- Author:
- Hanne Nielsen <hnie010@aucklanduni.ac.nz>
- Date:
- 2011-07-28 14:14:07+12:00
- Desc:
- Fixed session file.
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/olsen_hauser_kummer_2003/rawfile/d92916cd550f062607773de9010ca77880712aab/olsen_hauser_kummer_2003.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : olsen_model_2003.xml
CREATED : 22nd January 2004
LAST MODIFIED : 22nd January 2004
AUTHOR : Catherine Lloyd
Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the 16/1/02 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of Olsen et al.'s 2003 mathematical model of the peroxidase-oxidase reaction.
CHANGES:
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" cmeta:id="olsen_hauser_kummer_2003_version01" name="olsen_hauser_kummer_2003_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Mechanism of Protection of Peroxidase Activity by Oscillatory Dynamics</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This is the original unchecked version of the model imported from the previous
CellML model repository, 24-Jan-2006.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
In spite of their wide spread occurance, the functions of metabolic oscillations in cells are not well understood. They may be a side-effect of the nonlinear properties of metabolic enzymes, or they may actually serve an important fuction in their own right. Over the years several potential roles for metabolic oscillations have been suggested, such increasing the thermodynamic efficiency of metabolism, encoding transmembrane signalling, acting as a biological clock, and protecting proteins against substances such as reactive oxygen species, or radicals, that are synthesised as a by product of cell metabolism or signalling. </para>
<para>
The peroxidase-oxidase reaction is one such reaction which is known to have reactive oxygen species as intermediates. These intermediates are able to inactivate many types of biomolecules, including the peroxidase enzyme itself. Oscillatory dynamics seem to protect the enzyme from this inactivation, may be because the average concentration of the oscillating reactive oxygen species is lower than its steady state concentration.
</para>
<para>
In the Olsen <emphasis>et al.</emphasis> 2003 publication described here, the authors study the peroxidase-oxidase reaction with either 4-hydroxybenzoic acid or melatonin as cofactors. In both cases, the oscillatory dynamics of the reactive oxygen species had a protective effect. They then went onto to simulate these experimental results with a mathematical model (see the figure below). The simulation results support the hypothesis that enzyme protection is due to the lower average concentration of the reactive oxygen species during oscillations. In addition, increasing the cofactor concentrations further decreased the avaerage concentration of the radicals.
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
Mechanism of protection of peroxidase activity by oscillatory dynamics, Lars F. Olsen, Marcus J. B. Hauser and Ursula Kummer, 2003, <emphasis>European Journal of Biochemistry</emphasis>, 270, 2796-2804. <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12823550&dopt=Abstract">PubMed ID: 12823550</ulink>
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>reaction diagram</title>
</objectinfo>
<imagedata fileref="olsen_2003.png"/>
</imageobject>
</mediaobject>
<caption>Schematic diagram of the peroxidase-oxidase reaction. Per<superscript>3+</superscript> and Per<superscript>2+</superscript> indicate iron(III) and iron(II) peroxidase respectively. Enzyme intermediates compound I, II and III are represented as coI, coII, and coIII. ArH and Ar' indicate the aromatic compound 4-hydroxybenzoic acid, or melatonin, and its free radical respectively.</caption>
</informalfigure>
</sect1>
</article>
</documentation>
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<unit units="mole"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="micromolar">
<unit units="mole" prefix="micro"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="flux">
<unit units="molar"/>
<unit units="second" exponent="-1"/>
</units>
<units name="first_order_rate_constant">
<unit units="second" exponent="-1"/>
</units>
<units name="second_order_rate_constant">
<unit units="molar" exponent="-1"/>
<unit units="second" exponent="-1"/>
</units>
<component name="environment">
<variable units="second" public_interface="out" name="time"/>
</component>
<component cmeta:id="O2" name="O2">
<rdf:RDF>
<rdf:Description rdf:about="O2">
<dc:title>O2</dc:title>
<dcterms:alternative>oxygen</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="O2" initial_value="5.33"/>
<variable units="flux" public_interface="in" name="v1"/>
<variable units="flux" public_interface="in" name="v5"/>
<variable units="flux" public_interface="in" name="v7"/>
<variable units="flux" public_interface="in" name="v11"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
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<diff/>
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</bvar>
<ci>O2</ci>
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<ci>v5</ci>
<ci>v7</ci>
<ci>v11</ci>
</apply>
</apply>
</math>
</component>
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<rdf:RDF>
<rdf:Description rdf:about="O2_radical">
<dc:title>O2_radical</dc:title>
<dcterms:alternative>oxygen free radical</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="O2_radical"/>
<variable units="flux" public_interface="in" name="v5"/>
<variable units="flux" public_interface="in" name="v6"/>
<variable units="flux" public_interface="in" name="v7"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
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<ci>time</ci>
</bvar>
<ci>O2_radical</ci>
</apply>
<apply>
<plus/>
<ci>v6</ci>
<ci>v5</ci>
<ci>v7</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="O2_liquid" name="O2_liquid">
<rdf:RDF>
<rdf:Description rdf:about="O2_liquid">
<dc:title>O2_liquid</dc:title>
<dcterms:alternative>liquid oxygen</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="O2_liquid"/>
<variable units="flux" public_interface="in" name="v13_"/>
<variable units="flux" public_interface="in" name="v13"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>O2_liquid</ci>
</apply>
<apply>
<plus/>
<ci>v13</ci>
<ci>v13_</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="O2_gas" name="O2_gas">
<rdf:RDF>
<rdf:Description rdf:about="O2_gas">
<dc:title>O2_gas</dc:title>
<dcterms:alternative>oxygen gas</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="O2_gas"/>
<variable units="flux" public_interface="in" name="v13_"/>
<variable units="flux" public_interface="in" name="v13"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>O2_gas</ci>
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<apply>
<plus/>
<ci>v13</ci>
<ci>v13_</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="NADH" name="NADH">
<rdf:RDF>
<rdf:Description rdf:about="NADH">
<dc:title>NADH</dc:title>
<dcterms:alternative>nicotinamide adenine dinucleotide</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="NADH" initial_value="0.95"/>
<variable units="flux" public_interface="in" name="v1"/>
<variable units="flux" public_interface="in" name="v12"/>
<variable units="flux" public_interface="in" name="v14"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>NADH</ci>
</apply>
<apply>
<plus/>
<ci>v1</ci>
<ci>v12</ci>
<ci>v14</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="NAD" name="NAD">
<rdf:RDF>
<rdf:Description rdf:about="NAD">
<dc:title>NAD</dc:title>
<dcterms:alternative>oxidised nicotinamide adenine dinucleotide</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="NAD" initial_value="558.0"/>
<variable units="flux" public_interface="in" name="v1"/>
<variable units="flux" public_interface="in" name="v5"/>
<variable units="flux" public_interface="in" name="v8"/>
<variable units="flux" public_interface="in" name="v10"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>NAD</ci>
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<apply>
<plus/>
<ci>v1</ci>
<ci>v5</ci>
<ci>v8</ci>
<ci>v10</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="NAD_radical" name="NAD_radical">
<rdf:RDF>
<rdf:Description rdf:about="NAD">
<dc:title>NAD_radical</dc:title>
<dcterms:alternative>nicotinamide adenine dinucleotide free radical</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="NAD_radical" initial_value="5.0E-4"/>
<variable units="flux" public_interface="in" name="v9"/>
<variable units="flux" public_interface="in" name="v5"/>
<variable units="flux" public_interface="in" name="v8"/>
<variable units="flux" public_interface="in" name="v10"/>
<variable units="flux" public_interface="in" name="v14"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>NAD_radical</ci>
</apply>
<apply>
<plus/>
<ci>v9</ci>
<ci>v5</ci>
<ci>v8</ci>
<ci>v10</ci>
<ci>v14</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="NAD2" name="NAD2">
<rdf:RDF>
<rdf:Description rdf:about="NAD2">
<dc:title>NAD2</dc:title>
<dcterms:alternative>nicotinamide adenine dinucleotide</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="NAD2" initial_value="0.12"/>
<variable units="flux" public_interface="in" name="v9"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>NAD2</ci>
</apply>
<ci>v9</ci>
</apply>
</math>
</component>
<component cmeta:id="H2O2" name="H2O2">
<rdf:RDF>
<rdf:Description rdf:about="H2O2">
<dc:title>H2O2</dc:title>
<dcterms:alternative>peroxide</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="H2O2" initial_value="0.013"/>
<variable units="flux" public_interface="in" name="v1"/>
<variable units="flux" public_interface="in" name="v2"/>
<variable units="flux" public_interface="in" name="v7"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>H2O2</ci>
</apply>
<apply>
<plus/>
<ci>v1</ci>
<ci>v2</ci>
<ci>v7</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="H" name="H">
<rdf:RDF>
<rdf:Description rdf:about="H">
<dc:title>H</dc:title>
<dcterms:alternative>proton</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="H"/>
<variable units="flux" public_interface="in" name="v1"/>
<variable units="flux" public_interface="in" name="v7"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>H</ci>
</apply>
<apply>
<plus/>
<ci>v1</ci>
<ci>v7</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Per3" name="Per3">
<rdf:RDF>
<rdf:Description rdf:about="Per3">
<dc:title>Per3</dc:title>
<dcterms:alternative>ferric peroxidase</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Per3" initial_value="0.059"/>
<variable units="flux" public_interface="in" name="v2"/>
<variable units="flux" public_interface="in" name="v4"/>
<variable units="flux" public_interface="in" name="v6"/>
<variable units="flux" public_interface="in" name="v10"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
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<ci>time</ci>
</bvar>
<ci>Per3</ci>
</apply>
<apply>
<plus/>
<ci>v2</ci>
<ci>v4</ci>
<ci>v6</ci>
<ci>v10</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Per2" name="Per2">
<rdf:RDF>
<rdf:Description rdf:about="Per2">
<dc:title>Per2</dc:title>
<dcterms:alternative>ferrous peroxidase</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Per2" initial_value="1.0E-4"/>
<variable units="flux" public_interface="in" name="v10"/>
<variable units="flux" public_interface="in" name="v11"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Per2</ci>
</apply>
<apply>
<plus/>
<ci>v11</ci>
<ci>v10</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="coI" name="coI">
<rdf:RDF>
<rdf:Description rdf:about="coI">
<dc:title>coI</dc:title>
<dcterms:alternative>compound I</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="coI" initial_value="8.9E-4"/>
<variable units="flux" public_interface="in" name="v2"/>
<variable units="flux" public_interface="in" name="v3"/>
<variable units="flux" public_interface="in" name="v8"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
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<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>coI</ci>
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<apply>
<plus/>
<ci>v2</ci>
<ci>v3</ci>
<ci>v8</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="coII" name="coII">
<rdf:RDF>
<rdf:Description rdf:about="coII">
<dc:title>coII</dc:title>
<dcterms:alternative>compound II</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="coII" initial_value="0.026"/>
<variable units="flux" public_interface="in" name="v3"/>
<variable units="flux" public_interface="in" name="v4"/>
<variable units="second" public_interface="in" name="time"/>
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<diff/>
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<ci>time</ci>
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<ci>coII</ci>
</apply>
<apply>
<plus/>
<ci>v3</ci>
<ci>v4</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="coIII" name="coIII">
<rdf:RDF>
<rdf:Description rdf:about="coIII">
<dc:title>coIII</dc:title>
<dcterms:alternative>compound III</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="coIII" initial_value="1.31"/>
<variable units="flux" public_interface="in" name="v6"/>
<variable units="flux" public_interface="in" name="v8"/>
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<apply>
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<apply>
<diff/>
<bvar>
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</bvar>
<ci>coIII</ci>
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<apply>
<plus/>
<ci>v6</ci>
<ci>v8</ci>
<ci>v11</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Ar_radical" name="Ar_radical">
<rdf:RDF>
<rdf:Description rdf:about="Ar_radical">
<dc:title>Ar_radical</dc:title>
<dcterms:alternative>aromatic compound free radical</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Ar_radical" initial_value="0.12"/>
<variable units="flux" public_interface="in" name="v3"/>
<variable units="flux" public_interface="in" name="v4"/>
<variable units="flux" public_interface="in" name="v14"/>
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<apply>
<plus/>
<ci>v3</ci>
<ci>v4</ci>
<ci>v14</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="ArH" name="ArH">
<rdf:RDF>
<rdf:Description rdf:about="ArH">
<dc:title>ArH</dc:title>
<dcterms:alternative>aromatic compound</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="ArH" initial_value="299.88"/>
<variable units="flux" public_interface="in" name="v3"/>
<variable units="flux" public_interface="in" name="v4"/>
<variable units="flux" public_interface="in" name="v14"/>
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<plus/>
<ci>v3</ci>
<ci>v4</ci>
<ci>v14</ci>
</apply>
</apply>
</math>
</component>
<component name="v1">
<variable units="flux" public_interface="out" name="v1"/>
<variable units="micromolar" public_interface="in" name="NADH"/>
<variable units="micromolar" public_interface="in" name="O2"/>
<variable units="second_order_rate_constant" name="k1" initial_value="3.0"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="v1_calculation">
<eq/>
<ci> v1 </ci>
<apply>
<times/>
<ci> k1 </ci>
<ci> NADH </ci>
<ci> O2 </ci>
</apply>
</apply>
</math>
</component>
<component name="v2">
<variable units="flux" public_interface="out" name="v2"/>
<variable units="micromolar" public_interface="in" name="H2O2"/>
<variable units="micromolar" public_interface="in" name="Per3"/>
<variable units="second_order_rate_constant" name="k2" initial_value="1.8E7"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="v2_calculation">
<eq/>
<ci> v2 </ci>
<apply>
<times/>
<ci> k2 </ci>
<ci> H2O2 </ci>
<ci> Per3 </ci>
</apply>
</apply>
</math>
</component>
<component name="v3">
<variable units="flux" public_interface="out" name="v3"/>
<variable units="micromolar" public_interface="in" name="coI"/>
<variable units="micromolar" public_interface="in" name="ArH"/>
<variable units="second_order_rate_constant" name="k3" initial_value="1.5E5"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="v3_calculation">
<eq/>
<ci> v3 </ci>
<apply>
<times/>
<ci> k3 </ci>
<ci> coI </ci>
<ci> ArH </ci>
</apply>
</apply>
</math>
</component>
<component name="v4">
<variable units="flux" public_interface="out" name="v4"/>
<variable units="micromolar" public_interface="in" name="coII"/>
<variable units="micromolar" public_interface="in" name="ArH"/>
<variable units="second_order_rate_constant" name="k4" initial_value="5.2E3"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="v4_calculation">
<eq/>
<ci> v4 </ci>
<apply>
<times/>
<ci> k4 </ci>
<ci> coII </ci>
<ci> ArH </ci>
</apply>
</apply>
</math>
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This is the CellML description of Olsen et al.'s 2003 mathematical model of the peroxidase-oxidase reaction.
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Mechanism of protection of peroxidase activity by oscillatory dynamics
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<bqs:volume>270</bqs:volume>
<bqs:first_page>2796</bqs:first_page>
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