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Title:           Broad-spectrum ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD from Bradyrhizobium (sp. XS1150)
Subject:         Communications Biology, doi:10.1038/s42003-024-06344-w
Keywords:        
Author:          Ying Li
Creator:         Springer
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      Title: Broad-spectrum ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD from Bradyrhizobium (sp.’XS1150)
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       Item: 
        Title: Results
        Destination: A1
        Children: 
         Item: 
          Title: NopD has an unusual multiple activity for SUMO, ubiquitin and’Nedd8
          Destination: B1
         Item: 
          Title: Overall complex structures of NopD with Arabidopsis SUMO2 and ubiquitin
          Destination: B2
         Item: 
          Title: C-terminal tail comparison of SUMO2 and ubiquitin in’NopD
          Destination: B3
         Item: 
          Title: Unraveling the SUMO2 and ubiquitin interface with’NopD
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         Item: 
          Title: Dissecting the deconjugation activities in tobacco leaves infiltration’assays
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       Item: 
        Title: Discussion
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       Item: 
        Title: Materials and methods
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        Children: 
         Item: 
          Title: Plasmids, Cloning and Point Mutation
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         Item: 
          Title: Protein expression and purification
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         Item: 
          Title: Preparation of the NopD complexes with AtSUMO2 and ubiquitin
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         Item: 
          Title: Crystallization and data collection
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         Item: 
          Title: Activity-based binding probe’assays
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         Item: 
          Title: AMC-substrate hydrolysis’assays
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         Item: 
          Title: In vitro de-ubiquitination’assays
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         Item: 
          Title: In vitro de-SUMOyation’assays
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         Item: 
          Title: Cell-Death Tobacco Leaves’assays
          Destination: B14
         Item: 
          Title: Statistics and reproducibility
          Destination: B15
       Item: 
        Title: Data availability
        Destination: A4
       Item: 
        Title: References
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       Item: 
        Title: Acknowledgements
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       Item: 
        Title: Author contributions
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       Item: 
        Title: Competing interests
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       Item: 
        Title: Additional information
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    Title: Broad-spectrum ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD from Bradyrhizobium (sp. XS1150)
    Author: Ying Li
    Subject: Communications Biology, doi:10.1038/s42003-024-06344-w
    Keywords: 
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               <rdf:li>springerlink.com</rdf:li>
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         <crossmark:MajorVersionDate>2010-04-23</crossmark:MajorVersionDate>
         <crossmark:CrossmarkDomainExclusive>True</crossmark:CrossmarkDomainExclusive>
         <crossmark:DOI>10.1038/s42003-024-06344-w</crossmark:DOI>
         <crossmark:CrossMarkDomains>
            <rdf:Seq>
               <rdf:li>springer.com</rdf:li>
               <rdf:li>springerlink.com</rdf:li>
            </rdf:Seq>
         </crossmark:CrossMarkDomains>
         <xmp:CreatorTool>Springer</xmp:CreatorTool>
         <xmp:ModifyDate>2024-05-27T14:10:07+02:00</xmp:ModifyDate>
         <xmp:CreateDate>2024-05-27T15:21:59+05:30</xmp:CreateDate>
         <xmp:MetadataDate>2024-05-27T14:10:07+02:00</xmp:MetadataDate>
         <xmpRights:Marked>True</xmpRights:Marked>
         <pdf:Keywords></pdf:Keywords>
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         <xmpMM:History>
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                  <stEvt:parameters>converted to PDF/A-2b</stEvt:parameters>
                  <stEvt:softwareAgent>pdfToolbox</stEvt:softwareAgent>
                  <stEvt:when>2024-05-27T15:23:18+05:30</stEvt:when>
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                  <author:name>Ying Li</author:name>
                  <author:orcid>http://orcid.org/0000-0002-5377-6262</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Jordi Perez-Gil</author:name>
                  <author:orcid>http://orcid.org/0000-0002-5632-9556</author:orcid>
               </rdf:li>
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                  <author:name>L. Maria Lois</author:name>
                  <author:orcid>http://orcid.org/0000-0003-0638-1484</author:orcid>
               </rdf:li>
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                  <author:name>Nathalia Varejão</author:name>
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               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>David Reverter</author:name>
                  <author:orcid>http://orcid.org/0000-0002-5347-0992</author:orcid>
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                  <pdfaSchema:schema>XMP Media Management Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
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                        <rdf:li rdf:parseType="Resource">
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                           <pdfaProperty:name>InstanceID</pdfaProperty:name>
                           <pdfaProperty:valueType>URI</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
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                           <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:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>A reference to the original document from which this one is derived. It is a minimal reference; missing components can be assumed to be unchanged. For example, a new version might only need to specify the instance ID and version number of the previous version, or a rendition might only need to specify the instance ID and rendition class of the original.</pdfaProperty:description>
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                           <pdfaProperty:valueType>ResourceRef</pdfaProperty:valueType>
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                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
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                           <pdfaType:namespaceURI>http://ns.adobe.com/xap/1.0/sType/Part#</pdfaType:namespaceURI>
                           <pdfaType:prefix>stPart</pdfaType:prefix>
                           <pdfaType:type>Part</pdfaType:type>
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                  <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>
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                  </pdfaSchema:property>
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               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://ns.adobe.com/xap/1.0/t/pg/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>xmpTPg</pdfaSchema:prefix>
                  <pdfaSchema:schema>XMP Paged-Text</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>XMP08 Spec: An ordered array of plate names that are needed to print the document (including any in contained documents).</pdfaProperty:description>
                           <pdfaProperty:name>PlateNames</pdfaProperty:name>
                           <pdfaProperty:valueType>Seq Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>A structure containing the characteristics of a font used in a document</pdfaProperty:description>
                           <pdfaProperty:name>Fonts</pdfaProperty:name>
                           <pdfaProperty:valueType>Bag Font</pdfaProperty:valueType>
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                     </rdf:Seq>
                  </pdfaSchema:property>
                  <pdfaSchema:valueType>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaType:description>A structure containing the characteristics of a font used in a document.</pdfaType:description>
                           <pdfaType:namespaceURI>http://ns.adobe.com/xap/1.0/sType/Font#</pdfaType:namespaceURI>
                           <pdfaType:prefix>stFnt</pdfaType:prefix>
                           <pdfaType:type>Font</pdfaType:type>
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                  <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://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">
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                  <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>
      <pdf:Producer>iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version)</pdf:Producer></rdf:Description>
   </rdf:RDF>
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