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<model id="M3492" metaid="_45b369b9-e1c1-4cb5-86fd-4f9f0b1db383" name="Bordetella bronchiseptica">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">Co-infections alter the host immune response but how the systemic and local processes at the site of infection interact is still unclear. The majority of studies on co-infections concentrate on one of the infecting species, an immune function or group of cells and often focus on the initial phase of the infection. Here, we used a combination of experiments and mathematical modelling to investigate the network of immune responses against single and co-infections with the respiratory bacterium Bordetella bronchiseptica and the gastrointestinal helminth Trichostrongylus retortaeformis. Our goal was to identify representative mediators and functions that could capture the essence of the host immune response as a whole, and to assess how their relative contribution dynamically changed over time and between single and co-infected individuals. Network-based discrete dynamic models of single infections were built using current knowledge of bacterial and helminth immunology; the two single infection models were combined into a co-infection model that was then verified by our empirical findings. Simulations showed that a T helper cell mediated antibody and neutrophil response led to phagocytosis and clearance of B. bronchiseptica from the lungs. This was consistent in single and co-infection with no significant delay induced by the helminth. In contrast, T. retortaeformis intensity decreased faster when co-infected with the bacterium. Simulations suggested that the robust recruitment of neutrophils in the co-infection, added to the activation of IgG and eosinophil driven reduction of larvae, which also played an important role in single infection, contributed to this fast clearance. Perturbation analysis of the models, through the knockout of individual nodes (immune cells), identified the cells critical to parasite persistence and clearance both in single and co-infections. Our integrated approach captured the within-host immuno-dynamics of bacteria-helminth infection and identified key components that can be crucial for explaining individual variability between single and co-infections in natural populations.</body>
</notes>
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<vCard:Family>Helikar</vCard:Family>
<vCard:Given>Tomas</vCard:Given>
</vCard:N>
<vCard:EMAIL>thelika@unmc.edu</vCard:EMAIL>
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<vCard:Orgname>University of Nebraska - Lincoln</vCard:Orgname>
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<dcterms:W3CDTF>2013-06-16T07:46:41Z</dcterms:W3CDTF>
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<dcterms:W3CDTF>2016-01-22T07:08:46Z</dcterms:W3CDTF>
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Pro-inflammatory cytokines (mouse) for more info:<div>http://www.ncbi.nlm.nih.gov/mesh/68016207</div></p></body>
</notes>
<annotation>
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><font face="Arial, Verdana" size="2">O-antigen (mouse) for more info:</font><div><font face="Arial, Verdana" size="2">http://www.ncbi.nlm.nih.gov/mesh/68019081</font></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>respiratory bacterium&nbsp;Bordetella bronchiseptica&nbsp;</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_14dadb4f-0528-445f-9122-2857658249e2">
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<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">Th2\r\ncells in systemic compartment (mouse) for more info:</span><div><span lang="EN-GB">http://www.ncbi.nlm.nih.gov/mesh/68018418</span></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#b80e95a0-c96b-4b14-9d82-4f96cd8ebba4">
<dcterms:modified rdf:parseType="Resource">
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<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
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<qual:qualitativeSpecies metaid="e517b0bf-8542-4475-b2bb-9f23e1deef95" qual:compartment="cytosol" qual:constant="false" qual:id="S_5" qual:initialLevel="0" qual:maxLevel="1" qual:name="DCI">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><font face="Arial, Verdana" size="2">Dendritic cells in lungs/small intestine, for more info:</font><div><font face="Arial, Verdana" size="2">http://www.ncbi.nlm.nih.gov/mesh/68003713</font></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#e517b0bf-8542-4475-b2bb-9f23e1deef95">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
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<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">T\r\nregulatory cells in systemic compartment (mouse) for more info:</span><div><span lang="EN-GB">http://www.ncbi.nlm.nih.gov/mesh/68050378</span></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_515e5bf2-c237-4d05-877d-062e983170a3">
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<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
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</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="f8d8ec71-1f9d-4abe-be9f-d8c46f285738" qual:compartment="cytosol" qual:constant="false" qual:id="S_7" qual:initialLevel="0" qual:maxLevel="1" qual:name="IgA">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Antibody A (mouse)</p></body>
</notes>
<annotation>
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<rdf:Description rdf:about="#f8d8ec71-1f9d-4abe-be9f-d8c46f285738">
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<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:17591791"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:12654784"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:14971044"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="ad935c33-3005-45de-9f09-7813ca42fef5" qual:compartment="cytosol" qual:constant="false" qual:id="S_8" qual:initialLevel="0" qual:maxLevel="1" qual:name="TTSSII">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">Type\r\nthree secretion system in systemic compartment (mouse)</span></p></body>
</notes>
<annotation>
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<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
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</rdf:RDF>
</annotation>
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<qual:qualitativeSpecies metaid="e40010f6-c40b-410e-987b-bd8d97754e44" qual:compartment="cytosol" qual:constant="false" qual:id="S_9" qual:initialLevel="0" qual:maxLevel="1" qual:name="AgAb">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Antigen-antibody complexes</p></body>
</notes>
<annotation>
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Interleukin 4 in the small intestines/lungs (mouse)<div>UniProt AccessionID:&nbsp;<a href="http://www.uniprot.org/uniprot/P07750" style="font-size: small; text-decoration: none; font-family: sans-serif; background-color: rgb(255, 255, 255);">P07750</a></div></p></body>
</notes>
<annotation>
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<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
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</annotation>
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<qual:qualitativeSpecies metaid="bfb2b86f-5b29-4305-8826-de9c8836c786" qual:compartment="cytosol" qual:constant="false" qual:id="S_11" qual:initialLevel="0" qual:maxLevel="1" qual:name="IgG">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Antibody G (mouse)</p></body>
</notes>
<annotation>
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<rdf:li rdf:resource="urn:miriam:pubmed:17591791"/>
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<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:12654784"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:14971044"/>
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</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
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<qual:qualitativeSpecies metaid="_13b155a4-808f-4e68-b8d3-c505dfc3c874" qual:compartment="cytosol" qual:constant="false" qual:id="S_12" qual:initialLevel="0" qual:maxLevel="1" qual:name="IL4II">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">Interleukin\r\n4 in systemic compartment (mouse)</span><div><span lang="EN-GB">UniProt AccessionID:&nbsp;</span><a href="http://www.uniprot.org/uniprot/P07750" style="text-decoration: none; font-family: sans-serif; font-size: small; background-color: rgb(255, 255, 255);">P07750</a></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_13b155a4-808f-4e68-b8d3-c505dfc3c874">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
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</annotation>
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<qual:qualitativeSpecies metaid="_74e4fdff-ebdf-4947-9619-dc97634dad8d" qual:compartment="cytosol" qual:constant="false" qual:id="S_13" qual:initialLevel="0" qual:maxLevel="1" qual:name="Th1I">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">T\r\nhelper cells subtype I in lungs/small intestine (mouse)&nbsp;</span></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_74e4fdff-ebdf-4947-9619-dc97634dad8d">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_78fa4847-dbee-4f78-abb8-1f457bb1a545" qual:compartment="cytosol" qual:constant="false" qual:id="S_14" qual:initialLevel="0" qual:maxLevel="1" qual:name="MPI">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><font face="Arial, Verdana" size="2">Macrophages in the lungs (mouse) for more info:</font><div><font face="Arial, Verdana" size="2">http://www.ncbi.nlm.nih.gov/mesh/68008264</font><br/><div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><br/></div></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
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<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_6ffb26cf-b35e-4db9-840a-dbf25a4d593e" qual:compartment="cytosol" qual:constant="false" qual:id="S_15" qual:initialLevel="0" qual:maxLevel="1" qual:name="IL10II">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">Interleukin\r\n10 in systemic compartment (mouse)</span><div><span lang="EN-GB">UniProt AccessionID:&nbsp;</span><a href="http://www.uniprot.org/uniprot/P18893" style="text-decoration: none; font-family: sans-serif; font-size: small; background-color: rgb(255, 255, 255);">P18893</a></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_6ffb26cf-b35e-4db9-840a-dbf25a4d593e">
<dcterms:modified rdf:parseType="Resource">
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<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
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<qual:qualitativeSpecies metaid="_07a2ceb4-0440-4c34-ad4e-31f1358e3974" qual:compartment="cytosol" qual:constant="false" qual:id="S_16" qual:initialLevel="0" qual:maxLevel="1" qual:name="IL12I">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Interleukin 12 in lungs/intestine (mouse)</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_07a2ceb4-0440-4c34-ad4e-31f1358e3974">
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<rdf:Bag>
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<qual:qualitativeSpecies metaid="_914601df-f927-457c-9595-dff5284f537f" qual:compartment="cytosol" qual:constant="false" qual:id="S_17" qual:initialLevel="0" qual:maxLevel="1" qual:name="IL10I">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">Interleukin\r\n10 in lungs/small intestine (mouse)</span><div><span lang="EN-GB">UniProt AccessionID:&nbsp;</span><a href="http://www.uniprot.org/uniprot/P18893" style="font-size: small; text-decoration: none; font-family: sans-serif; background-color: rgb(255, 255, 255);">P18893</a></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_914601df-f927-457c-9595-dff5284f537f">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
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<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
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<qual:qualitativeSpecies metaid="ab7a0af3-f01a-4181-a034-0eab6dce96ce" qual:compartment="cytosol" qual:constant="false" qual:id="S_18" qual:initialLevel="0" qual:maxLevel="1" qual:name="NE">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB" style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">Recruited\r\nneutrophils (mouse) for more info:</span><div><span lang="EN-GB"><font face="Arial, Verdana" size="2">http://www.ncbi.nlm.nih.gov/mesh/68009504</font></span></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#ab7a0af3-f01a-4181-a034-0eab6dce96ce">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
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<qual:qualitativeSpecies metaid="e2f65584-2f29-49a6-86ca-3544c7a72c0b" qual:compartment="cytosol" qual:constant="false" qual:id="S_19" qual:initialLevel="0" qual:maxLevel="1" qual:name="Th1II">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">T\r\nhelper cells subtype I in systemic compartment (mouse)</span></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#e2f65584-2f29-49a6-86ca-3544c7a72c0b">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_117145d4-c648-4084-8dea-e995814acb8f" qual:compartment="cytosol" qual:constant="false" qual:id="S_20" qual:initialLevel="0" qual:maxLevel="1" qual:name="IFNgI">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Interferon gamma in lungs/small intestine (mouse)</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_117145d4-c648-4084-8dea-e995814acb8f">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:16428751"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:12654784"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:14971044"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_7187c556-ca5e-4a35-adac-7e63bd5f614d" qual:compartment="cytosol" qual:constant="false" qual:id="S_21" qual:initialLevel="0" qual:maxLevel="1" qual:name="EC">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><font face="Arial, Verdana" size="2">Epithelial cells in lung/intestine (mouse) for more info:</font><div><font face="Arial, Verdana" size="2">http://www.ncbi.nlm.nih.gov/mesh/68004847</font></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_7187c556-ca5e-4a35-adac-7e63bd5f614d">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_6a7ace8c-653b-4cd7-b31a-811944ddcaa7" qual:compartment="cytosol" qual:constant="false" qual:id="S_22" qual:initialLevel="0" qual:maxLevel="1" qual:name="C">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><font face="Arial, Verdana" size="2">Complement cascade for more info:</font><div><font face="Arial, Verdana" size="2">http://www.ncbi.nlm.nih.gov/mesh/?term=complement+cascade</font></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_6a7ace8c-653b-4cd7-b31a-811944ddcaa7">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="f932f552-0064-45b3-99f3-c5b606079a9c" qual:compartment="cytosol" qual:constant="false" qual:id="S_23" qual:initialLevel="0" qual:maxLevel="1" qual:name="DP">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Referred to as DNE (dead neutrophils) in Thakar et. al paper</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#f932f552-0064-45b3-99f3-c5b606079a9c">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="d3e5bb7e-01a5-46e2-b7f3-7429d3e19939" qual:compartment="cytosol" qual:constant="false" qual:id="S_24" qual:initialLevel="0" qual:maxLevel="1" qual:name="DCII">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Dendritic cells in the systemic compartment, more info:<div>http://www.ncbi.nlm.nih.gov/mesh/68003713</div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#d3e5bb7e-01a5-46e2-b7f3-7429d3e19939">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_0b16d3e5-4b72-4e81-b642-13a676a2e0d6" qual:compartment="cytosol" qual:constant="false" qual:id="S_25" qual:initialLevel="0" qual:maxLevel="1" qual:name="BC">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><font face="Arial, Verdana" size="2">B-Lymphocytes. See link:</font><div><font face="Arial, Verdana" size="2">http://www.ncbi.nlm.nih.gov/mesh/68001402</font></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_0b16d3e5-4b72-4e81-b642-13a676a2e0d6">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="ef2f0c27-323e-47d0-aeee-e7c268b028a3" qual:compartment="cytosol" qual:constant="false" qual:id="S_26" qual:initialLevel="0" qual:maxLevel="1" qual:name="T0">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Naive T cells (mouse)</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#ef2f0c27-323e-47d0-aeee-e7c268b028a3">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_83fea7db-486a-433d-ba1e-76f220d08cb0" qual:compartment="cytosol" qual:constant="false" qual:id="S_27" qual:initialLevel="0" qual:maxLevel="1" qual:name="AP">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Activated phagocytes</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_83fea7db-486a-433d-ba1e-76f220d08cb0">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_2f09a914-9874-49cb-8781-9e5758d4f767" qual:compartment="cytosol" qual:constant="false" qual:id="S_28" qual:initialLevel="0" qual:maxLevel="1" qual:name="TTSSI">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Type three secretion system in the lungs (mouse)</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_2f09a914-9874-49cb-8781-9e5758d4f767">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_5def2d8b-6294-4828-8a90-826630aeca13" qual:compartment="cytosol" qual:constant="false" qual:id="S_29" qual:initialLevel="0" qual:maxLevel="1" qual:name="TrI">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">T\r\nregulatory cells in lungs/small intestine (mouse) for more info:</span><div><span lang="EN-GB">http://www.ncbi.nlm.nih.gov/mesh/68050378</span></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_5def2d8b-6294-4828-8a90-826630aeca13">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_4fe5013b-025e-4bea-9313-7a712f397dee" qual:compartment="cytosol" qual:constant="false" qual:id="S_30" qual:initialLevel="0" qual:maxLevel="1" qual:name="IFNgII">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="font-family: arial, sans-serif; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: 18.0049991607666px; color: rgb(51, 51, 51); background-color: rgb(255, 255, 255);">Interferon gamma in systemic compartment (mouse) more info:</span><div><span style="background-color: rgb(255, 255, 255); line-height: 18.0049991607666px;"><font color="#333333" face="arial, sans-serif" size="2">http://www.ncbi.nlm.nih.gov/mesh/68007371</font></span></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_4fe5013b-025e-4bea-9313-7a712f397dee">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_49980c0b-1bee-4e46-991c-7d5232038171" qual:compartment="cytosol" qual:constant="false" qual:id="S_31" qual:initialLevel="0" qual:maxLevel="1" qual:name="Th2I">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB" style="font-size:12.0pt;line-height:\r\n115%;font-family:"Times New Roman","serif";mso-fareast-font-family:"Times New Roman";\r\nmso-ansi-language:EN-GB;mso-fareast-language:EN-US;mso-bidi-language:AR-SA">Th2\r\ncells in lungs/small intestine (mouse)</span></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_49980c0b-1bee-4e46-991c-7d5232038171">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="bc562e2c-8f6c-46c0-8fe5-ba45497cd81a" qual:compartment="cytosol" qual:constant="false" qual:id="S_32" qual:initialLevel="0" qual:maxLevel="1" qual:name="PH">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Represents pH<div><br/></div><div>Phagocytosis (mouse) in coninfection for more info:</div><div>http://www.ncbi.nlm.nih.gov/mesh/68010587</div><div><hr/></div><div><br/></div><div>PH protein in the Drosophila segmentation model (2013)</div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#bc562e2c-8f6c-46c0-8fe5-ba45497cd81a">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
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</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="b912d04d-b24c-4513-80b3-9554ffd213cc" qual:compartment="cytosol" qual:constant="false" qual:id="S_33" qual:initialLevel="0" qual:maxLevel="1" qual:name="IL12II">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">Interleukin\r\n12 in systemic compartment (mouse)</span></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#b912d04d-b24c-4513-80b3-9554ffd213cc">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-12-19T22:12:58Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:22253585"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
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<qual:listOfTransitions xmlns:qual="http://www.sbml.org/sbml/level3/version1/qual/version1">
<qual:transition qual:id="tr_S_1">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>EC positively regulates PIC [1]. DP positively regulates PIC [1]. AP activates PIC [1]. IL10I negatively regulates PIC [1].</div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_1_in_S_27" qual:qualitativeSpecies="S_27" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">AP activates PIC [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_1_in_S_21" qual:qualitativeSpecies="S_21" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"Upon detection, epithelial cells activate pro-inflammatory cytokines" [1]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_1_in_S_23" qual:qualitativeSpecies="S_23" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">DP activates PIC [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_1_in_S_17" qual:qualitativeSpecies="S_17" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">IL10I negatively regulates PIC [1]</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_1" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_23 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_2">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb positively regulates Oag [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_2_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb positively regulates Oag [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_2" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_3">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb self regulates. PH negatively regulates Bb [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_3_in_S_32" qual:qualitativeSpecies="S_32" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PH negatively regulates Bb [1].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_3_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb positively regulates itself [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_3" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_32 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_4">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>DCII in conjunction with T0 activates Th2II [1]. IL12II inhibites Th2II [1].</div><div><p class="MsoNormal" style="margin-bottom: 0.0001pt;"><br/></p></div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_4_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCII in conjunction with T0 activates Th2II [1].&nbsp;</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_4_in_S_33" qual:qualitativeSpecies="S_33" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>IL12II inhibites Th2II [1].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_4_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCII in conjunction with T0 activates Th2II [1].&nbsp;</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_4" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_5">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>Bb in conjunction with IFNgI activates DCI [1]. Bb in conjunction with PIC positively regulates DCI [1].</div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_5_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">Bb in conjunction with IFNgI activates DCI [1]. Bb in conjunction with PIC positively regulates DCI [1].</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_5_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">Bb in conjunction with IFNgI activates DCI [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_5_in_S_1" qual:qualitativeSpecies="S_1" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">Bb in conjunction with PIC positively regulates DCI [1].</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_5" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_6">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCII in conjunction with T0 positively regulate TrII [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_6_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCII in conjunction with T0 positively regulate TrII [1]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_6_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCII in conjunction with T0 positively regulate TrII [1]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_6" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_7">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>Bb in conjunction with BC positively regulates IgA [1,2,3,4].&nbsp;Bb in conjunction with IgA positively regulates IgA [1].</div><div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><br/></div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_7_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">Bb in conjunction with IgA positively regulates IgA [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_7_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb in conjunction with BC positively regulates IgA [1,2,3,4].&nbsp;<div>Bb in conjunction with IgA positively regulates IgA [1].</div></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_7_in_S_25" qual:qualitativeSpecies="S_25" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"<span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">Activation of B cells by T helper cells led to the prompt increase of peripheral antibodies (serum IgG and IgA)</span>" [1,2,3,4]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_7" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_8">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>TTSSI positively regulates TTSSII [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_8_in_S_28" qual:qualitativeSpecies="S_28" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>TTSSI positively regulates TTSSII [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_8" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_9">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB" style="font-size:12.0pt;line-height:\r\n115%;font-family:&quot;Times New Roman&quot;,&quot;serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;;\r\nmso-ansi-language:EN-GB;mso-fareast-language:EN-US;mso-bidi-language:AR-SA">Bb positively regulates AgAb in conjunction with IgG [1]. &nbsp;</span><span style="font-family: 'Times New Roman', serif; font-size: 16px; line-height: 18.399999618530273px;">Bb positively regulates AgAb in conjunction with IgA [1].&nbsp;</span></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_9_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="font-family: 'Times New Roman', serif; font-size: 16px; line-height: 18.399999618530273px;">Bb positively regulates AgAb in conjunction with IgA [1].</span><span style="font-family: 'Times New Roman', serif; font-size: 16px; line-height: 18.399999618530273px;">&nbsp;</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_9_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="font-family: 'Times New Roman', serif; font-size: 16px; line-height: 18.399999618530273px;">Bb positively regulates AgAb in conjunction with IgA [1].</span><span style="font-family: 'Times New Roman', serif; font-size: 16px; line-height: 18.399999618530273px;">&nbsp;</span><div><span style="font-family: 'Times New Roman', serif; font-size: 16px; line-height: 18.399999618530273px;">Bb positively regulates AgAb in conjunction with IgG [1].</span><span style="font-family: 'Times New Roman', serif; font-size: 16px; line-height: 18.399999618530273px;">&nbsp;</span></div></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_9_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="font-family: 'Times New Roman', serif; font-size: 16px; line-height: 18.399999618530273px;">Bb positively regulates AgAb in conjunction with IgG [1].</span><span style="font-family: 'Times New Roman', serif; font-size: 16px; line-height: 18.399999618530273px;">&nbsp;</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_9" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_10">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>IL4II positively regulates IL4I [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_10_in_S_12" qual:qualitativeSpecies="S_12" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>IL4II positively regulates IL4I [1]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_10" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_12 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_11">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BC positively regulates IgG [1,2,3,4]. IgG positively regulates itself [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_11_in_S_25" qual:qualitativeSpecies="S_25" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span lang="EN-GB">Activation of B cells by T helper cells led to\r\nthe prompt increase of peripheral antibodies (serum IgG and IgA) [1,2,3,4]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_11_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 18px; orphans: 3; widows: 3; background-color: rgb(255, 255, 255);">IgG positively regulates itself [1]</span></p></body>
</notes>
</qual:input>
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<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_11" qual:transitionEffect="assignmentLevel"/>
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<ci> S_25 </ci>
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<qual:transition qual:id="tr_S_12">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>DCII in conjunction with T0 positively regulates IL4II [1]. Th2II positively regulates IL4II [1]. IL12II negatively regulates IL4II [1]. IFNgII negatively regulates IL4II [1].</div><div><br/></div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_12_in_S_30" qual:qualitativeSpecies="S_30" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">IFNgII negatively regulates IL4II [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_12_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">&nbsp;"Dendritic cells induce differentiation of naïve T cells (T0) by producing IL4" [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_12_in_S_4" qual:qualitativeSpecies="S_4" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">"IL4 is also produced by differentiated Th2 cells" [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_12_in_S_33" qual:qualitativeSpecies="S_33" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">"IL4 and IL12 inhibit each other" [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_12_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">&nbsp;"Dendritic cells induce differentiation of naïve T cells (T0) by producing IL4" [1]</span></p></body>
</notes>
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<qual:output qual:qualitativeSpecies="S_12" qual:transitionEffect="assignmentLevel"/>
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<qual:transition qual:id="tr_S_13">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Th1II positively regulates Th1I [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_13_in_S_19" qual:qualitativeSpecies="S_19" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Th1II positively regulates Th1I [1]</p></body>
</notes>
</qual:input>
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<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_13" qual:transitionEffect="assignmentLevel"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
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<qual:transition qual:id="tr_S_14">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>Bb in combination with PIC activates MPI [1]. Bb in combination with IFNgI activates MPI [1].&nbsp;</div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_14_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb in combination with PIC activates MPI [1].<div>Bb in combination with IFNgI activates MPI [1].&nbsp;</div></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_14_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"macrophages were recruited by IFN? secreted by Th1 cells" [1]<div><br/></div><div>Bb in combination with IFNgI activates MPI [1].</div></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_14_in_S_1" qual:qualitativeSpecies="S_1" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb in combination with PIC activates MPI [1].&nbsp;</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_14" qual:transitionEffect="assignmentLevel"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
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<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
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<apply>
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<apply>
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<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
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<ci> S_3 </ci>
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<qual:transition qual:id="tr_S_15">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>IL10I positively regulates Il10II [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_15_in_S_17" qual:qualitativeSpecies="S_17" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>IL10I positively regulates Il10II [1]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_15" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
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</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
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</qual:transition>
<qual:transition qual:id="tr_S_16">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>DCII in conjunction with T0 positively regulates IL12I [1]. IL4II negatively regulates IL12I [1].</div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_16_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">DCII in conjunction with T0 positively regulates IL12I [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_16_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">DCII in conjunction with T0 positively regulates IL12I [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_16_in_S_12" qual:qualitativeSpecies="S_12" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>IL4II inhibits IL12I [1]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_16" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_12 </ci>
<cn type="integer"> 1 </cn>
</apply>
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<qual:transition qual:id="tr_S_17">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>Th2I in conjunction with TTSSI positively regulates IL10I [1]. TrI positively regulates IL10I [1]. MPI positively regulates IL10I [1].</div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_17_in_S_29" qual:qualitativeSpecies="S_29" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><font color="#333333" face="arial, sans-serif"><span style="line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">"</span></font><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">T regulatory (Treg) cells are stimulated by the type III secretion system of&nbsp;</span><em style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">B. bronchiseptica</em><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">&nbsp;to produce IL10" [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_17_in_S_28" qual:qualitativeSpecies="S_28" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">Th2I in conjunction with TTSSI positively regulates IL10I [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_17_in_S_14" qual:qualitativeSpecies="S_14" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">MPI positively regulates IL10I [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_17_in_S_31" qual:qualitativeSpecies="S_31" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">Th2I in conjunction with TTSSI positively regulates IL10I [1]</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_17" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_29 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_14 </ci>
<cn type="integer"> 1 </cn>
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</apply>
<apply>
<and/>
<apply>
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<ci> S_31 </ci>
<cn type="integer"> 1 </cn>
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<apply>
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<ci> S_28 </ci>
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</apply>
</apply>
</apply>
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</qual:transition>
<qual:transition qual:id="tr_S_18">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PIC positively regulates NE [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_18_in_S_1" qual:qualitativeSpecies="S_1" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"<span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">The rapid recruitment of peripheral neutrophils to the lungs was possible through pro-inflammatory cytokine mediated signalling" [1]</span></p></body>
</notes>
</qual:input>
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<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_18" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
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</qual:transition>
<qual:transition qual:id="tr_S_19">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>DCII in conjuction with T0 and Il12II positively regulates Th1II [1].&nbsp;</div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_19_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCII in conjuction with T0 and Il12II positively regulates Th1II [1]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_19_in_S_33" qual:qualitativeSpecies="S_33" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCII in conjuction with T0 and Il12II positively regulates Th1II [1]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_19_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCII in conjuction with T0 and Il12II positively regulates Th1II [1]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_19" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
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</qual:transition>
<qual:transition qual:id="tr_S_20">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><p class="MsoNormal" style="margin-bottom: 0.0001pt;"><span lang="EN-GB">Th1I positively regulates IFNgI, while IL10I negatively regulates IFNgI and is dominant over Th1I activity [1]. MPI positively regulates IFNgI [1]. DCI positively regulates IFNgI [1]. IL4I negatively regulates IFNgI [1].</span></p></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_20_in_S_10" qual:qualitativeSpecies="S_10" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 18px; orphans: 3; widows: 3; background-color: rgb(255, 255, 255);">IL4I negatively regulates IFNgI [1].</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_20_in_S_13" qual:qualitativeSpecies="S_13" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">"hosts successfully counteract the pathogen mediated inhibitions by activating a protective Th1 cell mediated IFN? response" [1,2,3,4]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_20_in_S_5" qual:qualitativeSpecies="S_5" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 18px; orphans: 3; widows: 3; background-color: rgb(255, 255, 255);">&nbsp;DCI positively regulates IFNgI [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_20_in_S_17" qual:qualitativeSpecies="S_17" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><em style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">B. bronchiseptica</em><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">&nbsp;has been suggested to induce IL10 production by T cell subtypes, which inhibits IFN? in the lower respiratory tract [1,2]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_20_in_S_14" qual:qualitativeSpecies="S_14" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 18px; orphans: 3; widows: 3; background-color: rgb(255, 255, 255);">MPI positively regulates IFNgI [1]</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_20" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_14 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_13 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_21">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb positively regulates EC [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_21_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>B. brontiseptica activates EC [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_21" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_22">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>AgAb in conjunction with IgG positively regulates C [1]. Oag negatively regulates C [1]. Bb positively regulates C [1].</div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_22_in_S_9" qual:qualitativeSpecies="S_9" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">AgAb in conjunction with IgG positively regulates C [1].</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_22_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; line-height: 18.0049991607666px; background-color: rgb(255, 255, 255);">Activation of complement by bacteria is inhibited by O-antigen [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_22_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Oag negatively regulates C, with dominance over positive regulator Bb [1].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_22_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">AgAb in conjunction with IgG positively regulates C [1].</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_22" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_23">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>NE in conjuction with TTSSI positively regulate DP (DNE) [1].</div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_23_in_S_18" qual:qualitativeSpecies="S_18" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>NE in conjuction with TTSSI positively regulate DP (DNE) [1].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_23_in_S_28" qual:qualitativeSpecies="S_28" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>NE in conjuction with TTSSI positively regulate DP (DNE) [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_23" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_18 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_24">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCI positively regulates DCII [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_24_in_S_5" qual:qualitativeSpecies="S_5" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCI positively regulates DCII [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_24" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_25">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>T0 positively regulates BC. BC positively regulates itself [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_25_in_S_25" qual:qualitativeSpecies="S_25" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BC positively regulates itself [1].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_25_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>T0 positively regulates BC [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_25" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_26">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>DCII positively regulates T0 [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_26_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"Dendritic cells induce differentiation of naïve T cells (T0) by producing IL4 and IL12" [1]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_26" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_27">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>Bb, MPI, and Th1I in combination with C and IgG activate AP [1].&nbsp;<span style="font-size: 10pt;">Bb, MPI, and Th11 in combination with AgAb activate AP [1].</span></div><div><br/></div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_27_in_S_22" qual:qualitativeSpecies="S_22" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb, MPI, and Th1I in combination with C and IgG activate AP [1].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_27_in_S_9" qual:qualitativeSpecies="S_9" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb, MPI, and Th11 in combination with AgAb activate AP [1].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_27_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb, MPI, and Th1I in combination with C and IgG or AgAb activate AP [1].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_27_in_S_13" qual:qualitativeSpecies="S_13" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb, MPI, and Th1I in combination with C and IgG or AgAb activate AP [1].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_27_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb, MPI, and Th1I in combination with C and IgG activate AP [1].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_27_in_S_14" qual:qualitativeSpecies="S_14" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Bb, MPI, and Th1I in combination with C and IgG or AgAb activate AP [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_27" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_13 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_14 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_22 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_13 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_14 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_28">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>Bb activates TTSSI [1]. IgG inhibits TTSSI [1].&nbsp;<span style="font-size: 10pt;">IgA inhibits TTSSI [1].</span></div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_28_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">IgA inhibits TTSSI [1].</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_28_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">Bb activates TTSSI [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_28_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">IgG inhibits TTSSI [1].</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_28" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_29">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>TrII positively regulates TrI [1].&nbsp;</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_29_in_S_6" qual:qualitativeSpecies="S_6" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>TrII positively regulates TrI [1]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_29" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_30">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>IFNgI positively regulates IFNgII [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_30_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>IFNgI positively regulates IFNgII [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_30" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_31">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Th2II positively regulates Th2I [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_31_in_S_4" qual:qualitativeSpecies="S_4" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Th2II positively regulates Th2I [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_31" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_4 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_32">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>AP in conjunction with Bb activate PH [1].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_32_in_S_27" qual:qualitativeSpecies="S_27" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"The node “activated phagocytic cells†represents the outcome of the stimulation of neutrophils and macrophages by antibody-antigen complex and complement. These cells induce the node phagocytosis that depletes bacteria" [1]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_32_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>AP in conjunction with Bb activate PH [1].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_32" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_33">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>DCII in conjunction with T0 positively regulates IL12II [1]. IL4II negatively regulates IL12II [1].</div></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_33_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">DCII in conjunction with T0 positively regulates IL12II [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_33_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">DCII in conjunction with T0 positively regulates IL12II [1]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_33_in_S_12" qual:qualitativeSpecies="S_12" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">IL4II negatively regulates IL12II [1].</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_33" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_12 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
</qual:listOfTransitions>
<listOfCompartments>
<compartment constant="true" id="cytosol" name="cytosol"/>
</listOfCompartments>
</model>
</sbml>