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        <div class="dc:title">Proctor2017- Role of microRNAs in
osteoarthritis (Positive Feedback By Micro RNA)</div>
        <div class="dc:bibliographicCitation">
          <p>This model is described in the article:</p>
          <div class="bibo:title">
            <a href="http://identifiers.org/pubmed/29095952" title="Access to this publication">Computer simulation models
    as a tool to investigate the role of microRNAs in
    osteoarthritis.</a>
          </div>
          <div class="bibo:authorList">Proctor CJ, Smith GR.</div>
          <div class="bibo:Journal">PLoS ONE 2017; 12(11): e0187568</div>
          <p>Abstract:</p>
          <div class="bibo:abstract">
            <p>The aim of this study was to show how computational models
    can be used to increase our understanding of the role of
    microRNAs in osteoarthritis (OA) using miR-140 as an example.
    Bioinformatics analysis and experimental results from the
    literature were used to create and calibrate models of gene
    regulatory networks in OA involving miR-140 along with key
    regulators such as NF-?B, SMAD3, and RUNX2. The individual
    models were created with the modelling standard, Systems
    Biology Markup Language, and integrated to examine the overall
    effect of miR-140 on cartilage homeostasis. Down-regulation of
    miR-140 may have either detrimental or protective effects for
    cartilage, indicating that the role of miR-140 is complex.
    Studies of individual networks in isolation may therefore lead
    to different conclusions. This indicated the need to combine
    the five chosen individual networks involving miR-140 into an
    integrated model. This model suggests that the overall effect
    of miR-140 is to change the response to an IL-1 stimulus from a
    prolonged increase in matrix degrading enzymes to a pulse-like
    response so that cartilage degradation is temporary. Our
    current model can easily be modified and extended as more
    experimental data become available about the role of miR-140 in
    OA. In addition, networks of other microRNAs that are important
    in OA could be incorporated. A fully integrated model could not
    only aid our understanding of the mechanisms of microRNAs in
    ageing cartilage but could also provide a useful tool to
    investigate the effect of potential interventions to prevent
    cartilage loss.</p>
          </div>
        </div>
        <div class="dc:publisher">
          <p>This model is hosted on 
  <a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a>
  and identified by: 
  <a href="http://identifiers.org/biomodels.db/MODEL1610100000">MODEL1610100000</a>.</p>
          <p>To cite BioModels Database, please use: 
  <a href="http://identifiers.org/pubmed/25414348" target="_blank">Chelliah V et al. BioModels: ten-year
  anniversary. Nucl. Acids Res. 2015, 43(Database
  issue):D542-8</a>.</p>
        </div>
        <div class="dc:license">
          <p>To the extent possible under law, all copyright and related or
  neighbouring rights to this encoded model have been dedicated to
  the public domain worldwide. Please refer to 
  <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication">CC0
  Public Domain Dedication</a> for more information.</p>
        </div>
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            <bvar>
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            </bvar>
            <bvar>
              <ci> miR_gene_TF2 </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> krelTF2miRgene </ci>
                <ci> miR_gene_TF2 </ci>
                <ci> cell </ci>
              </apply>
              <ci> cell </ci>
            </apply>
          </lambda>
        </math>
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        <math xmlns="http://www.w3.org/1998/Math/MathML">        
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            <bvar>
              <ci> TF2 </ci>
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            <bvar>
              <ci> cell </ci>
            </bvar>
            <bvar>
              <ci> kbinTF2miRgene </ci>
            </bvar>
            <bvar>
              <ci> miR_gene </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> kbinTF2miRgene </ci>
                <ci> miR_gene </ci>
                <ci> cell </ci>
                <ci> TF2 </ci>
                <ci> cell </ci>
              </apply>
              <ci> cell </ci>
            </apply>
          </lambda>
        </math>
            </functionDefinition>
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        <math xmlns="http://www.w3.org/1998/Math/MathML">        
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            <bvar>
              <ci> cell </ci>
            </bvar>
            <bvar>
              <ci> krelTF1miRgene </ci>
            </bvar>
            <bvar>
              <ci> miR_gene_TF1 </ci>
            </bvar>
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              <divide/>
              <apply>
                <times/>
                <ci> krelTF1miRgene </ci>
                <ci> miR_gene_TF1 </ci>
                <ci> cell </ci>
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              <ci> cell </ci>
            </apply>
          </lambda>
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        <math xmlns="http://www.w3.org/1998/Math/MathML">        
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            <bvar>
              <ci> TF1 </ci>
            </bvar>
            <bvar>
              <ci> cell </ci>
            </bvar>
            <bvar>
              <ci> kbinTF1miRgene </ci>
            </bvar>
            <bvar>
              <ci> miR_gene </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> kbinTF1miRgene </ci>
                <ci> miR_gene </ci>
                <ci> cell </ci>
                <ci> TF1 </ci>
                <ci> cell </ci>
              </apply>
              <ci> cell </ci>
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          </lambda>
        </math>
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        <math xmlns="http://www.w3.org/1998/Math/MathML">        
          <lambda>
            <bvar>
              <ci> Signal </ci>
            </bvar>
            <bvar>
              <ci> cell </ci>
            </bvar>
            <bvar>
              <ci> ksynTF1mRNA </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> ksynTF1mRNA </ci>
                <ci> Signal </ci>
                <ci> cell </ci>
              </apply>
              <ci> cell </ci>
            </apply>
          </lambda>
        </math>
            </functionDefinition>
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        <math xmlns="http://www.w3.org/1998/Math/MathML">        
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            <bvar>
              <ci> TF1_mRNA </ci>
            </bvar>
            <bvar>
              <ci> cell </ci>
            </bvar>
            <bvar>
              <ci> kdegTF1mRNA </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> kdegTF1mRNA </ci>
                <ci> TF1_mRNA </ci>
                <ci> cell </ci>
              </apply>
              <ci> cell </ci>
            </apply>
          </lambda>
        </math>
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            </bvar>
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            <bvar>
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            </bvar>
            <bvar>
              <ci> miR </ci>
            </bvar>
            <apply>
              <divide/>
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                <times/>
                <ci> kdegTF1mRNAbyMiR </ci>
                <ci> TF1_mRNA </ci>
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                <ci> cell </ci>
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          </lambda>
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              <ci> cell </ci>
            </bvar>
            <bvar>
              <ci> ksynTF1 </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> ksynTF1 </ci>
                <ci> TF1_mRNA </ci>
                <ci> cell </ci>
              </apply>
              <ci> cell </ci>
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          </lambda>
        </math>
            </functionDefinition>
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            <bvar>
              <ci> kdegTF1 </ci>
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              <divide/>
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                <times/>
                <ci> kdegTF1 </ci>
                <ci> TF1 </ci>
                <ci> cell </ci>
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              <ci> cell </ci>
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          </lambda>
        </math>
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              <divide/>
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                <times/>
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                <ci> miR_gene_TF2 </ci>
                <ci> cell </ci>
              </apply>
              <ci> cell </ci>
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          </lambda>
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      <parameter constant="true" id="kbinTF2miRgene" metaid="_18c98925-f446-47a8-bff3-01b5a6617431" name="kbinTF2miRgene" value="0.0001"/>
      <parameter constant="true" id="kdegMiR" metaid="_22f42120-6395-4de3-be85-aaab6ad0674a" name="kdegMiR" value="0.0004"/>
      <parameter constant="true" id="kdegTF1" metaid="_16ac7031-ba64-4e56-91dc-95e47eb3c4fe" name="kdegTF1" value="1E-5"/>
      <parameter constant="true" id="kdegTF1mRNA" metaid="a1cd6970-7832-4c8f-968c-4b55b8d9e6e9" name="kdegTF1mRNA" value="0.0001"/>
      <parameter constant="true" id="kdegTF1mRNAbyMiR" metaid="ce6c942c-5a76-4cf7-9fdf-9f321a9d5bf5" name="kdegTF1mRNAbyMiR" value="1E-6"/>
      <parameter constant="true" id="krelTF1miRgene" metaid="_890193c5-db6d-4b68-a94f-4786da8ae570" name="krelTF1miRgene" value="0.001"/>
      <parameter constant="true" id="krelTF2miRgene" metaid="fd28c7bd-200b-443d-a6fd-146a2368a3df" name="krelTF2miRgene" value="0.001"/>
      <parameter constant="true" id="ksynMiR" metaid="_34240524-4d95-47fe-a1b2-931084d2cfc5" name="ksynMiR" value="0.2"/>
      <parameter constant="true" id="ksynTF1" metaid="df2fb646-f52c-4f3a-b759-f21c532dd762" name="ksynTF1" value="0.0003"/>
      <parameter constant="true" id="ksynTF1mRNA" metaid="_269832ec-3723-45c9-976f-3fa002bba825" name="ksynTF1mRNA" value="0.01"/>
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        <kineticLaw>
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            <apply>
              <times/>
              <ci> cell </ci>
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                <ci> Function_for_miR_gene_TF1_binding </ci>
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                <ci> cell </ci>
                <ci> kbinTF1miRgene </ci>
                <ci> miR_gene </ci>
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                </kineticLaw>
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        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="_025dfbc7-7fb0-4a3b-aac5-0f8b9661e673" species="miR_gene_TF2" stoichiometry="1"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <ci> Function_for_miR_gene_TF2_binding </ci>
                <ci> TF2 </ci>
                <ci> cell </ci>
                <ci> kbinTF2miRgene </ci>
                <ci> miR_gene </ci>
              </apply>
            </apply>
          </math>
                </kineticLaw>
      </reaction>
      <reaction id="miR_gene_TF2_release" metaid="_3716d21f-3934-4b7e-b3f7-9d97447c19de" name="miR_gene_TF2_release" reversible="false">
        <listOfReactants>
          <speciesReference metaid="_1e10dc83-666f-4f39-9056-111d2a9b0843" species="miR_gene_TF2" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="a37b7660-95aa-46bb-a350-0a5bd9012a3d" species="miR_gene" stoichiometry="1"/>
          <speciesReference metaid="_5b36d615-c9e7-4b0a-848f-ce1a36d04083" species="TF2" stoichiometry="1"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <ci> Function_for_miR_gene_TF2_release </ci>
                <ci> cell </ci>
                <ci> krelTF2miRgene </ci>
                <ci> miR_gene_TF2 </ci>
              </apply>
            </apply>
          </math>
                </kineticLaw>
      </reaction>
      <reaction id="miR_synthesis" metaid="_70950600-1c7e-4783-83e9-d497f0b7a960" name="miR_synthesis" reversible="false">
        <listOfReactants>
          <speciesReference metaid="d1197d5e-6808-450a-8623-4fc5db2f744a" species="miR_gene_TF2" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="ced396e0-309b-4eba-a109-c3b429d19ee5" species="miR_gene_TF2" stoichiometry="1"/>
          <speciesReference metaid="_1443778d-a2e4-426a-93e1-0e3bb970ccb9" species="miR" stoichiometry="1"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <ci> Function_for_miR_synthesis_2 </ci>
                <ci> cell </ci>
                <ci> ksynMiR </ci>
                <ci> miR_gene_TF2 </ci>
              </apply>
            </apply>
          </math>
                </kineticLaw>
      </reaction>
      <reaction id="miR_degradation" metaid="_128aabc5-ec9a-459f-a2b1-b2253de22330" name="miR_degradation" reversible="false">
        <listOfReactants>
          <speciesReference metaid="cca7a5db-7627-46a9-b2c3-b54121b8e551" species="miR" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="daea383f-df29-4f8a-b63e-93973c4b859e" species="Sink" stoichiometry="1"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <ci> Function_for_miR_degradation </ci>
                <ci> cell </ci>
                <ci> kdegMiR </ci>
                <ci> miR </ci>
              </apply>
            </apply>
          </math>
                </kineticLaw>
      </reaction>
      <reaction id="TF1_transcription" metaid="_73ceeb58-7611-49fd-8389-115b47dd45e2" name="TF1_transcription" reversible="false">
        <listOfReactants>
          <speciesReference metaid="_72d72dd9-d7bd-4ca0-89ed-498e8796270a" species="Signal" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="_3018b3d0-292e-404a-a1e7-52de69ab3f79" species="Signal" stoichiometry="1"/>
          <speciesReference metaid="_126bc4be-b1ae-435d-a043-ce35be396f28" species="TF1_mRNA" stoichiometry="1"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <ci> Function_for_TF1_transcription </ci>
                <ci> Signal </ci>
                <ci> cell </ci>
                <ci> ksynTF1mRNA </ci>
              </apply>
            </apply>
          </math>
                </kineticLaw>
      </reaction>
      <reaction id="TF1_mRNA_degradation" metaid="_87e85824-3812-4f9e-93c7-54eaaf82d6d4" name="TF1_mRNA_degradation" reversible="false">
        <listOfReactants>
          <speciesReference metaid="ee835bbd-1c08-4827-93ef-e83dad1385a0" species="TF1_mRNA" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="_3414fa2f-26d5-4e10-a587-3fbd9dff1b4d" species="Sink" stoichiometry="1"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <ci> Function_for_TF1_mRNA_degradation </ci>
                <ci> TF1_mRNA </ci>
                <ci> cell </ci>
                <ci> kdegTF1mRNA </ci>
              </apply>
            </apply>
          </math>
                </kineticLaw>
      </reaction>
      <reaction id="TF1_mRNA_degradation_via_miR" metaid="b66e95ed-e825-4551-bea3-ae349190f07a" name="TF1_mRNA_degradation_via_miR" reversible="false">
        <listOfReactants>
          <speciesReference metaid="_18ce4d1e-9b91-4732-9971-3a3f5ec3a950" species="TF1_mRNA" stoichiometry="1"/>
          <speciesReference metaid="_188abb86-28c2-460f-92f8-2f57f03d7557" species="miR" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="_48289d9c-0c86-4e47-b333-4598fda22518" species="miR" stoichiometry="1"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <ci> Function_for_TF1_mRNA_degradation_via_miR </ci>
                <ci> TF1_mRNA </ci>
                <ci> cell </ci>
                <ci> kdegTF1mRNAbyMiR </ci>
                <ci> miR </ci>
              </apply>
            </apply>
          </math>
                </kineticLaw>
      </reaction>
      <reaction id="TF1_translation" metaid="_3c8d5d8d-50dd-49b7-9a69-9d9fe3d4027a" name="TF1_translation" reversible="false">
        <listOfReactants>
          <speciesReference metaid="b6a4800f-a2e3-4ae9-a499-3eb18f48d681" species="TF1_mRNA" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="_1ed341ca-e344-4c3e-b70b-b584dabd425d" species="TF1_mRNA" stoichiometry="1"/>
          <speciesReference metaid="e8f681b4-eae7-44d7-a6e0-50b8b10717f3" species="TF1" stoichiometry="1"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <ci> Function_for_TF1_translation </ci>
                <ci> TF1_mRNA </ci>
                <ci> cell </ci>
                <ci> ksynTF1 </ci>
              </apply>
            </apply>
          </math>
                </kineticLaw>
      </reaction>
      <reaction id="TF1_degradation" metaid="d8040f90-c492-4569-bd7e-2df7cdea0f16" name="TF1_degradation" reversible="false">
        <listOfReactants>
          <speciesReference metaid="_0f41362d-0552-443f-943e-50e2fe46acad" species="TF1" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="_2682ec3f-1c54-4ef6-b71e-e5719eb23d43" species="Sink" stoichiometry="1"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <ci> Function_for_TF1_degradation </ci>
                <ci> TF1 </ci>
                <ci> cell </ci>
                <ci> kdegTF1 </ci>
              </apply>
            </apply>
          </math>
                </kineticLaw>
      </reaction>
    </listOfReactions>
    <listOfEvents>
      <event id="ActivateSignal" metaid="_5d275ee5-aa41-4d24-9c62-29b5fc5b688a" name="ActivateSignal">
        <trigger>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <gt/>
              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
              <cn> 3600 </cn>
            </apply>
          </math>
                </trigger>
        <delay>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <cn> 0 </cn>
          </math>
                </delay>
        <listOfEventAssignments>
          <eventAssignment metaid="_3e29b852-7e0e-4266-9dc1-d5af7d2c3292" variable="Signal">
            <math xmlns="http://www.w3.org/1998/Math/MathML">            
              <apply>
                <divide/>
                <cn> 100 </cn>
                <ci> cell </ci>
              </apply>
            </math>
                    </eventAssignment>
        </listOfEventAssignments>
      </event>
      <event id="DeactivateSignal" metaid="f3a891ae-bf8c-420a-bab5-dcfa51c9e20e" name="DeactivateSignal">
        <trigger>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <apply>
              <gt/>
              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
              <cn> 7200 </cn>
            </apply>
          </math>
                </trigger>
        <delay>
          <math xmlns="http://www.w3.org/1998/Math/MathML">          
            <cn> 0 </cn>
          </math>
                </delay>
        <listOfEventAssignments>
          <eventAssignment metaid="_6926285d-138f-41d7-848e-00229e0a946e" variable="Signal">
            <math xmlns="http://www.w3.org/1998/Math/MathML">            
              <apply>
                <divide/>
                <cn> 0 </cn>
                <ci> cell </ci>
              </apply>
            </math>
                    </eventAssignment>
        </listOfEventAssignments>
      </event>
    </listOfEvents>
  </model>
</sbml>