UNC-Utah NA-MIC framework for DTI fiber tract analysis
Identifieur interne : 000A40 ( Main/Exploration ); précédent : 000A39; suivant : 000A41UNC-Utah NA-MIC framework for DTI fiber tract analysis
Auteurs : Audrey R. Verde [États-Unis] ; Francois Budin [États-Unis] ; Jean-Baptiste Berger [États-Unis] ; Aditya Gupta [États-Unis] ; Mahshid Farzinfar [États-Unis] ; Adrien Kaiser [États-Unis] ; Mihye Ahn [États-Unis] ; Hans Johnson [États-Unis] ; Joy Matsui [États-Unis] ; Heather C. Hazlett [États-Unis] ; Anuja Sharma [États-Unis] ; Casey Goodlett [États-Unis] ; Yundi Shi [États-Unis] ; Sylvain Gouttard [États-Unis] ; Clement Vachet [États-Unis] ; Joseph Piven [États-Unis] ; Hongtu Zhu [États-Unis] ; Guido Gerig [États-Unis] ; Martin Styner [États-Unis]Source :
- Frontiers in Neuroinformatics [ 1662-5196 ] ; 2014.
Abstract
Diffusion tensor imaging has become an important modality in the field of neuroimaging to capture changes in micro-organization and to assess white matter integrity or development. While there exists a number of tractography toolsets, these usually lack tools for preprocessing or to analyze diffusion properties along the fiber tracts. Currently, the field is in critical need of a coherent end-to-end toolset for performing an along-fiber tract analysis, accessible to non-technical neuroimaging researchers. The UNC-Utah NA-MIC DTI framework represents a coherent, open source, end-to-end toolset for atlas fiber tract based DTI analysis encompassing DICOM data conversion, quality control, atlas building, fiber tractography, fiber parameterization, and statistical analysis of diffusion properties. Most steps utilize graphical user interfaces (GUI) to simplify interaction and provide an extensive DTI analysis framework for non-technical researchers/investigators. We illustrate the use of our framework on a small sample, cross sectional neuroimaging study of eight healthy 1-year-old children from the Infant Brain Imaging Study (IBIS) Network. In this limited test study, we illustrate the power of our method by quantifying the diffusion properties at 1 year of age on the genu and splenium fiber tracts.
Url:
DOI: 10.3389/fninf.2013.00051
PubMed: 24409141
PubMed Central: 3885811
Affiliations:
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
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<country>Chapel Hill, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Kaiser, Adrien" sort="Kaiser, Adrien" uniqKey="Kaiser A" first="Adrien" last="Kaiser">Adrien Kaiser</name>
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<country>Chapel Hill, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Ahn, Mihye" sort="Ahn, Mihye" uniqKey="Ahn M" first="Mihye" last="Ahn">Mihye Ahn</name>
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<country>Chapel Hill, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Johnson, Hans" sort="Johnson, Hans" uniqKey="Johnson H" first="Hans" last="Johnson">Hans Johnson</name>
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<country>Iowa City, IA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Matsui, Joy" sort="Matsui, Joy" uniqKey="Matsui J" first="Joy" last="Matsui">Joy Matsui</name>
<affiliation wicri:level="4"><nlm:aff id="aff4"><institution>Iowa Institute for Biomedical Imaging, University of Iowa</institution>
<country>Iowa City, IA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Hazlett, Heather C" sort="Hazlett, Heather C" uniqKey="Hazlett H" first="Heather C." last="Hazlett">Heather C. Hazlett</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><institution>Neuro Image Research and Analysis Laboratory, Department of Psychiatry, University of North Carolina</institution>
<country>Chapel Hill, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Sharma, Anuja" sort="Sharma, Anuja" uniqKey="Sharma A" first="Anuja" last="Sharma">Anuja Sharma</name>
<affiliation wicri:level="4"><nlm:aff id="aff5"><institution>Scientific Computing and Imaging Institute, University of Utah</institution>
<country>Salt Lake City, UT, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Goodlett, Casey" sort="Goodlett, Casey" uniqKey="Goodlett C" first="Casey" last="Goodlett">Casey Goodlett</name>
<affiliation wicri:level="4"><nlm:aff id="aff6"><institution>Kitware Inc.</institution>
<country>Clifton Park, NY, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Shi, Yundi" sort="Shi, Yundi" uniqKey="Shi Y" first="Yundi" last="Shi">Yundi Shi</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><institution>Neuro Image Research and Analysis Laboratory, Department of Psychiatry, University of North Carolina</institution>
<country>Chapel Hill, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Gouttard, Sylvain" sort="Gouttard, Sylvain" uniqKey="Gouttard S" first="Sylvain" last="Gouttard">Sylvain Gouttard</name>
<affiliation wicri:level="4"><nlm:aff id="aff5"><institution>Scientific Computing and Imaging Institute, University of Utah</institution>
<country>Salt Lake City, UT, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Vachet, Clement" sort="Vachet, Clement" uniqKey="Vachet C" first="Clement" last="Vachet">Clement Vachet</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><institution>Neuro Image Research and Analysis Laboratory, Department of Psychiatry, University of North Carolina</institution>
<country>Chapel Hill, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="aff5"><institution>Scientific Computing and Imaging Institute, University of Utah</institution>
<country>Salt Lake City, UT, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Piven, Joseph" sort="Piven, Joseph" uniqKey="Piven J" first="Joseph" last="Piven">Joseph Piven</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><institution>Neuro Image Research and Analysis Laboratory, Department of Psychiatry, University of North Carolina</institution>
<country>Chapel Hill, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Zhu, Hongtu" sort="Zhu, Hongtu" uniqKey="Zhu H" first="Hongtu" last="Zhu">Hongtu Zhu</name>
<affiliation wicri:level="4"><nlm:aff id="aff3"><institution>Department of Biostatistics, University of North Carolina</institution>
<country>Chapel Hill, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Gerig, Guido" sort="Gerig, Guido" uniqKey="Gerig G" first="Guido" last="Gerig">Guido Gerig</name>
<affiliation wicri:level="4"><nlm:aff id="aff5"><institution>Scientific Computing and Imaging Institute, University of Utah</institution>
<country>Salt Lake City, UT, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
<author><name sortKey="Styner, Martin" sort="Styner, Martin" uniqKey="Styner M" first="Martin" last="Styner">Martin Styner</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><institution>Neuro Image Research and Analysis Laboratory, Department of Psychiatry, University of North Carolina</institution>
<country>Chapel Hill, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="aff7"><institution>Department of Computer Science, University of North Carolina</institution>
<country>Chapel Hill, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh, Pittsburgh</wicri:regionArea>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université de Pittsburgh</orgName>
</affiliation>
</author>
</analytic>
<series><title level="j">Frontiers in Neuroinformatics</title>
<idno type="eISSN">1662-5196</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
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<front><div type="abstract" xml:lang="en"><p>Diffusion tensor imaging has become an important modality in the field of neuroimaging to capture changes in micro-organization and to assess white matter integrity or development. While there exists a number of tractography toolsets, these usually lack tools for preprocessing or to analyze diffusion properties along the fiber tracts. Currently, the field is in critical need of a coherent end-to-end toolset for performing an along-fiber tract analysis, accessible to non-technical neuroimaging researchers. The UNC-Utah NA-MIC DTI framework represents a coherent, open source, end-to-end toolset for atlas fiber tract based DTI analysis encompassing DICOM data conversion, quality control, atlas building, fiber tractography, fiber parameterization, and statistical analysis of diffusion properties. Most steps utilize graphical user interfaces (GUI) to simplify interaction and provide an extensive DTI analysis framework for non-technical researchers/investigators. We illustrate the use of our framework on a small sample, cross sectional neuroimaging study of eight healthy 1-year-old children from the Infant Brain Imaging Study (IBIS) Network. In this limited test study, we illustrate the power of our method by quantifying the diffusion properties at 1 year of age on the genu and splenium fiber tracts.</p>
</div>
</front>
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<author><name sortKey="Rueckert, D" uniqKey="Rueckert D">D. Rueckert</name>
</author>
<author><name sortKey="Nichols, T E" uniqKey="Nichols T">T. E. Nichols</name>
</author>
<author><name sortKey="Mackay, C E" uniqKey="Mackay C">C. E. MacKay</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Song, S K" uniqKey="Song S">S. K. Song</name>
</author>
<author><name sortKey="Sun, S W" uniqKey="Sun S">S. W. Sun</name>
</author>
<author><name sortKey="Ju, W K" uniqKey="Ju W">W. K. Ju</name>
</author>
<author><name sortKey="Lin, S J" uniqKey="Lin S">S. J. Lin</name>
</author>
<author><name sortKey="Cross, A H" uniqKey="Cross A">A. H. Cross</name>
</author>
<author><name sortKey="Neufeld, A H" uniqKey="Neufeld A">A. H. Neufeld</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Van Ginneken, B" uniqKey="Van Ginneken B">B. Van Ginneken</name>
</author>
<author><name sortKey="Heimann, T" uniqKey="Heimann T">T. Heimann</name>
</author>
<author><name sortKey="Styner, M" uniqKey="Styner M">M. Styner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yushkevich, P A" uniqKey="Yushkevich P">P. A. Yushkevich</name>
</author>
<author><name sortKey="Piven, J" uniqKey="Piven J">J. Piven</name>
</author>
<author><name sortKey="Hazlett, H C" uniqKey="Hazlett H">H. C. Hazlett</name>
</author>
<author><name sortKey="Smith, R G" uniqKey="Smith R">R. G. Smith</name>
</author>
<author><name sortKey="Ho, S" uniqKey="Ho S">S. Ho</name>
</author>
<author><name sortKey="Gee, J C" uniqKey="Gee J">J. C. Gee</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhu, H" uniqKey="Zhu H">H. Zhu</name>
</author>
<author><name sortKey="Kong, L" uniqKey="Kong L">L. Kong</name>
</author>
<author><name sortKey="Li, R" uniqKey="Li R">R. Li</name>
</author>
<author><name sortKey="Styner, M" uniqKey="Styner M">M. Styner</name>
</author>
<author><name sortKey="Gerig, G" uniqKey="Gerig G">G. Gerig</name>
</author>
<author><name sortKey="Lin, W" uniqKey="Lin W">W. Lin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhu, T" uniqKey="Zhu T">T. Zhu</name>
</author>
<author><name sortKey="Hu, R" uniqKey="Hu R">R. Hu</name>
</author>
<author><name sortKey="Tian, W" uniqKey="Tian W">W. Tian</name>
</author>
<author><name sortKey="Ekholm, S" uniqKey="Ekholm S">S. Ekholm</name>
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<author><name sortKey="Schifitto, G" uniqKey="Schifitto G">G. Schifitto</name>
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<author><name sortKey="Qiu, X" uniqKey="Qiu X">X. Qiu</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Pennsylvanie</li>
</region>
<settlement><li>Pittsburgh</li>
</settlement>
<orgName><li>Université de Pittsburgh</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Verde, Audrey R" sort="Verde, Audrey R" uniqKey="Verde A" first="Audrey R." last="Verde">Audrey R. Verde</name>
</region>
<name sortKey="Ahn, Mihye" sort="Ahn, Mihye" uniqKey="Ahn M" first="Mihye" last="Ahn">Mihye Ahn</name>
<name sortKey="Berger, Jean Baptiste" sort="Berger, Jean Baptiste" uniqKey="Berger J" first="Jean-Baptiste" last="Berger">Jean-Baptiste Berger</name>
<name sortKey="Budin, Francois" sort="Budin, Francois" uniqKey="Budin F" first="Francois" last="Budin">Francois Budin</name>
<name sortKey="Farzinfar, Mahshid" sort="Farzinfar, Mahshid" uniqKey="Farzinfar M" first="Mahshid" last="Farzinfar">Mahshid Farzinfar</name>
<name sortKey="Gerig, Guido" sort="Gerig, Guido" uniqKey="Gerig G" first="Guido" last="Gerig">Guido Gerig</name>
<name sortKey="Goodlett, Casey" sort="Goodlett, Casey" uniqKey="Goodlett C" first="Casey" last="Goodlett">Casey Goodlett</name>
<name sortKey="Gouttard, Sylvain" sort="Gouttard, Sylvain" uniqKey="Gouttard S" first="Sylvain" last="Gouttard">Sylvain Gouttard</name>
<name sortKey="Gupta, Aditya" sort="Gupta, Aditya" uniqKey="Gupta A" first="Aditya" last="Gupta">Aditya Gupta</name>
<name sortKey="Gupta, Aditya" sort="Gupta, Aditya" uniqKey="Gupta A" first="Aditya" last="Gupta">Aditya Gupta</name>
<name sortKey="Hazlett, Heather C" sort="Hazlett, Heather C" uniqKey="Hazlett H" first="Heather C." last="Hazlett">Heather C. Hazlett</name>
<name sortKey="Johnson, Hans" sort="Johnson, Hans" uniqKey="Johnson H" first="Hans" last="Johnson">Hans Johnson</name>
<name sortKey="Kaiser, Adrien" sort="Kaiser, Adrien" uniqKey="Kaiser A" first="Adrien" last="Kaiser">Adrien Kaiser</name>
<name sortKey="Matsui, Joy" sort="Matsui, Joy" uniqKey="Matsui J" first="Joy" last="Matsui">Joy Matsui</name>
<name sortKey="Piven, Joseph" sort="Piven, Joseph" uniqKey="Piven J" first="Joseph" last="Piven">Joseph Piven</name>
<name sortKey="Sharma, Anuja" sort="Sharma, Anuja" uniqKey="Sharma A" first="Anuja" last="Sharma">Anuja Sharma</name>
<name sortKey="Shi, Yundi" sort="Shi, Yundi" uniqKey="Shi Y" first="Yundi" last="Shi">Yundi Shi</name>
<name sortKey="Styner, Martin" sort="Styner, Martin" uniqKey="Styner M" first="Martin" last="Styner">Martin Styner</name>
<name sortKey="Styner, Martin" sort="Styner, Martin" uniqKey="Styner M" first="Martin" last="Styner">Martin Styner</name>
<name sortKey="Vachet, Clement" sort="Vachet, Clement" uniqKey="Vachet C" first="Clement" last="Vachet">Clement Vachet</name>
<name sortKey="Vachet, Clement" sort="Vachet, Clement" uniqKey="Vachet C" first="Clement" last="Vachet">Clement Vachet</name>
<name sortKey="Zhu, Hongtu" sort="Zhu, Hongtu" uniqKey="Zhu H" first="Hongtu" last="Zhu">Hongtu Zhu</name>
</country>
</tree>
</affiliations>
</record>
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