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TLR7 and -8 (when activated by ssRNA) and TLR9 (when activated by CpG-rich DNA) mediate MyD88-dependent adaptor signaling.</csml:comment>
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TLR7 and -8 (when activated by ssRNA) and TLR9 (when activated by CpG-rich DNA) mediate MyD88-dependent adaptor signaling.</csml:comment>
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TLR7 and -8 (when activated by ssRNA) and TLR9 (when activated by CpG-rich DNA) mediate MyD88-dependent adaptor signaling.</csml:comment>
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TLR7 and -8 (when activated by ssRNA) and TLR9 (when activated by CpG-rich DNA) mediate MyD88-dependent adaptor signaling.</csml:comment>
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TLR7 and -8 (when activated by ssRNA) and TLR9 (when activated by CpG-rich DNA) mediate MyD88-dependent adaptor signaling.</csml:comment>
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TLR7 and -8 (when activated by ssRNA) and TLR9 (when activated by CpG-rich DNA) mediate MyD88-dependent adaptor signaling.</csml:comment>
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TLR3 when activated by dsRNA mediates MyD88-independent signaling via the TRIF adaptor protein.</csml:comment>
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TLR3 when activated by dsRNA mediates MyD88-independent signaling via the TRIF adaptor protein.</csml:comment>
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The interaction of RNA with the RIG-I or MDA5 cytosolic cellular helicase mediates signaling via CARD domain interactions between the helicase sensor and a mitochondrial membrane-associated adaptor protein known variously as IPS-1, CARDIF, MAVS, and VISA.</csml:comment>
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The interaction of RNA with the RIG-I or MDA5 cytosolic cellular helicase mediates signaling via CARD domain interactions between the helicase sensor and a mitochondrial membrane-associated adaptor protein known variously as IPS-1, CARDIF, MAVS, and VISA.</csml:comment>
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<csml:processKinetic calcStyle="csml-calcStyle:speed" fast="false" kineticStyle="csml-kineticStyle:mass">
<csml:parameter key="coefficient1" value="0.1"/>
<csml:parameter key="coefficient2" value="1.0"/>
</csml:processKinetic>
</csml:processSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="578.0" y="166.0"/>
<csml:shape shapeID="default" visible="true">
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<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_Binding" refCellComponentID="cso30:i:CC_Cytosol"/>
<csml:comments>
<csml:comment type="text">PMID: 17395579
The interaction of RNA with the RIG-I or MDA5 cytosolic cellular helicase mediates signaling via CARD domain interactions between the helicase sensor and a mitochondrial membrane-associated adaptor protein known variously as IPS-1, CARDIF, MAVS, and VISA.</csml:comment>
</csml:comments>
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<csml:viewProperty>
<csml:position position="auto" positionID="default" x="242.0" y="532.0"/>
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</csml:connector>
<csml:connector id="c42" name="c42" refID="e46" type="cso30:c:InputAssociation">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
<csml:parameter key="stoichiometry" value="1"/>
</csml:connectorKinetic>
</csml:connectorSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="238.0" y="490.0"/>
<csml:shape shapeID="default" visible="true">
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<figure xmlns="http://www.csml.org/csml/cigraphics">
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</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
<csml:comments>
<csml:comment type="text">Indirect</csml:comment>
</csml:comments>
</csml:connector>
<csml:connector id="c41" name="c41" refID="e48" type="cso30:c:OutputProcess">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
<csml:parameter key="stoichiometry" value="1"/>
</csml:connectorKinetic>
</csml:connectorSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="280.0" y="544.0"/>
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<figure xmlns="http://www.csml.org/csml/cigraphics">
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</csml:viewProperty>
</csml:connector>
<csml:processSimulationProperty>
<csml:priority value="0"/>
<csml:firing firingOnce="false" firingStyle="csml-firingStyle:and" type="csml-variable:Boolean" value="true"/>
<csml:delay delayStyle="nodelay" value="0.0"/>
<csml:processKinetic calcStyle="csml-calcStyle:speed" fast="false" kineticStyle="csml-kineticStyle:mass">
<csml:parameter key="coefficient1" value="0.1"/>
<csml:parameter key="coefficient2" value="1.0"/>
</csml:processKinetic>
</csml:processSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="268.0" y="520.0"/>
<csml:shape shapeID="default" visible="true">
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<csml:toolSpecificGraphics/>
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<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_UnknownActivation" refCellComponentID="cso30:i:CC_Cytosol"/>
<csml:comments>
<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
</csml:comments>
</csml:process>
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<csml:parameter key="stoichiometry" value="1"/>
</csml:connectorKinetic>
</csml:connectorSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="266.0" y="676.0"/>
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<figure xmlns="http://www.csml.org/csml/cigraphics">
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</csml:viewProperty>
</csml:connector>
<csml:connector id="c47" name="c47" refID="e48" type="cso30:c:InputAssociation">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
<csml:parameter key="stoichiometry" value="1"/>
</csml:connectorKinetic>
</csml:connectorSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="286.0" y="621.0"/>
<csml:shape shapeID="default" visible="true">
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<figure xmlns="http://www.csml.org/csml/cigraphics">
<associationConnector depth="0" points="286.0 621.0 299.09166011477834 654.5473790441196" visible="true"/>
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</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
<csml:comments>
<csml:comment type="text">Indirect</csml:comment>
</csml:comments>
</csml:connector>
<csml:connector id="c44" name="c44" refID="e63" type="cso30:c:OutputProcess">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
<csml:parameter key="stoichiometry" value="1"/>
</csml:connectorKinetic>
</csml:connectorSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="270.6564023547028" y="685.0"/>
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<figure xmlns="http://www.csml.org/csml/cigraphics">
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<csml:processSimulationProperty>
<csml:priority value="0"/>
<csml:firing firingOnce="false" firingStyle="csml-firingStyle:and" type="csml-variable:Boolean" value="true"/>
<csml:delay delayStyle="nodelay" value="0.0"/>
<csml:processKinetic calcStyle="csml-calcStyle:speed" fast="false" kineticStyle="csml-kineticStyle:mass">
<csml:parameter key="coefficient1" value="0.1"/>
<csml:parameter key="coefficient2" value="1.0"/>
</csml:processKinetic>
</csml:processSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="294.0" y="662.0"/>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
</csml:comments>
</csml:process>
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<csml:position position="auto" positionID="default" x="384.0" y="680.0"/>
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<figure xmlns="http://www.csml.org/csml/cigraphics">
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</csml:viewProperty>
</csml:connector>
<csml:connector id="c48" name="c48" refID="e48" type="cso30:c:InputAssociation">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
<csml:parameter key="stoichiometry" value="1"/>
</csml:connectorKinetic>
</csml:connectorSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="294.0" y="616.0"/>
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</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
<csml:comments>
<csml:comment type="text">Indirect</csml:comment>
</csml:comments>
</csml:connector>
<csml:connector id="c46" name="c46" refID="e65" type="cso30:c:OutputProcess">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
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</csml:connectorSimulationProperty>
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</csml:processKinetic>
</csml:processSimulationProperty>
<csml:viewProperty>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
</csml:comments>
</csml:process>
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<csml:parameter key="stoichiometry" value="1"/>
</csml:connectorKinetic>
</csml:connectorSimulationProperty>
<csml:viewProperty>
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<csml:comments>
<csml:comment type="text">Indirect</csml:comment>
</csml:comments>
</csml:connector>
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<csml:connectorSimulationProperty>
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<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
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</csml:processKinetic>
</csml:processSimulationProperty>
<csml:viewProperty>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
</csml:comments>
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</csml:connectorSimulationProperty>
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</csml:connector>
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<csml:parameter key="stoichiometry" value="1"/>
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<csml:comments>
<csml:comment type="text">Indirect</csml:comment>
</csml:comments>
</csml:connector>
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<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
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<csml:comments>
<csml:comment type="text">Indirect</csml:comment>
</csml:comments>
</csml:connector>
<csml:connector id="c56" name="c56" refID="e71" type="cso30:c:OutputProcess">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
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</csml:processKinetic>
</csml:processSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="711.0" y="419.0"/>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
</csml:comments>
</csml:process>
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<csml:comments>
<csml:comment type="text">Indirect</csml:comment>
</csml:comments>
</csml:connector>
<csml:connector id="c58" name="c58" refID="e71" type="cso30:c:OutputProcess">
<csml:connectorSimulationProperty>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
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<csml:comments>
<csml:comment type="text">Indirect</csml:comment>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
</csml:comments>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
</csml:comments>
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<csml:position position="auto" positionID="default" x="463.0" y="723.0"/>
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<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
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<csml:parameter key="coefficient1" value="0.1"/>
<csml:parameter key="coefficient2" value="1.0"/>
</csml:processKinetic>
</csml:processSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="315.0" y="763.0"/>
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<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
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<csml:comment type="text">PMID: 17395579
Translocation into the nucleus of IRF dimers (IRF-3, IRF-7) and activated NF-kappaB lead to transcriptional activation of type I interferon gene expression (for example IFN-beta and IFN-alpha4).</csml:comment>
</csml:comments>
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<csml:comment type="text">Indirect</csml:comment>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
Translocation into the nucleus of IRF dimers (IRF-3, IRF-7) and activated NF-kappaB lead to transcriptional activation of type I interferon gene expression (for example IFN-beta and IFN-alpha4).</csml:comment>
</csml:comments>
</csml:process>
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<csml:parameter key="coefficient1" value="0.1"/>
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</csml:processKinetic>
</csml:processSimulationProperty>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
</csml:comments>
</csml:process>
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<csml:parameter key="stoichiometry" value="1"/>
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</csml:connector>
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<csml:comment type="text">Indirect</csml:comment>
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<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
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</csml:processKinetic>
</csml:processSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="269.0" y="385.0"/>
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<csml:comment type="text">PMID: 17395579
The IPS-1, TRIF, and MyD88 adaptors then lead to IRF and NF-kappaB activation via IKK (inhibitor of nuclear factor-{kappa}B kinase), IRAK (interleukin 1 receptor-associated kinase), TBK (TANK-binding kinase), and TRAF (tumor necrosis factor receptor-associated factor) proteins.</csml:comment>
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<csml:viewProperty>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
Translocation into the nucleus of IRF dimers (IRF-3, IRF-7) and activated NF-kappaB lead to transcriptional activation of type I interferon gene expression (for example IFN-beta and IFN-alpha4).</csml:comment>
</csml:comments>
</csml:process>
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<csml:comment type="text">PMID: 17395579
Translocation into the nucleus of IRF dimers (IRF-3, IRF-7) and activated NF-kappaB lead to transcriptional activation of type I interferon gene expression (for example IFN-beta and IFN-alpha4).</csml:comment>
</csml:comments>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
Translocation into the nucleus of IRF dimers (IRF-3, IRF-7) and activated NF-kappaB lead to transcriptional activation of type I interferon gene expression (for example IFN-beta and IFN-alpha4).</csml:comment>
</csml:comments>
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<csml:comments>
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<csml:comments>
<csml:comment type="text">PMID: 17395579
Translocation into the nucleus of IRF dimers (IRF-3, IRF-7) and activated NF-kappaB lead to transcriptional activation of type I interferon gene expression (for example IFN-beta and IFN-alpha4).</csml:comment>
</csml:comments>
</csml:process>
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<csml:participant id="participant-g12" name="participant-g12" refID="g12" type="csml-element:participant"/>
<csml:participant id="participant-e7" name="participant-e7" refID="e7" type="csml-element:participant"/>
<csml:participant id="participant-e9" name="participant-e9" refID="e9" type="csml-element:participant"/>
</csml:fact>
<csml:fact id="g14" name="g1" type="cso30:c:FactViewGroup"/>
<csml:fact id="g1" name="g1" type="cso30:c:FactViewGroup">
<csml:participant id="participant-e3" name="participant-e3" refID="e3" type="csml-element:participant"/>
<csml:participant id="participant-e2" name="participant-e2" refID="e2" type="csml-element:participant"/>
<csml:participant id="participant-e4" name="participant-e4" refID="e4" type="csml-element:participant"/>
<csml:participant id="participant-e1" name="participant-e1" refID="e1" type="csml-element:participant"/>
</csml:fact>
<csml:fact id="g12" name="g2" type="cso30:c:FactViewGroup">
<csml:participant id="participant-e52" name="participant-e52" refID="e52" type="csml-element:participant"/>
<csml:participant id="participant-e50" name="participant-e50" refID="e50" type="csml-element:participant"/>
<csml:participant id="participant-e59" name="participant-e59" refID="e59" type="csml-element:participant"/>
<csml:participant id="participant-e51" name="participant-e51" refID="e51" type="csml-element:participant"/>
<csml:participant id="participant-g13" name="participant-g13" refID="g13" type="csml-element:participant"/>
<csml:participant id="participant-e57" name="participant-e57" refID="e57" type="csml-element:participant"/>
<csml:participant id="participant-e54" name="participant-e54" refID="e54" type="csml-element:participant"/>
<csml:participant id="participant-e55" name="participant-e55" refID="e55" type="csml-element:participant"/>
<csml:participant id="participant-e56" name="participant-e56" refID="e56" type="csml-element:participant"/>
<csml:participant id="participant-e53" name="participant-e53" refID="e53" type="csml-element:participant"/>
<csml:participant id="participant-e58" name="participant-e58" refID="e58" type="csml-element:participant"/>
</csml:fact>
<csml:fact id="g13" name="g2" type="cso30:c:FactViewGroup">
<csml:participant id="participant-e62" name="participant-e62" refID="e62" type="csml-element:participant"/>
<csml:participant id="participant-e61" name="participant-e61" refID="e61" type="csml-element:participant"/>
<csml:participant id="participant-e60" name="participant-e60" refID="e60" type="csml-element:participant"/>
</csml:fact>
<csml:fact id="g3" name="g1" type="cso30:c:FactViewGroup">
<csml:participant id="participant-e11" name="participant-e11" refID="e11" type="csml-element:participant"/>
<csml:participant id="participant-e6" name="participant-e6" refID="e6" type="csml-element:participant"/>
<csml:participant id="participant-e5" name="participant-e5" refID="e5" type="csml-element:participant"/>
</csml:fact>
<csml:fact id="g4" name="g3" type="cso30:c:FactViewGroup">
<csml:participant id="participant-g6" name="participant-g6" refID="g6" type="csml-element:participant"/>
<csml:participant id="participant-g5" name="participant-g5" refID="g5" type="csml-element:participant"/>
</csml:fact>
<csml:fact id="g6" name="g1" type="cso30:c:FactViewGroup">
<csml:participant id="participant-e41" name="participant-e41" refID="e41" type="csml-element:participant"/>
<csml:participant id="participant-e40" name="participant-e40" refID="e40" type="csml-element:participant"/>
<csml:participant id="participant-e39" name="participant-e39" refID="e39" type="csml-element:participant"/>
<csml:participant id="participant-e38" name="participant-e38" refID="e38" type="csml-element:participant"/>
<csml:participant id="participant-e37" name="participant-e37" refID="e37" type="csml-element:participant"/>
<csml:participant id="participant-e36" name="participant-e36" refID="e36" type="csml-element:participant"/>
<csml:participant id="participant-e35" name="participant-e35" refID="e35" type="csml-element:participant"/>
</csml:fact>
<csml:fact id="g5" name="g2" type="cso30:c:FactViewGroup">
<csml:participant id="participant-e34" name="participant-e34" refID="e34" type="csml-element:participant"/>
<csml:participant id="participant-e33" name="participant-e33" refID="e33" type="csml-element:participant"/>
</csml:fact>
</csml:factSet>
<csml:modelSimulationProperty>
<csml:parameter key="enhancedFiring" value="true"/>
<csml:parameter key="discreteWeakFiring" value="false"/>
<csml:parameter key="continousWeakFiring" value="false"/>
<csml:parameter key="samplingInterval" value="0.1"/>
<csml:parameter key="plotUpdateInterval" value="1.0"/>
<csml:parameter key="logUpdateInterval" value="1.0"/>
<csml:parameter key="simulationTime" value="1000.0"/>
<csml:parameter key="firingAccuracy" value="1.0E-10"/>
</csml:modelSimulationProperty>
</csml:model>
<csml:subModelSet/>
<csml:viewSet>
<csml:view name="Default View" refAnimationID="default" refModelID="undef" refPositionID="default" refShapeID="default" viewID="default"/>
</csml:viewSet>
</csml:project>
