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PMID: 17405910
association of single LPS molecules with plasmaderived LPS-binding protein (LBP)
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PMID: 17405910
one LPS bound to one LBP, the so formed protein–glycolipid complex is recognized, with high specificity, by CD14</csml:comment>
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PMID: 17405910, 11034352
activation of TLR4, which is thought to initiate intracellular signaling upon association with a CD14 molecule that is occupied by an LPS–LBP complex.</csml:comment>
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</csml:comment>
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</csml:comment>
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PMID: 17405910
TLR4 signaling depends on the presence of MD2, a secretory glycoprotein
that associates with TLR4.</csml:comment>
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PMID: 17405910
Subsequent to the association of MyD88 with TLR4, MyD88 recruits the IL-1
receptor-associated kinase 1 (IRAK1).</csml:comment>
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PMID: 17405910
Subsequent to the association of MyD88 with TLR4, MyD88 recruits the IL-1
receptor-associated kinase 1 (IRAK1).</csml:comment>
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PMID: 17405910
Phosphorylation of IRAK1 by IRAK4 and other kinases results in the dissociation of IRAK1 from TLR4.</csml:comment>
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<csml:comment type="text">

</csml:comment>
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</csml:comment>
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PMID: 17405910
Phosphorylated IRAK1 associates, in the cytosol, with tumor necrosis factor receptor (TNFR)-associated factor 6 (TRAF6).
</csml:comment>
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</csml:comment>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
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<csml:priority value="0"/>
<csml:firing firingOnce="false" firingStyle="csml-firingStyle:and" type="csml-variable:Boolean" value="true"/>
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<csml:processKinetic calcStyle="csml-calcStyle:speed" fast="false" kineticStyle="csml-kineticStyle:mass">
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<csml:parameter key="coefficient2" value="1.0"/>
</csml:processKinetic>
</csml:processSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="925.0" y="97.0"/>
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PMID: 17405910
Phosphorylation of IRAK1 by IRAK4 and other kinases results in the dissociation of IRAK1 from TLR4.</csml:comment>
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Indirect</csml:comment>
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<csml:comment type="text">

</csml:comment>
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PMID: 17405910
TRAF6, a RING domain-containing E3 ubiquitin ligase, activates mitogen-activated protein kinase kinase kinases
(MAP3K), transforming growth factor beta (TGF-beta)-activating kinase 1 (TAK1), mitogen-activated protein kinase/extracellular signal-regulated kinase kinase
kinase (MEKK3, and apoptosis signal-regulating kinase 1 (ASK1).</csml:comment>
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</csml:comment>
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Indirect</csml:comment>
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PMID: 17405910
TRAF6, a RING domain-containing E3 ubiquitin ligase, activates mitogen-activated protein kinase kinase kinases
(MAP3K), transforming growth factor beta (TGF-beta)-activating kinase 1 (TAK1), mitogen-activated protein kinase/extracellular signal-regulated kinase kinase
kinase (MEKK3, and apoptosis signal-regulating kinase 1 (ASK1).
</csml:comment>
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<csml:comments>
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Indirect</csml:comment>
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</csml:connector>
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</csml:comment>
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<csml:comments>
<csml:comment type="text">

PMID: 17405910
TRAF6, a RING domain-containing E3 ubiquitin ligase, activates mitogen-activated protein kinase kinase kinases
(MAP3K), transforming growth factor beta (TGF-beta)-activating kinase 1 (TAK1), mitogen-activated protein kinase/extracellular signal-regulated kinase kinase
kinase (MEKK3, and apoptosis signal-regulating kinase 1 (ASK1).</csml:comment>
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</csml:comment>
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Indirect</csml:comment>
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PMID: 17405910
MAP3K family (T1, TAK1; M3, MEKK3; A1, ASK1) which, in turn, activate Jnk (J), IKK (I), and p38 (p).</csml:comment>
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Indirect</csml:comment>
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<csml:comments>
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PMID: 17405910
MAP3K family (T1, TAK1; M3, MEKK3; A1, ASK1) which, in turn, activate Jnk (J), IKK (I), and p38 (p).</csml:comment>
</csml:comments>
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<csml:comment type="text">

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Indirect</csml:comment>
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<csml:comment type="text">

PMID: 17405910
MAP3K family (T1, TAK1; M3, MEKK3; A1, ASK1) which, in turn, activate Jnk (J), IKK (I), and p38 (p).</csml:comment>
</csml:comments>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
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<csml:comments>
<csml:comment type="text">

PMID: 17405910
Subsequent activation of cJun N-terminal kinase (Jnk), I-kappaB kinase (IKK) complex (consisting of alpha, beta and gamma subunits), and p38, leads to phosphorylation of cJun, I-kappaB, and ATF2, respectively.</csml:comment>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
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PMID: 17405910
Subsequent activation of cJun N-terminal kinase (Jnk), I-kappaB kinase (IKK) complex (consisting of alpha, beta and gamma subunits), and p38, leads to phosphorylation of cJun, I-kappaB, and ATF2, respectively.</csml:comment>
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Indirect</csml:comment>
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PMID: 17405910
Subsequent activation of cJun N-terminal kinase (Jnk), I-kappaB kinase (IKK) complex (consisting of alpha, beta and gamma subunits), and p38, leads to phosphorylation of cJun, I-kappaB, and ATF2, respectively.</csml:comment>
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PMID: 17405910
Phosphorylated I-kappaB is ubiquitinated and degraded by the 26S proteosome, leaving the p65-p50 dimer (NF-kappaB), which is now free to translocate to the nucleus.</csml:comment>
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PMID: 17405910
Phosphorylated I-kappaB is ubiquitinated and degraded by the 26S proteosome, leaving the p65-p50 dimer (NF-kappaB), which is now free to translocate to the nucleus.</csml:comment>
</csml:comments>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
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<csml:comment type="text">

PMID: 17405910, 15356101
The generation of ROS appears to result from a direct activation of membrane-bound NADPH oxidase 4 by TLR4.</csml:comment>
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Indirect</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="249.0" y="369.0"/>
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<csml:comments>
<csml:comment type="text">

PMID: 17405910, 15356101
The generation of ROS appears to result from a direct activation of membrane-bound NADPH oxidase 4 by TLR4.</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p25" name="p25" type="cso30:c:ProcessBiological">
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
</csml:connector>
<csml:connector id="c78" name="c78" refID="e68" type="cso30:c:InputProcess">
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
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</csml:viewProperty>
<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
</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="1165.0" y="705.0"/>
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<csml:comments>
<csml:comment type="text">

PMID: 17405910, 9564042
ASK1 can only be activated by TRAF6 if the associated thioredoxin (TrX) is displaced from TRAF6.</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p26" name="p26" type="cso30:c:ProcessBiological">
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<csml:comments>
<csml:comment type="text">

</csml:comment>
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<csml:comments>
<csml:comment type="text">

Indirect</csml:comment>
</csml:comments>
</csml:connector>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
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<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_Dissociation" refCellComponentID="cso30:i:CC_Extracellular"/>
<csml:comments>
<csml:comment type="text">PMID: 17405910, 15864310
This dissociation depends on the formation of ROS.</csml:comment>
</csml:comments>
</csml:process>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
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<csml:comments>
<csml:comment type="text">

PMID: 17405910, 12062447, 12062447
TIRAP, another TLR4 adapter protein appears to be involved in the activation of interferon regulatory factor 3 (IRF3), a transcription factor, which induces the type I interferon gene, and further evidence suggests that this activation is mediated by a double-stranded RNA responsive protein kinase (PKR).</csml:comment>
</csml:comments>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
</csml:connector>
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<csml:connectorKinetic>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
</csml:connector>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
</csml:connector>
<csml:processSimulationProperty>
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</csml:processSimulationProperty>
<csml:viewProperty>
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<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_Binding" refCellComponentID="cso30:i:CC_Cytosol"/>
<csml:comments>
<csml:comment type="text">

PMID: 17405910, 12062447, 12062447
TIRAP, another TLR4 adapter protein appears to be involved in the activation of interferon regulatory factor 3 (IRF3), a transcription factor, which induces the type I interferon gene, and further evidence suggests that this activation is mediated by a double-stranded RNA responsive protein kinase (PKR).
 </csml:comment>
</csml:comments>
</csml:process>
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PMID: 17405910
Phosphorylated I-kappaB is ubiquitinated and degraded by the 26S proteosome, leaving the p65-p50 dimer (NF-kappaB), which is now free to translocate to the nucleus.</csml:comment>
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PMID: 17405910
Apart from MyD88 and TIRAP, additional TLR4 adapter proteins have been identified.</csml:comment>
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</csml:comment>
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PMID: 17405910, 12062447, 15029200, 16006187
TIRAP, another TLR4 adapter protein appears to be involved in the activation of interferon regulatory factor 3 (IRF3), a transcription factor, which induces the type I interferon gene, and further evidence suggests that this activation is mediated by a double-stranded RNA responsive protein kinase (PKR). 
</csml:comment>
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<csml:comment type="text">

</csml:comment>
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Indirect</csml:comment>
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<csml:comment type="text">

</csml:comment>
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PMID: 17405910, 16006187
TIR domain-containing adapter inducing interferon (TRIF) and TRIF-related adapter molecule (TRAM), both  involved in the activation of IRF3 and IRF7.</csml:comment>
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PMID: 17405910, 9820516
macrophages express several other LPS receptors, for example,
CD11b/CD18</csml:comment>
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PMID: 17405910, 1852209
macrophages express several other LPS receptors, for example,
CD11b/CD18, class A macrophage scavenger receptor (MSR)</csml:comment>
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PMID: 17405910, 1852209
MSR acts as a scavenger for LPS, that is, rather than eliciting a proinflammatory response, the MSR–LPS complex is internalized
and LPS is partially degraded.</csml:comment>
</csml:comments>
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</csml:comment>
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</csml:comment>
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PMID: 17405910, 16021602
NOD-1 and -2 agonists also act in synergy with LPS to stimulate cytokine production.</csml:comment>
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<csml:comment type="text">

</csml:comment>
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<csml:comment type="text">

</csml:comment>
</csml:comments>
</csml:connector>
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<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="337.0" y="125.0"/>
<csml:shape shapeID="default" visible="true">
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<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_Binding" refCellComponentID="cso30:i:CC_Extracellular"/>
<csml:comments>
<csml:comment type="text">

PMID: 17405910, 15275964
Cationic proteins, e.g., protamines and CAP37, associate with LPS and bind to
cellular surfaces.</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p38" name="p38" type="cso30:c:ProcessBiological">
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
</csml:connector>
<csml:connector id="c120" name="c120" refID="e91" type="cso30:c:OutputProcess">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
<csml:parameter key="stoichiometry" value="1"/>
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</csml:connectorSimulationProperty>
<csml:viewProperty>
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</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
</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="253.0" y="53.0"/>
<csml:shape shapeID="default" visible="true">
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<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_Binding" refCellComponentID="cso30:i:CC_Extracellular"/>
<csml:comments>
<csml:comment type="text">

PMID: 17405910
Heparin exerts its anticoagulant effect through binding to AT III and thrombin. Apart from its interaction with
proteins of the coagulation pathway, heparin binds to LBP and displaces LPS</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p39" name="p39" type="cso30:c:ProcessBiological">
<csml:connector id="c121" name="c121" refID="e12" type="cso30:c:InputProcess">
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<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="83.0208260313957" y="126.0"/>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
</csml:connector>
<csml:connector id="c122" name="c122" refID="e92" type="cso30:c:InputProcess">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
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</csml:connectorSimulationProperty>
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</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
</csml:connector>
<csml:connector id="c123" name="c123" refID="e93" type="cso30:c:OutputProcess">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
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</csml:connectorKinetic>
</csml:connectorSimulationProperty>
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</csml:toolSpecificGraphics>
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</csml:viewProperty>
<csml:comments>
<csml:comment type="text">

</csml:comment>
</csml:comments>
</csml:connector>
<csml:connector id="c66" name="c66" refID="e11" 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>
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</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="65.0" y="297.0"/>
<csml:shape shapeID="default" visible="true">
<csml:image fileFormat="svg" filePath="" fileType="resourceFile" height="30.0" outlineColor="0 0 0 0" resourceID="10005" width="30.0"/>
<csml:toolSpecificGraphics/>
</csml:shape>
</csml:viewProperty>
<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_Binding" refCellComponentID="cso30:i:CC_Extracellular"/>
<csml:comments>
<csml:comment type="text">

PMID: 17405910, 14550561
LPS is bound and neutralized by poly-L-histidine.</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p40" name="p12" type="cso30:c:ProcessBiological">
<csml:connector id="c125" name="c125" refID="e31" type="cso30:c:InputProcess">
<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="941.0" y="498.0"/>
<csml:shape shapeID="default" visible="true">
<csml:toolSpecificGraphics>
<figure xmlns="http://www.csml.org/csml/cigraphics">
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</csml:connector>
<csml:connector id="c127" name="c127" refID="e24" type="cso30:c:InputAssociation">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
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</csml:connectorKinetic>
</csml:connectorSimulationProperty>
<csml:viewProperty>
<csml:position position="auto" positionID="default" x="978.3861999450876" y="497.0"/>
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<figure xmlns="http://www.csml.org/csml/cigraphics">
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</csml:connector>
<csml:connector id="c126" name="c126" refID="e32" type="cso30:c:OutputProcess">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
<csml:parameter key="stoichiometry" value="1"/>
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</csml:connectorSimulationProperty>
<csml:viewProperty>
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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="957.0" y="529.0"/>
<csml:shape shapeID="default" visible="true">
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<csml:toolSpecificGraphics/>
</csml:shape>
</csml:viewProperty>
<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_UnknownActivation" refCellComponentID="cso30:i:CC_Cytosol"/>
<csml:comments>
<csml:comment type="text">PMID: 17405910, 9564042
ASK1 can only be activated by TRAF6 if the associated thioredoxin (TrX) is displaced from TRAF6.</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p41" name="p15" type="cso30:c:ProcessBiological">
<csml:connector id="c44" name="c44" refID="e34" 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>
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</csml:toolSpecificGraphics>
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</csml:viewProperty>
</csml:connector>
<csml:connector id="c84" name="c84" refID="e27" type="cso30:c:InputProcess">
<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
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</csml:connectorKinetic>
</csml:connectorSimulationProperty>
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</csml:connector>
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<csml:connectorSimulationProperty>
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</csml:viewProperty>
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<csml:processSimulationProperty>
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<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="869.0" y="693.0"/>
<csml:shape shapeID="default" visible="true">
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</csml:viewProperty>
<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_UnknownActivation" refCellComponentID="cso30:i:CC_Cytosol"/>
<csml:comments>
<csml:comment type="text">

PMID: 17405910
MAP3K family (T1, TAK1; M3, MEKK3; A1, ASK1) which, in turn, activate Jnk (J), IKK (I), and p38 (p).</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p42" name="p15" type="cso30:c:ProcessBiological">
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<csml:connectorSimulationProperty>
<csml:connectorFiring connectorFiringStyle="csml-connectorFiringStyle:threshold" value="0"/>
<csml:connectorKinetic>
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<csml:viewProperty>
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</csml:connector>
<csml:connector id="c129" name="c129" refID="e27" type="cso30:c:InputProcess">
<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="933.6064078549882" y="698.0"/>
<csml:shape shapeID="default" visible="true">
<csml:toolSpecificGraphics>
<figure xmlns="http://www.csml.org/csml/cigraphics">
<processConnector depth="0" points="968.0 698.0 933.6064078549882 721.4883068307397" visible="true"/>
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<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<processConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="935.2982927934609 723.9657097763603 931.9145229165157 719.0109038851191 927.0 726.0" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
</csml:connector>
<csml:connector id="c130" name="c130" refID="e36" 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="822.3577934305443" y="697.1405215862079"/>
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</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="897.0" y="721.0"/>
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<csml:toolSpecificGraphics/>
</csml:shape>
</csml:viewProperty>
<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_UnknownActivation" refCellComponentID="cso30:i:CC_Cytosol"/>
<csml:comments>
<csml:comment type="text">

PMID: 17405910
MAP3K family (T1, TAK1; M3, MEKK3; A1, ASK1) which, in turn, activate Jnk (J), IKK (I), and p38 (p).</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p43" name="p15" type="cso30:c:ProcessBiological">
<csml:connector id="c47" name="c47" refID="e34" 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="862.0" y="646.0"/>
<csml:shape shapeID="default" visible="true">
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<figure xmlns="http://www.csml.org/csml/cigraphics">
<associationConnector depth="0" points="862.0 646.0 880.9762292989584 793.0657770669278" visible="true"/>
</figure>
<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
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</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
</csml:connector>
<csml:connector id="c131" name="c131" refID="e28" type="cso30:c:InputProcess">
<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="906.7611400011626" y="796.0"/>
<csml:shape shapeID="default" visible="true">
<csml:toolSpecificGraphics>
<figure xmlns="http://www.csml.org/csml/cigraphics">
<processConnector depth="0" points="963.0 796.0 906.7611400011626 810.0597149997093" visible="true"/>
</figure>
<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<processConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="907.4887468762716 812.9701425001452 906.0335331260536 807.1492874992732 899.0 811.9999999999999" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
</csml:connector>
<csml:connector id="c132" name="c132" refID="e37" 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="814.7462185896749" y="797.9990241521741"/>
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<figure xmlns="http://www.csml.org/csml/cigraphics">
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<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<processConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="813.9965845326095 800.9038561233021 815.4958526467401 795.094192181046 807.0 795.9999999999999" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</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="869.0" y="801.0"/>
<csml:shape shapeID="default" visible="true">
<csml:image fileFormat="svg" filePath="" fileType="resourceFile" height="30.0" outlineColor="0 0 0 0" resourceID="10003" width="30.0"/>
<csml:toolSpecificGraphics/>
</csml:shape>
</csml:viewProperty>
<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_UnknownActivation" refCellComponentID="cso30:i:CC_Cytosol"/>
<csml:comments>
<csml:comment type="text">

PMID: 17405910
MAP3K family (T1, TAK1; M3, MEKK3; A1, ASK1) which, in turn, activate Jnk (J), IKK (I), and p38 (p).</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p44" name="p15" type="cso30:c:ProcessBiological">
<csml:connector id="c48" name="c48" refID="e32" 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="907.0183849426446" y="642.0"/>
<csml:shape shapeID="default" visible="true">
<csml:toolSpecificGraphics>
<figure xmlns="http://www.csml.org/csml/cigraphics">
<associationConnector depth="0" points="930.0 642.0 907.0183849426446 821.0650839885608" visible="true"/>
</figure>
<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<associationConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="909.9939784469343 821.4469783420525 904.0427914383549 820.6831896350691 906.0 829.0" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
</csml:connector>
<csml:connector id="c133" name="c133" refID="e28" type="cso30:c:InputProcess">
<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="925.5398594650478" y="803.0"/>
<csml:shape shapeID="default" visible="true">
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<figure xmlns="http://www.csml.org/csml/cigraphics">
<processConnector depth="0" points="963.0 803.0 925.5398594650478 829.3923717405345" visible="true"/>
</figure>
<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<processConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="927.2677200623474 831.8448190399274 923.8119988677482 826.9399244411416 919.0 834.0" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
</csml:connector>
<csml:connector id="c134" name="c134" refID="e37" 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="814.2584848522703" y="802.3636881022716"/>
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<figure xmlns="http://www.csml.org/csml/cigraphics">
<processConnector depth="0" points="889.0 837.0 814.2584848522703 802.3636881022716" visible="true"/>
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<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<processConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="812.9971018139184 805.0856199218729 815.5198678906221 799.6417562826701 807.0 799.0" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</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="889.0" y="829.0"/>
<csml:shape shapeID="default" visible="true">
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<csml:toolSpecificGraphics/>
</csml:shape>
</csml:viewProperty>
<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_UnknownActivation" refCellComponentID="cso30:i:CC_Cytosol"/>
<csml:comments>
<csml:comment type="text">

PMID: 17405910
MAP3K family (T1, TAK1; M3, MEKK3; A1, ASK1) which, in turn, activate Jnk (J), IKK (I), and p38 (p).</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p45" name="p15" type="cso30:c:ProcessBiological">
<csml:connector id="c50" name="c50" refID="e34" 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="861.0" y="646.0"/>
<csml:shape shapeID="default" visible="true">
<csml:toolSpecificGraphics>
<figure xmlns="http://www.csml.org/csml/cigraphics">
<associationConnector depth="0" points="861.0 646.0 886.2246412896499 905.0376624744813" visible="true"/>
</figure>
<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<associationConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="889.2105178617194 904.7469029581 883.2387647175804 905.3284219908626 887.0 913.0000000000001" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
</csml:connector>
<csml:connector id="c135" name="c135" refID="e35" type="cso30:c:InputProcess">
<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="910.6048436519278" y="907.0"/>
<csml:shape shapeID="default" visible="true">
<csml:toolSpecificGraphics>
<figure xmlns="http://www.csml.org/csml/cigraphics">
<processConnector depth="0" points="952.0 907.0 910.6048436519278 920.5167857463093" visible="true"/>
</figure>
<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<processConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="911.5360489970618 923.3686021157822 909.6736383067938 917.6649693768363 903.0 923.0" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
</csml:connector>
<csml:connector id="c136" name="c136" refID="e38" 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="824.6550446131422" y="908.3238528289896"/>
<csml:shape shapeID="default" visible="true">
<csml:toolSpecificGraphics>
<figure xmlns="http://www.csml.org/csml/cigraphics">
<processConnector depth="0" points="873.0 923.0 824.6550446131422 908.3238528289896" visible="true"/>
</figure>
<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<processConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="823.783599802271 911.194494558918 825.5264894240132 905.4532110990614 817.0 906.0000000000001" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</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="873.0" y="913.0"/>
<csml:shape shapeID="default" visible="true">
<csml:image fileFormat="svg" filePath="" fileType="resourceFile" height="30.0" outlineColor="0 0 0 0" resourceID="10003" width="30.0"/>
<csml:toolSpecificGraphics/>
</csml:shape>
</csml:viewProperty>
<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_UnknownActivation" refCellComponentID="cso30:i:CC_Cytosol"/>
<csml:comments>
<csml:comment type="text">

PMID: 17405910
MAP3K family (T1, TAK1; M3, MEKK3; A1, ASK1) which, in turn, activate Jnk (J), IKK (I), and p38 (p).</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p46" name="p15" type="cso30:c:ProcessBiological">
<csml:connector id="c51" name="c51" refID="e32" 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="913.4807350181795" y="642.0"/>
<csml:shape shapeID="default" visible="true">
<csml:toolSpecificGraphics>
<figure xmlns="http://www.csml.org/csml/cigraphics">
<associationConnector depth="0" points="931.0 642.0 913.4807350181795 933.0144571980175" visible="true"/>
</figure>
<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<associationConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="916.475313568923 933.1947328298348 910.486156467436 932.8341815662002 912.9999999999999 941.0000000000001" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
</csml:connector>
<csml:connector id="c137" name="c137" refID="e35" type="cso30:c:InputProcess">
<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="932.9278956114879" y="913.0"/>
<csml:shape shapeID="default" visible="true">
<csml:toolSpecificGraphics>
<figure xmlns="http://www.csml.org/csml/cigraphics">
<processConnector depth="0" points="959.0 913.0 932.9278956114879 936.6278446020891" visible="true"/>
</figure>
<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<processConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="934.9424538857045 938.8508054563971 930.9133373372713 934.4048837477812 927.0 942.0" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</csml:viewProperty>
</csml:connector>
<csml:connector id="c138" name="c138" refID="e38" 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="824.1910112359551" y="913.5056179775281"/>
<csml:shape shapeID="default" visible="true">
<csml:toolSpecificGraphics>
<figure xmlns="http://www.csml.org/csml/cigraphics">
<processConnector depth="0" points="897.0 949.0 824.1910112359551 913.5056179775281" visible="true"/>
</figure>
<targetArrow xmlns="http://www.csml.org/csml/cigraphics">
<processConnectorArrow points="0.0 0.0 0.0 6.0 8.0 3.0" pointsInAbsoluteCoordinate="822.8764044943821 916.2022471910112 825.5056179775281 910.8089887640449 817.0000000000001 910.0" size="8.0 6.0"/>
</targetArrow>
</csml:toolSpecificGraphics>
</csml:shape>
</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="897.0" y="941.0"/>
<csml:shape shapeID="default" visible="true">
<csml:image fileFormat="svg" filePath="" fileType="resourceFile" height="30.0" outlineColor="0 0 0 0" resourceID="10003" width="30.0"/>
<csml:toolSpecificGraphics/>
</csml:shape>
</csml:viewProperty>
<csml:biologicalProperty refBiologicalEventID="cso30:i:ME_UnknownActivation" refCellComponentID="cso30:i:CC_Cytosol"/>
<csml:comments>
<csml:comment type="text">

PMID: 17405910
MAP3K family (T1, TAK1; M3, MEKK3; A1, ASK1) which, in turn, activate Jnk (J), IKK (I), and p38 (p).</csml:comment>
</csml:comments>
</csml:process>
<csml:process id="p47" name="p24" type="cso30:c:ProcessBiological">
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PMID: 17405910, 15356101
The generation of ROS appears to result from a direct activation of membrane-bound NADPH oxidase 4 by TLR4.</csml:comment>
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PMID: 17405910, 12062447, 12062447
TIRAP, another TLR4 adapter protein appears to be involved in the activation of interferon regulatory factor 3 (IRF3), a transcription factor, which induces the type I interferon gene, and further evidence suggests that this activation is mediated by a double-stranded RNA responsive protein kinase (PKR).
 </csml:comment>
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<csml:comment type="text">PMID: 17405910, 12062447, 15029200, 16006187
TIR domain-containing adapter inducing interferon (TRIF) and TRIF-related adapter molecule (TRAM), both  involved in the activation of IRF3 and IRF7.</csml:comment>
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<csml:comments>
<csml:comment type="text">

</csml:comment>
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