- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2007-10-09 05:29:49+13:00
- Desc:
- committing version01 of thomas_2000
- Permanent Source URI:
- https://models.cellml.org/workspace/thomas_2000/rawfile/a5a4deeb1cf8b85adbb1fb7b7e3ddddd96370a12/thomas_2000.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : thomas_model_2000.xml
CREATED : 27th September 2007
LAST MODIFIED : 27th September 2007
AUTHOR : Catherine Lloyd
Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.1 Specification.
DESCRIPTION : This file contains a CellML description of Thomas's 2000 mathematical model of inner medullary lactate production and accumulation: a vasa recta model.
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="thomas_model_2000_version01" name="thomas_model_2000_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<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>
<ulink url="http://ajprenal.physiology.org/cgi/content/abstract/279/3/F468">Inner medullary lactate production and accumulation: a vasa recta model</ulink>, S. Randall Thomas, 2000, <ulink url="http://ajprenal.physiology.org/">
<emphasis>American Journal of Physiology</emphasis>
</ulink>, 279, F468-F481. (<ulink url="http://ajprenal.physiology.org/cgi/content/full/279/3/F468">full text</ulink> and <ulink url="http://ajprenal.physiology.org/cgi/reprint/279/3/F468">PDF</ulink> versions of the article are available to journal subscribers on the <emphasis>American Journal of Physiology</emphasis> website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=10966926&query_hl=1&itool=pubmed_docsum">PubMed ID: 10966926</ulink>
</para>
</sect1>
</article>
</documentation>
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as a whole, as indicated by the empty about attribute on the
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<!--
The Model Builder Metadata. The Dublin Core "creator" element is used
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-->
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<vCard:Family>Lloyd</vCard:Family>
<vCard:Given>Catherine</vCard:Given>
<vCard:Other>May</vCard:Other>
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<!--
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-->
<!-- The Publisher metadata. -->
<dc:publisher>
The University of Auckland, Bioengineering Institute
</dc:publisher>
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<!--
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reference to the ID "thomas_model_2000", which is declared
on the <model> element.
-->
<rdf:Description rdf:about="#thomas_model_2000">
<!-- A human readable name for the model. -->
<dc:title>
Thomas's 2000 mathematical model of inner medullary lactate production and accumulation: a vasa recta model.
</dc:title>
<!-- A comment regarding the model. -->
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
This is the CellML description of Thomas's 2000 mathematical model of inner medullary lactate production and accumulation: a vasa recta model.
</rdf:value>
<!-- The creator of the comment. -->
<dc:creator rdf:parseType="Resource">
<vCard:FN>Catherine Lloyd</vCard:FN>
</dc:creator>
</cmeta:comment>
<cmeta:bio_entity>descending vasa recta</cmeta:bio_entity>
<cmeta:bio_entity>kidney</cmeta:bio_entity>
<!-- Keyword(s) -->
<bqs:reference rdf:parseType="Resource">
<dc:subject rdf:parseType="Resource">
<bqs:subject_type>keyword</bqs:subject_type>
<rdf:value>
<rdf:Bag>
<rdf:li>glucose</rdf:li>
<rdf:li>vasa recta</rdf:li>
<rdf:li>lactate</rdf:li>
</rdf:Bag>
</rdf:value>
</dc:subject>
</bqs:reference>
<!--
The CellML Metadata Specification recommends that bibliographic metadata
is used to provide information about the original model reference. The
"identifier" attribute on the "BibliographicReference" class provides an
elegant way to identify a cited reference using a database identifier
such as Pubmed. All associated data such as author, journal title,
date, etc can be looked up on the database.
-->
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<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Thomas</vCard:Family>
<vCard:Given>S</vCard:Given>
<vCard:Other>Randall</vCard:Other>
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</rdf:li>
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<dc:title>
Inner medullary lactate production and accumulation: a vasa recta model
</dc:title>
<dcterms:issued rdf:parseType="Resource">
<dcterms:W3CDTF>2000</dcterms:W3CDTF>
</dcterms:issued>
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<dc:title>American Journal of Physiology</dc:title>
</bqs:Journal>
<bqs:volume>279</bqs:volume>
<bqs:first_page>F468</bqs:first_page>
<bqs:last_page>F481</bqs:last_page>
</bqs:JournalArticle>
</bqs:reference>
</rdf:Description>
</rdf:RDF>
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Inner medullary lactate production and accumulation: a vasa recta model
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The University of Auckland, Bioengineering Institute
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Thomas's 2000 mathematical model of inner medullary lactate production and accumulation: a vasa recta model.
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