- Author:
- AnandR <a.rampadarath@auckland.ac.nz>
- Date:
- 2019-09-16 15:51:41+12:00
- Desc:
- added combine archives
- Permanent Source URI:
- https://models.cellml.org/workspace/5b6/rawfile/3e2a4710066924ebb1f3dd02d0a7be650b348962/thomas_2000.rdf
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<articleinfo>
<title>Inner medullary lactate production and accumulation: a vasa recta model</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 CellML version of the model has been checked in COR and PCEnv and it runs in PCEnv. The model will not run in COR because it does not contain any time derivatives - COR expects the units of the differential equations to be a function of time (not length as it is in this case). However, COR did allow for the units to be checked and they are consistent. The model runs in PCEnv but as yet it does not recreate the published results. This may be due to differences in the defined set of initial conditions. The model author has been contacted and we are currently receiving their help and advice.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>S. Randall Thomas here investigates the possibility that recycling of lactate produced by anaerobic glycolysis in the inner medulla of the kidney can provide sufficient of a lactate gradient to contributes significantly to the urine concentrating mechanism.</para>
<para>Assuming (from other sources) that 20% of the glucose delivered to the inner medulla, Thomas uses a mathematical model of the inner medullary vasa recta, based on observed mass distribution and distribution of loops, to investigate a range of plausible values of lactose and glucose permeabilities, to see which values would allow a sufficient accumulation of a lactate gradient to be a significant contributor to urine concentrating ability, in different circumstances of blood flow and diuresis.</para>
<para>The complete original paper reference is cited below:</para>
<para>
Inner medullary lactate production and accumulation: a vasa recta model, S. Randall Thomas, 2000,
<emphasis>American Journal of Physiology</emphasis>
, 279, F468-F481.
<ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=10966926&amp;query_hl=1&amp;itool=pubmed_docsum">PubMed ID: 10966926</ulink>
</para>
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<semsim:hasSinkParticipant rdf:resource="./thomas_2000.cellml#sink_5"/>
<semsim:hasSourceParticipant rdf:resource="./thomas_2000.cellml#source_6"/>
<semsim:name>glycolytic glucose flow from DVR to AVR</semsim:name>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#process_1">
<semsim:hasMediatorParticipant rdf:resource="./thomas_2000.cellml#mediator_1"/>
<semsim:hasSinkParticipant rdf:resource="./thomas_2000.cellml#sink_1"/>
<semsim:hasSourceParticipant rdf:resource="./thomas_2000.cellml#source_1"/>
<semsim:name>lactate flow from DVR to AVR</semsim:name>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#J_ABS_V.N_x">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_01001"/>
<dcterms:description>number of descending vasa recta (DVR) at depth x in the inner medullary vasa recta model</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#entity_2">
<bqbiol:is rdf:resource="http://identifiers.org/fma/FMA_272225"/>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#sink_4">
<semsim:hasMultiplier>1.0</semsim:hasMultiplier>
<semsim:hasPhysicalEntityReference rdf:resource="./thomas_2000.cellml#entity_3"/>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#entity_6">
<bqbiol:is rdf:resource="http://identifiers.org/ma/MA:0002598"/>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#kv.N_0">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_01001"/>
<dcterms:description>number of entering descending vasa recta in the inner medullary vasa recta model</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#entity_14">
<bqbiol:is rdf:resource="https://identifiers.org/cl/CL:1001286"/>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#F_AVR_LAC.F_AVR_LAC">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#process_6"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00592"/>
<dcterms:description>tubular outlow of lactate in the ascending vasa recta from the long descending Henle's loop</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#F_AVR_v.F_AVR_v">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#process_2"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00299"/>
<dcterms:description>tubular outflow of volume (blood) in the ascending vasa recta from the long descending Henle's loop</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#JGLY.JGLY">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#process_5"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>flux of glycolytic glucose consumption from all DVR to AVR treating the capillary walls as a single barrier (no distinction here between transcellular and paracellular transport)</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#JGLY.L">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#entity_12"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_01064"/>
<dcterms:description>total length of the inner medulla (depth at the papillary tip)</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#F_AVR_GLU.F_AVR_GLU">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#process_4"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00592"/>
<dcterms:description>tubular outflow of glucose in the ascending vasa recta from the long descending Henle's loop</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#source_1">
<semsim:hasMultiplier>1.0</semsim:hasMultiplier>
<semsim:hasPhysicalEntityReference rdf:resource="./thomas_2000.cellml#entity_2"/>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#source_5">
<semsim:hasMultiplier>1.0</semsim:hasMultiplier>
<semsim:hasPhysicalEntityReference rdf:resource="./thomas_2000.cellml#entity_5"/>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#mediator_1">
<semsim:hasPhysicalEntityReference rdf:resource="./thomas_2000.cellml#entity_4"/>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#JGLY.N_0">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#entity_0"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_01001"/>
<dcterms:description>number of entering descending vasa recta in the inner medullary vasa recta model</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#process_6">
<semsim:hasSinkParticipant rdf:resource="./thomas_2000.cellml#sink_6"/>
<semsim:hasSourceParticipant rdf:resource="./thomas_2000.cellml#source_7"/>
<semsim:name>lactate flow in the ascending vasa rceta</semsim:name>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#c_AVR_GLU.c_AVR_GLU">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#entity_9"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00340"/>
<dcterms:description>concentration of glucose in the ascending vasa recta</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#process_2">
<semsim:hasSinkParticipant rdf:resource="./thomas_2000.cellml#sink_2"/>
<semsim:hasSourceParticipant rdf:resource="./thomas_2000.cellml#source_2"/>
<semsim:name>volume (blood) flow in the ascending vasa recta</semsim:name>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#F_AVR_LAC.JGLY">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#process_5"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>flux of glycolytic glucose consumption from all DVR to AVR treating the capillary walls as a single barrier (no distinction here between transcellular and paracellular transport)</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#entity_3">
<bqbiol:is rdf:resource="http://identifiers.org/fma/FMA_272227"/>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#entity_10">
<bqbiol:is rdf:resource="http://identifiers.org/fma/FMA_272227"/>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#F_DVR_LAC.JLAC">
<bqbiol:isPropertyOf rdf:resource="./thomas_2000.cellml#process_1"/>
<bqbiol:isVersionOf rdf:resource="https://identifiers.org/opb/OPB_00593"/>
<dcterms:description>flux of lactate from all DVR to AVR treating the capillary walls as a single barrier (no distinction here between transcellular and paracellular transport)</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#entity_7">
<bqbiol:isPartOf rdf:resource="./thomas_2000.cellml#entity_8"/>
<bqbiol:is rdf:resource="https://identifiers.org/chebi/CHEBI:24996"/>
</rdf:Description>
<rdf:Description rdf:about="./thomas_2000.cellml#sink_3">
<semsim:hasMultiplier>1.0</semsim:hasMultiplier>
<semsim:hasPhysicalEntityReference rdf:resource="./thomas_2000.cellml#entity_3"/>
</rdf:Description>
</rdf:RDF>
