, ~ )
        % We need to accept the new position, so remove the appdata before
        % redrawing
        if isappdata( ax, 'OriginalAxesPosition' )
            rmappdata( ax, 'OriginalAxesPosition' );
        end
        if isappdata( ax, 'OriginalXLabelPosition' )
            rmappdata( ax, 'OriginalXLabelPosition' );
        end
        repositionAxes( ax );
        repositionXLabel( ax );
    end % onAxesPositionChanged

%-------------------------------------------------------------------------%
    function onXAxisLocationChanged( ~, ~ )
        updateAlignment();
        repositionAxes( ax );
        repositionXLabel( ax );
    end % onXAxisLocationChanged

%-------------------------------------------------------------------------%
    function onAxesLimitsChanged( ~, ~ )
        % The limits have moved, so make sure the labels are still ok
        textLabels = findall( ax, 'Tag', 'RotatedXTickLabel' );
        xlim = get( ax, 'XLim' );
        pos = [0 getYPositionToUse( ax )];
        for tt=1:numel( textLabels )
            xval = get( textLabels(tt), 'UserData' );
            pos(1) = xval;
            % If the tick is off the edge, make it invisible
            if xval<xlim(1) || xval>xlim(2)
                set( textLabels(tt), 'Visible', 'off', 'Position', pos )
            elseif ~strcmpi( get( textLabels(tt), 'Visible' ), 'on' )
                set( textLabels(tt), 'Visible', 'on', 'Position', pos )
            else
                % Just set the position
                set( textLabels(tt), 'Position', pos );
            end
        end
        
        repositionXLabel( ax );
    end % onAxesPositionChanged

%-------------------------------------------------------------------------%
    function onTextLabelDeleted( ~, ~ )
        % The final text label has been deleted. This is likely from a
        % "cla" or "close" call, so we should remove all of our dirty
        % hacks.
        restoreDefaultLabels(ax);
    end

%-------------------------------------------------------------------------%
    function addListeners( ax )
        % Create listeners. We store the array of listeners in the axes to make
        % sure that they have the same life-span as the axes they are listening to.
        axh = handle( ax );
        listeners = [
            handle.listener( axh, findprop( axh, 'FontName' ), 'PropertyPostSet', @onAxesFontChanged )
            handle.listener( axh, findprop( axh, 'FontSize' ), 'PropertyPostSet', @onAxesFontChanged )
            handle.listener( axh, findprop( axh, 'FontWeight' ), 'PropertyPostSet', @onAxesFontChanged )
            handle.listener( axh, findprop( axh, 'FontAngle' ), 'PropertyPostSet', @onAxesFontChanged )
            handle.listener( axh, findprop( axh, 'FontUnits' ), 'PropertyPostSet', @onAxesFontChanged )
            handle.listener( axh, findprop( axh, 'OuterPosition' ), 'PropertyPostSet', @onAxesPositionChanged )
            handle.listener( axh, findprop( axh, 'XLim' ), 'PropertyPostSet', @onAxesLimitsChanged )
            handle.listener( axh, findprop( axh, 'YLim' ), 'PropertyPostSet', @onAxesLimitsChanged )
            handle.listener( axh, findprop( axh, 'XAxisLocation' ), 'PropertyPostSet', @onXAxisLocationChanged )
            ];
        setappdata( ax, 'RotateXLabelsListeners', listeners );
    end % addListeners

%-------------------------------------------------------------------------%
    function removeListeners( ax )
        % Rempove any property listeners whilst we are fiddling with the axes
        if isappdata( ax, 'RotateXLabelsListeners' )
            delete( getappdata( ax, 'RotateXLabelsListeners' ) );
            rmappdata( ax, 'RotateXLabelsListeners' );
        end
    end % removeListeners

%-------------------------------------------------------------------------%
    function y = getYPositionToUse( ax )
        % Use the direction and XAxisLocation properties to work out which
        % Y-value to draw the labels at.
        whichYLim = 1;
        % If YDir is reversed, switch where we position
        if strcmpi( get( ax, 'YDir' ), 'Reverse' )
            whichYLim = 3-whichYLim;
        end
        % If set to "top", then switch (again?)
        if strcmpi( get( ax, 'XAxisLocation' ), 'Top' )
            whichYLim = 3-whichYLim;
        end
        % Now get the value
        ylim = get( ax, 'YLim' );
        y = ylim(whichYLim);
    end % getYPositionToUse

end % EOF

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