IndexRecordTransformerTest for producing a record that can be manually submitted to solr
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package eu.dnetlib.dhp.oa.provision;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import java.io.IOException;
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import java.io.StringReader;
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import java.io.StringWriter;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.List;
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import javax.xml.transform.Transformer;
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import javax.xml.transform.TransformerException;
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import javax.xml.transform.stream.StreamResult;
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import javax.xml.transform.stream.StreamSource;
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import org.apache.commons.io.IOUtils;
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import org.apache.solr.client.solrj.util.ClientUtils;
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import org.apache.solr.common.SolrInputDocument;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.collect.Lists;
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import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
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import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
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import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
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import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
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import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
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import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
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import eu.dnetlib.dhp.schema.oaf.Project;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
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public class IndexRecordTransformerTest {
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public static final String VERSION = "2021-04-15T10:05:53Z";
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public static final String DSID = "b9ee796a-c49f-4473-a708-e7d67b84c16d_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl";
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private ContextMapper contextMapper;
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@BeforeEach
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public void setUp() {
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contextMapper = new ContextMapper();
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}
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@Test
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public void testTrasformRecord() throws IOException, TransformerException {
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String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml"));
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public void testPreBuiltRecordTransformation() throws IOException, TransformerException {
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String record = IOUtils.toString(getClass().getResourceAsStream("record.xml"));
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testRecordTransformation(record);
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}
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@Test
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public void testPublicationRecordTransformation() throws IOException, TransformerException {
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XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation,
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XmlRecordFactoryTest.otherDsTypeId);
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Publication p = load("publication.json", Publication.class);
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Project pj = load("project.json", Project.class);
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Relation rel = load("relToValidatedProject.json", Relation.class);
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JoinedEntity je = new JoinedEntity<>(p);
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je
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.setLinks(
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Lists
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.newArrayList(
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new RelatedEntityWrapper(rel,
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CreateRelatedEntitiesJob_phase1.asRelatedEntity(pj, Project.class))));
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String record = xmlRecordFactory.build(je);
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assertNotNull(record);
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testRecordTransformation(record);
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}
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private void testRecordTransformation(String record) throws IOException, TransformerException {
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String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml"));
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String xslt = IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"));
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String transformer = XmlIndexingJob.getLayoutTransformer("DMF", fields, xslt);
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Transformer tr = SaxonTransformerFactory.newInstance(transformer);
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String a = XmlIndexingJob.toIndexRecord(tr, record);
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String indexRecordXML = XmlIndexingJob.toIndexRecord(tr, record);
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System.out.println(a);
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SolrInputDocument solrDoc = new StreamingInputDocumentFactory(VERSION, DSID).parseDocument(indexRecordXML);
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final String xmlDoc = ClientUtils.toXML(solrDoc);
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Assertions.assertNotNull(xmlDoc);
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System.out.println(xmlDoc);
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}
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private <T> T load(String fileName, Class<T> clazz) throws IOException {
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return XmlRecordFactoryTest.OBJECT_MAPPER
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.readValue(IOUtils.toString(getClass().getResourceAsStream(fileName)), clazz);
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}
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}
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@ -29,9 +29,9 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
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public class XmlRecordFactoryTest {
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private static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource";
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public static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource";
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private static ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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public static ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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@Test
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@ -61,7 +61,7 @@
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<FIELD indexable="true" name="funderoriginalname" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree/funder/originalname"/>
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<FIELD indexable="true" name="funderjurisdiction" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree/funder/jurisdiction"/><!-- RESULT FIELDS -->
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<FIELD indexable="true" name="resulttitle" result="false" stat="false" xpath="//*[local-name() = 'entity']/*[local-name() ='result']/title | //*[local-name()='entity']/*[local-name()='result']/children/result/title"/>
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<FIELD indexable="true" name="resultsubject" result="false" stat="false" type="string_ci" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/subject)"/>
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<FIELD indexable="true" name="resultsubject" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/subject)"/>
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<FIELD indexable="true" name="resultsubjectclass" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/subject/@classname)"/>
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<FIELD indexable="true" multivalued="false" name="resultembargoenddate" result="false" stat="false" type="pdate" value="//*[local-name()='entity']/*[local-name()='result']/embargoenddate"/>
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<FIELD indexable="true" multivalued="false" name="resultembargoendyear" result="false" stat="false" tokenizable="false" value="dnet:extractYear(//*[local-name()='entity']/*[local-name()='result']/embargoenddate)"/>
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@ -72,7 +72,6 @@
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<FIELD indexable="true" name="resultdescription" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='result']//*[local-name()='description']"/>
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<FIELD indexable="true" name="resultlicense" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='result']/children/instance/license"/>
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<FIELD indexable="true" name="resultaccessright" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='result']/children/instance/accessright/@classname"/>
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<FIELD indexable="true" name="resultresourcetypename" result="false" stat="false" type="string_ci" xpath="//*[local-name()='entity']/*[local-name()='result']/resourcetype/@classname"/>
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<FIELD indexable="true" multivalued="false" name="resultbestaccessright" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/bestaccessright/@classname)"/>
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<FIELD indexable="true" multivalued="false" name="resultdateofacceptance" result="false" stat="false" type="pdate" value="//*[local-name()='entity']/*[local-name()='result']/dateofacceptance"/>
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<FIELD indexable="true" multivalued="false" name="resultacceptanceyear" result="false" stat="false" tokenizable="false" value="dnet:extractYear(//*[local-name()='entity']/*[local-name()='result']/dateofacceptance)"/>
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@ -131,9 +130,9 @@
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<FIELD indexable="true" name="collectedfromdatasourceid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*/*[local-name()='collectedfrom']/@id | //*[local-name()='entity']/*//*[local-name() = 'instance']/*[local-name()='collectedfrom']/@id)"/>
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<FIELD indexable="true" name="collectedfromname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*/*[local-name()='collectedfrom']/@name | //*[local-name()='entity']/*//*[local-name() = 'instance']/*[local-name()='collectedfrom']/@name)"/>
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<FIELD indexable="true" name="originalid" result="false" stat="false" tokenizable="false" type="string_ci" xpath="//*[local-name()='entity']/*/*[local-name()='originalId']"/>
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<FIELD indexable="true" name="pid" result="false" stat="false" tokenizable="false" type="string_ci" xpath="//*[local-name()='entity']/*[local-name()='result']/pid/text()"/>
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<FIELD indexable="true" name="pidclassid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/pid/@classid)"/>
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<FIELD indexable="true" name="pidclassname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/pid/@classname)"/>
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<FIELD indexable="true" name="pid" result="false" stat="false" tokenizable="false" type="string_ci" xpath="//*[local-name()='entity']/*/pid/text()"/>
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<FIELD indexable="true" name="pidclassid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*/pid/@classid)"/>
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<FIELD indexable="true" name="pidclassname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*/pid/@classname)"/>
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<FIELD indexable="true" name="inferred" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//datainfo/inferred"/>
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<FIELD indexable="true" name="deletedbyinference" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//datainfo/deletedbyinference"/>
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<FIELD indexable="true" name="trust" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//datainfo/trust"/>
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@ -1,774 +1,78 @@
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<result xmlns:dri="http://www.driver-repository.eu/namespace/dri">
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<header xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<dri:objIdentifier>dedup_wf_001::113ca964590682d906a3588d3d6b4838</dri:objIdentifier>
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<dri:dateOfCollection>2020-03-15T05:46:43.509Z</dri:dateOfCollection>
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<dri:dateOfTransformation>2020-03-15T21:17:13.902Z</dri:dateOfTransformation>
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</header>
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<metadata>
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<oaf:entity xmlns:oaf="http://namespace.openaire.eu/oaf"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://namespace.openaire.eu/oaf https://www.openaire.eu/schema/1.0/oaf-1.0.xsd">
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<oaf:result>
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<collectedfrom name="scholExplorer"
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id="openaire____::e034d6a11054f5ade9221ebac484e864"/>
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<collectedfrom name="UnpayWall" id="openaire____::8ac8380272269217cb09a928c8caa993"/>
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<collectedfrom name="DOAJ-Articles"
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id="driver______::bee53aa31dc2cbb538c10c2b65fa5824"/>
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<collectedfrom name="Crossref" id="openaire____::081b82f96300b6a6e3d282bad31cb6e2"/>
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<collectedfrom name="Microsoft Academic Graph"
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id="openaire____::5f532a3fc4f1ea403f37070f59a7a53a"/>
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<collectedfrom name="PubMed Central"
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id="opendoar____::eda80a3d5b344bc40f3bc04f65b7a357"/>
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<originalId>oai:pubmedcentral.nih.gov:5657733</originalId>
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<originalId>oai:doaj.org/article:f26495a4c1d149099049e1a604fa1256</originalId>
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<originalId>10.1177/0963689717714320</originalId>
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<pid classid="pmid" classname="pmid" schemeid="dnet:pid_types"
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schemename="dnet:pid_types" inferred="false">28933215</pid>
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<pid classid="pmc" classname="pmc" schemeid="dnet:pid_types"
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schemename="dnet:pid_types" inferred="false">PMC5657733</pid>
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<pid classid="doi" classname="doi" schemeid="dnet:pid_types"
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schemename="dnet:pid_types" inferred="false">10.1177/0963689717714320</pid>
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<title classid="main title" classname="main title" schemeid="dnet:dataCite_title"
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schemename="dnet:dataCite_title" inferred="false">Extract Protects Model Neurons
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from Traumatic Injury</title>
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<bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
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schemename="dnet:access_modes"/>
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<creator rank="1">Jain, Subhash C.</creator>
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<creator rank="2">Citron, Bruce A.</creator>
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<creator rank="3">Vijayalakshmi Ravindranath</creator>
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<creator rank="4">Saykally, Jessica N.</creator>
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<creator rank="5">Keeley, Kristen L.</creator>
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<creator rank="6">Haris Hatic</creator>
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<creator rank="7" name="Miriam" surname="Baglioni" orcid_pending="0000-0002-2273-9004">Baglioni, Miriam</creator>
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<creator rank="8" name="Michele" surname="De Bonis" orcid="0000-0002-2273-9004">De Bonis, Michele</creator>
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<dateofacceptance>2017-06-01</dateofacceptance>
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<description>Withania somnifera has been used in traditional medicine for a variety
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of neural disorders. Recently, chronic neurodegenerative conditions have been
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shown to benefit from treatment with this extract. To evaluate the action of
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this extract on traumatically injured neurons, the efficacy of W. somnifera root
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extract as a neuroprotective agent was examined in cultured model neurons
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exposed to an in vitro injury system designed to mimic mild traumatic brain
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injury (TBI). Neuronal health was evaluated by staining with annexin V (an
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early, apoptotic feature) and monitoring released lactate dehydrogenase activity
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(a terminal cell loss parameter). Potential mechanisms underlying the observed
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neuroprotection were examined. Additionally, morphological changes were
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monitored following injury and treatment. Although no differences were found in
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the expression of the antioxidant transcription factor nuclear factor erythroid
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2-like 2 (Nrf2) or other Nrf2-related downstream components, significant changes
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were seen in apoptotic signaling. Treatment with the extract resulted in an
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increased length of neurites projecting from the neuronal cell body after
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injury. W. somnifera extract treatment also resulted in reduced cell death in
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the model neuron TBI system. The cell death factor Bax was involved (its
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expression was reduced 2-fold by the treatment) and injury-induced reduction in
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neurite lengths and numbers was reversed by the treatment. This all indicates
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that W. somnifera root extract was neuroprotective and could have therapeutic
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potential to target factors involved in secondary injury and long-term sequelae
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of mild TBI.</description>
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<embargoenddate/>
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<subject classid="keyword" classname="keyword"
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schemeid="dnet:subject_classification_typologies"
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schemename="dnet:subject_classification_typologies" inferred="false">Withania
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somnifera</subject>
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<subject classid="keyword" classname="keyword"
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schemeid="dnet:subject_classification_typologies"
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schemename="dnet:subject_classification_typologies" inferred="false">R</subject>
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<subject classid="keyword" classname="keyword" schemeid="dnet:subject"
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schemename="dnet:subject" inferred="false">Cell Biology</subject>
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<subject classid="keyword" classname="keyword"
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schemeid="dnet:subject_classification_typologies"
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schemename="dnet:subject_classification_typologies" inferred="false"
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>neuroprotection</subject>
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<subject classid="keyword" classname="keyword"
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schemeid="dnet:subject_classification_typologies"
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schemename="dnet:subject_classification_typologies" inferred="false"
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>SH-SY5Y</subject>
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<subject classid="keyword" classname="keyword" schemeid="dnet:subject"
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schemename="dnet:subject" inferred="false">Biomedical Engineering</subject>
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<subject classid="keyword" classname="keyword" schemeid="dnet:subject"
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schemename="dnet:subject" inferred="false">Transplantation</subject>
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<subject classid="keyword" classname="keyword"
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schemeid="dnet:subject_classification_typologies"
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schemename="dnet:subject_classification_typologies" inferred="false">traumatic
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brain injury</subject>
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<subject classid="keyword" classname="keyword"
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schemeid="dnet:subject_classification_typologies"
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schemename="dnet:subject_classification_typologies" inferred="false"
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>neurites</subject>
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<subject classid="keyword" classname="keyword"
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schemeid="dnet:subject_classification_typologies"
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schemename="dnet:subject_classification_typologies" inferred="false"
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>Ayurveda</subject>
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<subject classid="keyword" classname="keyword"
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schemeid="dnet:subject_classification_typologies"
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schemename="dnet:subject_classification_typologies" inferred="false"
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>Medicine</subject>
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<language classid="eng" classname="English" schemeid="dnet:languages"
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schemename="dnet:languages"/>
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<relevantdate classid="dnet:date" classname="dnet:date" schemeid="dnet:date"
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schemename="dnet:date" inferred="false">2018-11-13</relevantdate>
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<relevantdate classid="published-online" classname="published-online"
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schemeid="dnet:dataCite_date" schemename="dnet:dataCite_date" inferred="false"
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>2017-6-30</relevantdate>
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<relevantdate classid="published-print" classname="published-print"
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schemeid="dnet:dataCite_date" schemename="dnet:dataCite_date" inferred="false"
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>2017-7-1</relevantdate>
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<publisher>SAGE Publishing</publisher>
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<source>Cell Transplantation, Vol 26 (2017)</source>
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<source>Cell Transplantation</source>
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<resulttype classid="publication" classname="publication"
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schemeid="dnet:result_typologies" schemename="dnet:result_typologies"/>
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<resourcetype classid="Book" classname="Book" schemeid="dnet:dataCite_resource" schemename="dnet:dataCite_resource" />
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<journal issn="0963-6897" eissn="1555-3892" ep="1201" iss="7" sp="1193" vol="26"
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>Cell Transplantation</journal>
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<context id="NIH" label="National Institutes of Health" type="funding">
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<category id="NIH::VETERANS AFFAIRS" label="VETERANS AFFAIRS"/>
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</context>
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<datainfo>
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<inferred>true</inferred>
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<deletedbyinference>false</deletedbyinference>
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<trust>0.9</trust>
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<inferenceprovenance>dedup-similarity-result-levenstein</inferenceprovenance>
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<provenanceaction classid="sysimport:dedup" classname="sysimport:dedup"
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schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
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</datainfo>
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<rels>
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<rel inferred="true" trust="0.8998"
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inferenceprovenance="iis::document_affiliations" provenanceaction="iis">
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<to class="hasAuthorInstitution"
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scheme="dnet:organization_organization_relations" type="organization"
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>wt__________::4de25ac59f6cb729d5716260164bb67c</to>
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<legalname>Indian Institute Of Science</legalname>
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</rel>
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<rel inferred="true" trust="0.8998"
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inferenceprovenance="iis::document_affiliations" provenanceaction="iis">
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<to class="hasAuthorInstitution"
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scheme="dnet:organization_organization_relations" type="organization"
|
||||
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schemeid="dnet:datasourceCompatibilityLevel" schemename="dnet:datasourceCompatibilityLevel"/>
|
||||
<longitude>44.7</longitude>
|
||||
<datasourcetypeui
|
||||
classid="aggregator::pubsrepository::unknown"
|
||||
classname="Publication Repository Aggregator"
|
||||
schemeid="dnet:datasource_typologies" schemename="dnet:datasource_typologies"/>
|
||||
<datasourcetype classid="aggregator::pubsrepository::unknown"
|
||||
classname="Publication Repository Aggregator"
|
||||
schemeid="dnet:datasource_typologies" schemename="dnet:datasource_typologies"/>
|
||||
<latitude>20.4</latitude>
|
||||
<versioning>false</versioning>
|
||||
<odnumberofitems/>
|
||||
<odnumberofitemsdate/>
|
||||
<odpolicies/>
|
||||
<odlanguages/>
|
||||
<odcontenttypes/>
|
||||
<releasestartdate/>
|
||||
<releaseenddate/>
|
||||
<missionstatementurl/>
|
||||
<databaseaccesstype/>
|
||||
<datauploadtype/>
|
||||
<databaseaccessrestriction/>
|
||||
<datauploadrestriction/>
|
||||
<citationguidelineurl/>
|
||||
<qualitymanagementkind/>
|
||||
<pidsystems/>
|
||||
<certificates/>
|
||||
<policies id="" name=""/>
|
||||
<collectedfrom
|
||||
id="infrastruct_::f66f1bd369679b5b077dcdf006089556" name="OpenAIRE"/>
|
||||
<originalId>openaire____::UklGRFQgLSBSZXBvc2l0b3J5IG9mIEluc3RpdHV0ZSBmb3IgUGhpbG9zb3BoeSBhbmQgU29jaWFsIFRoZW9yeQ==</originalId>
|
||||
<originalId>piwik:121</originalId>
|
||||
<pid classid="" classname="" schemeid="" schemename=""/>
|
||||
<datainfo>
|
||||
<inferred>false</inferred>
|
||||
<deletedbyinference>false</deletedbyinference>
|
||||
<trust>0.9</trust>
|
||||
<inferenceprovenance/>
|
||||
<provenanceaction
|
||||
classid="sysimport:crosswalk:entityregistry"
|
||||
classname="sysimport:crosswalk:entityregistry"
|
||||
schemeid="dnet:provenance_actions" schemename="dnet:provenance_actions"/>
|
||||
</datainfo>
|
||||
<rels/>
|
||||
<children/>
|
||||
</oaf:datasource>
|
||||
</oaf:entity>
|
||||
</metadata>
|
||||
</result>
|
||||
</record>
|
||||
Loading…
Reference in New Issue