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Title:           Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures
Subject:         Nature Communications, doi:10.1038/s41467-021-23397-1
Keywords:        
Author:          Raquel García-Pérez
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      Title: Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures
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       Item: 
        Title: Results
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         Item: 
          Title: Comprehensive profiling of primate lymphoblastoid cell lines (LCLs)
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         Item: 
          Title: Annotation of RE
          Destination: B2
         Item: 
          Title: The evolutionary dynamics of promoters and enhancers in primate LCLs recapitulate previous observations in more distant mammals
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         Item: 
          Title: The activity of promoters and enhancers influences their epigenetic and sequence conservation
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         Item: 
          Title: Definition of different types of components in the regulatory architectures
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         Item: 
          Title: Regulatory components influence gene expression and its evolution differently
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         Item: 
          Title: Different regulatory components with poised and weak enhancer states appear in LCL-unrelated genes and functions
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         Item: 
          Title: Genes with novel human-specific intragenic weak enhancers are targeted by signals of adaptation and nucleotide changes
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        Title: Discussion
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        Title: Methods
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         Item: 
          Title: Cell line acquisition and cell growth
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         Item: 
          Title: DNA and RNA extractions
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         Item: 
          Title: Chromatin immunoprecipitation
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         Item: 
          Title: Assay of transposable chromatin
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         Item: 
          Title: Definition of RE
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         Item: 
          Title: Assignment of a regulatory state to RE
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         Item: 
          Title: Analysis of evolutionary conservation at orthologous regulatory regions
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         Item: 
          Title: Classification of RE in different types of components of gene regulatory architectures
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         Item: 
          Title: Gene expression levels and regulatory states in gene components
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         Item: 
          Title: Partial correlation analysis
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         Item: 
          Title: Differential gene expression analyses
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         Item: 
          Title: Over-representation analyses (ORA) of functional annotations
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         Item: 
          Title: Analysis of tissue-specific gene expression
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         Item: 
          Title: Association of genes containing gE with signals of positive selection and accelerated evolution
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         Item: 
          Title: Analyses of the density of human-fixed single nucleotide changes (hSNCs) in gE with weak enhancer states
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        Title: Data availability
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        Title: References
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        Title: Acknowledgements
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        Title: Competing interests
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    Author: Raquel García-Pérez
    Subject: Nature Communications, doi:10.1038/s41467-021-23397-1
    Keywords: 
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         <xmpMM:InstanceID>uuid:f901c753-10e9-4210-b60a-d7d75e425ef4</xmpMM:InstanceID>
         <xmpMM:RenditionClass>default</xmpMM:RenditionClass>
         <xmpMM:VersionID>1</xmpMM:VersionID>
         <xmpMM:History>
            <rdf:Seq>
               <rdf:li rdf:parseType="Resource">
                  <stEvt:action>converted</stEvt:action>
                  <stEvt:instanceID>uuid:c21457d8-a1b4-4bd7-9e4d-c9c8dde6a34d</stEvt:instanceID>
                  <stEvt:parameters>converted to PDF/A-2b</stEvt:parameters>
                  <stEvt:softwareAgent>pdfToolbox</stEvt:softwareAgent>
                  <stEvt:when>2021-05-19T09:44:25+05:30</stEvt:when>
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      </rdf:Description>
      <rdf:Description rdf:about="" xmlns:pdfaid="http://www.aiim.org/pdfa/ns/id/">
         <pdfaid:part>2</pdfaid:part>
         <pdfaid:conformance>B</pdfaid:conformance>
      </rdf:Description>
      <rdf:Description rdf:about="" xmlns:author="http://springernature.com/ns/xmpExtensions/2.0/authorInfo/" xmlns:sn="http://springernature.com/ns/xmpExtensions/2.0/">
         <sn:authorInfo>
            <rdf:Bag>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Raquel García-Pérez</author:name>
                  <author:orcid>http://orcid.org/0000-0002-2573-6984</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Paula Esteller-Cucala</author:name>
                  <author:orcid>http://orcid.org/0000-0003-3048-4280</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Valerio Carlo</author:name>
                  <author:orcid>http://orcid.org/0000-0002-5099-0685</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Martin Kuhlwilm</author:name>
                  <author:orcid>http://orcid.org/0000-0002-0115-1797</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Arcadi Navarro</author:name>
                  <author:orcid>http://orcid.org/0000-0003-2162-8246</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Antoine Blancher</author:name>
                  <author:orcid>http://orcid.org/0000-0002-6763-0539</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Luciano Croce</author:name>
                  <author:orcid>http://orcid.org/0000-0003-3488-6228</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>David Juan</author:name>
                  <author:orcid>http://orcid.org/0000-0003-1912-9667</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Tomàs Marquès-Bonet</author:name>
                  <author:orcid>http://orcid.org/0000-0002-5597-3075</author:orcid>
               </rdf:li>
            </rdf:Bag>
         </sn:authorInfo>
      </rdf:Description>
      <rdf:Description rdf:about="" xmlns:pdfaExtension="http://www.aiim.org/pdfa/ns/extension/" xmlns:pdfaField="http://www.aiim.org/pdfa/ns/field#" xmlns:pdfaProperty="http://www.aiim.org/pdfa/ns/property#" xmlns:pdfaSchema="http://www.aiim.org/pdfa/ns/schema#" xmlns:pdfaType="http://www.aiim.org/pdfa/ns/type#">
         <pdfaExtension:schemas>
            <rdf:Bag>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://ns.adobe.com/pdf/1.3/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>pdf</pdfaSchema:prefix>
                  <pdfaSchema:schema>Adobe PDF Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>A name object indicating whether the document has been modified to include trapping information</pdfaProperty:description>
                           <pdfaProperty:name>Trapped</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://ns.adobe.com/pdfx/1.3/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>pdfx</pdfaSchema:prefix>
                  <pdfaSchema:schema>pdfx</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>ID of PDF/X standard</pdfaProperty:description>
                           <pdfaProperty:name>GTS_PDFXVersion</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Conformance level of PDF/X standard</pdfaProperty:description>
                           <pdfaProperty:name>GTS_PDFXConformance</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Company creating the PDF</pdfaProperty:description>
                           <pdfaProperty:name>Company</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Date when document was last modified</pdfaProperty:description>
                           <pdfaProperty:name>SourceModified</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Mirrors crossmark:CrosMarkDomains</pdfaProperty:description>
                           <pdfaProperty:name>CrossMarkDomains</pdfaProperty:name>
                           <pdfaProperty:valueType>Seq Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Mirrors crossmark:DOI</pdfaProperty:description>
                           <pdfaProperty:name>doi</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://ns.adobe.com/xap/1.0/mm/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>xmpMM</pdfaSchema:prefix>
                  <pdfaSchema:schema>XMP Media Management Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>UUID based identifier for specific incarnation of a document</pdfaProperty:description>
                           <pdfaProperty:name>InstanceID</pdfaProperty:name>
                           <pdfaProperty:valueType>URI</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>The common identifier for all versions and renditions of a document.</pdfaProperty:description>
                           <pdfaProperty:name>OriginalDocumentID</pdfaProperty:name>
                           <pdfaProperty:valueType>URI</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://www.aiim.org/pdfa/ns/id/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>pdfaid</pdfaSchema:prefix>
                  <pdfaSchema:schema>PDF/A ID Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Part of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>part</pdfaProperty:name>
                           <pdfaProperty:valueType>Integer</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Amendment of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>amd</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Conformance level of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>conformance</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://crossref.org/crossmark/1.0/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>crossmark</pdfaSchema:prefix>
                  <pdfaSchema:schema>crossmark</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>CrossMarkDomains</pdfaProperty:description>
                           <pdfaProperty:name>CrossMarkDomains</pdfaProperty:name>
                           <pdfaProperty:valueType>Seq Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>CrossmarkDomainExclusive</pdfaProperty:description>
                           <pdfaProperty:name>CrossmarkDomainExclusive</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Usual same as prism:doi</pdfaProperty:description>
                           <pdfaProperty:name>DOI</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The date when a publication was published.</pdfaProperty:description>
                           <pdfaProperty:name>MajorVersionDate</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://prismstandard.org/namespaces/basic/2.0/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>prism</pdfaSchema:prefix>
                  <pdfaSchema:schema>Prism</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The aggregation type specifies the unit of aggregation for a content collection. 
Comment 
PRISM recommends that the PRISM Aggregation Type Controlled Vocabulary be used to provide values for this element. 
Note: PRISM recommends against the use of the #other value currently allowed in this controlled vocabulary. In lieu of using #other please reach out to the PRISM group at info@prismstandard.org to request addition of your term to the Aggregation Type Controlled Vocabulary. 

</pdfaProperty:description>
                           <pdfaProperty:name>aggregationType</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Copyright </pdfaProperty:description>
                           <pdfaProperty:name>copyright</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The Digital Object Identifier for the article.
The DOI may also be used as the dc:identifier. If used as a dc:identifier, the URI form should be captured, and the bare identifier should also be captured using prism:doi. If an alternate unique identifier is used as the required dc:identifier, then the DOI should be specified as a bare identifier within prism:doi only. 
If the URL associated with a DOI is to be specified, then prism:url may be used in conjunction with prism:doi in order to provide the service endpoint (i.e. the URL). 
</pdfaProperty:description>
                           <pdfaProperty:name>doi</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>ISSN for an electronic version of the issue in which the resource occurs. 
Permits publishers to include a second ISSN, identifying an electronic version of the issue in which the resource occurs (therefore e(lectronic)Issn. If used, prism:eIssn MUST contain the ISSN of the electronic version. See prism:issn. 
</pdfaProperty:description>
                           <pdfaProperty:name>issn</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Title of the magazine, or other publication, in which a resource was/will be published. 
Typically this will be used to provide the name of the magazine an article appeared in as metadata for the article, along with information such as the article title, the publisher, volume, number, and cover date. 

Note: Publication name can be used to differentiate between a print magazine and the online version if the names are different such as “magazine” and “magazine.com.” 
</pdfaProperty:description>
                           <pdfaProperty:name>publicationName</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>This element provides the url for an article or unit of content. 
The attribute platform is optionally allowed for situations in which multiple URLs must be specified. PRISM recommends that a subset of the PCV platform values, namely “mobile” and “web”, be used in conjunction with this element. 
NOTE: PRISM recommends against the use of the #other value allowed in the PRISM Platform controlled vocabulary. In lieu of using #other please reach out to the PRISM group at prism-wg@yahoogroups.com to request addition of your term to the Platform Controlled Vocabulary. 
</pdfaProperty:description>
                           <pdfaProperty:name>url</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://springernature.com/ns/xmpExtensions/2.0/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>sn</pdfaSchema:prefix>
                  <pdfaSchema:schema>Springer Nature ORCID Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Author information: contains the name of each author and his/her ORCID (ORCiD: Open Researcher and Contributor ID). An ORCID is a persistent identifier (a non-proprietary alphanumeric code) to uniquely identify scientific and other academic authors.</pdfaProperty:description>
                           <pdfaProperty:name>authorInfo</pdfaProperty:name>
                           <pdfaProperty:valueType>Bag AuthorInformation</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
                  <pdfaSchema:valueType>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaType:description>Specifies the types of author information: name and ORCID of an author.</pdfaType:description>
                           <pdfaType:namespaceURI>http://springernature.com/ns/xmpExtensions/2.0/authorInfo/</pdfaType:namespaceURI>
                           <pdfaType:prefix>author</pdfaType:prefix>
                           <pdfaType:type>AuthorInformation</pdfaType:type>
                           <pdfaType:field>
                              <rdf:Seq>
                                 <rdf:li rdf:parseType="Resource">
                                    <pdfaField:description>Gives the name of an author.</pdfaField:description>
                                    <pdfaField:name>name</pdfaField:name>
                                    <pdfaField:valueType>Text</pdfaField:valueType>
                                 </rdf:li>
                                 <rdf:li rdf:parseType="Resource">
                                    <pdfaField:description>Gives the ORCID of an author.</pdfaField:description>
                                    <pdfaField:name>orcid</pdfaField:name>
                                    <pdfaField:valueType>URI</pdfaField:valueType>
                                 </rdf:li>
                              </rdf:Seq>
                           </pdfaType:field>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:valueType>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://www.niso.org/schemas/jav/1.0/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>jav</pdfaSchema:prefix>
                  <pdfaSchema:schema>NISO</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Values for Journal Article Version are one of the following:
AO = Author’s Original
SMUR = Submitted Manuscript Under Review
AM = Accepted Manuscript
P = Proof
VoR = Version of Record
CVoR = Corrected Version of Record
EVoR = Enhanced Version of Record</pdfaProperty:description>
                           <pdfaProperty:name>journal_article_version</pdfaProperty:name>
                           <pdfaProperty:valueType>Closed Choice of Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
            </rdf:Bag>
         </pdfaExtension:schemas>
      </rdf:Description>
   </rdf:RDF>
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