From fb61051cac4b39131221031bcc431e222d5dd2d8 Mon Sep 17 00:00:00 2001
From: Fred Atherden <43879983+fred-atherden@users.noreply.github.com>
Date: Tue, 16 Jan 2024 08:28:07 +0000
Subject: [PATCH] Include pre and final versions of clintrial-conformance-9

---
 src/final-JATS-schematron.sch                 |    5 +-
 src/final-JATS-schematron.xsl                 |    4 +-
 src/final-package-JATS-schematron.sch         |    5 +-
 src/pre-JATS-schematron.sch                   |    5 +-
 src/pre-JATS-schematron.xsl                   |    8 +-
 src/schematron.sch                            |    8 +-
 .../final-clintrial-conformance-9/fail.xml    |   29 +
 .../final-clintrial-conformance-9.sch         | 1303 +++++++++++++++++
 .../final-clintrial-conformance-9/pass.xml    |   29 +
 .../pre-clintrial-conformance-9/fail.xml      |   29 +
 .../pre-clintrial-conformance-9/pass.xml      |   29 +
 .../pre-clintrial-conformance-9.sch           | 1303 +++++++++++++++++
 test/xspec/schematron.sch                     |    5 +-
 test/xspec/schematron.xspec                   |   22 +-
 14 files changed, 2767 insertions(+), 17 deletions(-)
 create mode 100644 test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/fail.xml
 create mode 100644 test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/final-clintrial-conformance-9.sch
 create mode 100644 test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/pass.xml
 create mode 100644 test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/fail.xml
 create mode 100644 test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/pass.xml
 create mode 100644 test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/pre-clintrial-conformance-9.sch

diff --git a/src/final-JATS-schematron.sch b/src/final-JATS-schematron.sch
index 039d94528a..d3259bd2d2 100644
--- a/src/final-JATS-schematron.sch
+++ b/src/final-JATS-schematron.sch
@@ -2132,7 +2132,10 @@
       
       <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-8" test="matches(@id,'^abs[1-9]$')" role="error" id="clintrial-conformance-8">[clintrial-conformance-8] <name/> must have an @id in the format 'abs1'. <value-of select="@id"/> does not conform to this convention.</assert>
       
-      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="error" id="clintrial-conformance-9">[clintrial-conformance-9] A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
+      <!-- temporarily doing pre and final versions -->
+      
+
+      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="error" id="final-clintrial-conformance-9">[final-clintrial-conformance-9] A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
     </rule></pattern><pattern id="abstract-sec-title-content-pattern"><rule context="abstract[not(@abstract-type)]/sec/title" id="abstract-sec-title-content">
       
       <report test="*" role="error" id="struct-abs-title-1">[struct-abs-title-1] A title in a structured abstract cannot contain a child element. It should only contain text. This title with the content '<value-of select="."/>' has the following element(s): <value-of select="string-join(*/name(),'; ')"/>.</report>
diff --git a/src/final-JATS-schematron.xsl b/src/final-JATS-schematron.xsl
index a12948d1c5..e99ccdc924 100644
--- a/src/final-JATS-schematron.xsl
+++ b/src/final-JATS-schematron.xsl
@@ -11018,13 +11018,13 @@
 		    <!--REPORT error-->
       <xsl:if test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])">
          <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])">
-            <xsl:attribute name="id">clintrial-conformance-9</xsl:attribute>
+            <xsl:attribute name="id">final-clintrial-conformance-9</xsl:attribute>
             <xsl:attribute name="see">https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5</xsl:attribute>
             <xsl:attribute name="role">error</xsl:attribute>
             <xsl:attribute name="location">
                <xsl:apply-templates select="." mode="schematron-select-full-path"/>
             </xsl:attribute>
-            <svrl:text>[clintrial-conformance-9] A section with the title <xsl:text/>
+            <svrl:text>[final-clintrial-conformance-9] A section with the title <xsl:text/>
                <xsl:value-of select="title"/>
                <xsl:text/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</svrl:text>
          </svrl:successful-report>
diff --git a/src/final-package-JATS-schematron.sch b/src/final-package-JATS-schematron.sch
index bf5d1a2423..e5b4f75d11 100644
--- a/src/final-package-JATS-schematron.sch
+++ b/src/final-package-JATS-schematron.sch
@@ -2138,7 +2138,10 @@
       
       <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-8" test="matches(@id,'^abs[1-9]$')" role="error" id="clintrial-conformance-8"><name/> must have an @id in the format 'abs1'. <value-of select="@id"/> does not conform to this convention.</assert>
       
-      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="error" id="clintrial-conformance-9">A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
+      <!-- temporarily doing pre and final versions -->
+      
+
+      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="error" id="final-clintrial-conformance-9">A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
     </rule></pattern><pattern id="abstract-sec-title-content-pattern"><rule context="abstract[not(@abstract-type)]/sec/title" id="abstract-sec-title-content">
       
       <report test="*" role="error" id="struct-abs-title-1">A title in a structured abstract cannot contain a child element. It should only contain text. This title with the content '<value-of select="."/>' has the following element(s): <value-of select="string-join(*/name(),'; ')"/>.</report>
diff --git a/src/pre-JATS-schematron.sch b/src/pre-JATS-schematron.sch
index fa44670316..4f1edc9801 100644
--- a/src/pre-JATS-schematron.sch
+++ b/src/pre-JATS-schematron.sch
@@ -2077,7 +2077,10 @@
       
       <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-8" test="matches(@id,'^abs[1-9]$')" role="error" id="clintrial-conformance-8">[clintrial-conformance-8] <name/> must have an @id in the format 'abs1'. <value-of select="@id"/> does not conform to this convention.</assert>
       
-      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="error" id="clintrial-conformance-9">[clintrial-conformance-9] A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
+      <!-- temporarily doing pre and final versions -->
+      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="warning" id="pre-clintrial-conformance-9">[pre-clintrial-conformance-9] A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
+
+      
     </rule></pattern><pattern id="abstract-sec-title-content-pattern"><rule context="abstract[not(@abstract-type)]/sec/title" id="abstract-sec-title-content">
       
       <report test="*" role="error" id="struct-abs-title-1">[struct-abs-title-1] A title in a structured abstract cannot contain a child element. It should only contain text. This title with the content '<value-of select="."/>' has the following element(s): <value-of select="string-join(*/name(),'; ')"/>.</report>
diff --git a/src/pre-JATS-schematron.xsl b/src/pre-JATS-schematron.xsl
index 5db07f02b9..98da489583 100644
--- a/src/pre-JATS-schematron.xsl
+++ b/src/pre-JATS-schematron.xsl
@@ -10902,16 +10902,16 @@
          </xsl:otherwise>
       </xsl:choose>
 
-		    <!--REPORT error-->
+		    <!--REPORT warning-->
       <xsl:if test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])">
          <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])">
-            <xsl:attribute name="id">clintrial-conformance-9</xsl:attribute>
+            <xsl:attribute name="id">pre-clintrial-conformance-9</xsl:attribute>
             <xsl:attribute name="see">https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5</xsl:attribute>
-            <xsl:attribute name="role">error</xsl:attribute>
+            <xsl:attribute name="role">warning</xsl:attribute>
             <xsl:attribute name="location">
                <xsl:apply-templates select="." mode="schematron-select-full-path"/>
             </xsl:attribute>
-            <svrl:text>[clintrial-conformance-9] A section with the title <xsl:text/>
+            <svrl:text>[pre-clintrial-conformance-9] A section with the title <xsl:text/>
                <xsl:value-of select="title"/>
                <xsl:text/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</svrl:text>
          </svrl:successful-report>
diff --git a/src/schematron.sch b/src/schematron.sch
index 0af22ceccb..eeab361b4f 100644
--- a/src/schematron.sch
+++ b/src/schematron.sch
@@ -2984,10 +2984,16 @@
         role="error" 
         id="clintrial-conformance-8"><name/> must have an @id in the format 'abs1'. <value-of select="@id"/> does not conform to this convention.</assert>
       
+      <!-- temporarily doing pre and final versions -->
+      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5"
+        test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" 
+        role="warning" 
+        id="pre-clintrial-conformance-9">A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
+
       <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5"
         test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" 
         role="error" 
-        id="clintrial-conformance-9">A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
+        id="final-clintrial-conformance-9">A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
     </rule>
     
     <rule context="abstract[not(@abstract-type)]/sec/title" id="abstract-sec-title-content">
diff --git a/test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/fail.xml b/test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/fail.xml
new file mode 100644
index 0000000000..2ce40990d9
--- /dev/null
+++ b/test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/fail.xml
@@ -0,0 +1,29 @@
+<?oxygen SCHSchema="final-clintrial-conformance-9.sch"?>
+<!--Context: abstract[not(@abstract-type)]/sec
+Test: report    starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])
+Message: A section with the title  in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not. -->
+<root xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:ali="http://www.niso.org/schemas/ali/1.0/">
+  <article>
+    <abstract>
+      <sec id="abs1">
+        <title>Background:</title>
+      </sec>
+      <sec id="abs2">
+        <title>Methods:</title>
+      </sec>
+      <sec id="abs3">
+        <title>Results:</title>
+      </sec>
+      <sec id="abs4">
+        <title>Conclusions:</title>
+      </sec>
+      <sec id="abs5">
+        <title>Funding:</title>
+      </sec>
+      <sec id="abs6">
+        <title>Clinical trial number:</title>
+        <p><ext-link ext-link-type="uri" xlink:href="https://clinicaltrials.gov/">https://clinicaltrials.gov/</ext-link> (CTN1234567890).</p>
+      </sec>
+    </abstract>
+  </article>
+</root>
\ No newline at end of file
diff --git a/test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/final-clintrial-conformance-9.sch b/test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/final-clintrial-conformance-9.sch
new file mode 100644
index 0000000000..bb52f08133
--- /dev/null
+++ b/test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/final-clintrial-conformance-9.sch
@@ -0,0 +1,1303 @@
+<schema xmlns="http://purl.oclc.org/dsdl/schematron" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:java="http://www.java.com/" xmlns:file="java.io.File" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:mml="http://www.w3.org/1998/Math/MathML" queryBinding="xslt2">
+  <title>eLife Schematron</title>
+  <ns uri="http://www.niso.org/schemas/ali/1.0/" prefix="ali"/>
+  <ns uri="http://www.w3.org/XML/1998/namespace" prefix="xml"/>
+  <ns uri="http://www.w3.org/1999/xlink" prefix="xlink"/>
+  <ns uri="http://www.w3.org/2001/XInclude" prefix="xi"/>
+  <ns uri="http://www.w3.org/1998/Math/MathML" prefix="mml"/>
+  <ns uri="http://saxon.sf.net/" prefix="saxon"/>
+  <ns uri="http://purl.org/dc/terms/" prefix="dc"/>
+  <ns uri="http://www.w3.org/2001/XMLSchema" prefix="xs"/>
+  <ns uri="https://elifesciences.org/namespace" prefix="e"/>
+  <ns uri="java.io.File" prefix="file"/>
+  <ns uri="http://www.java.com/" prefix="java"/>
+  <let name="features-subj" value="('Feature Article', 'Insight', 'Editorial')"/>
+  <let name="features-article-types" value="('article-commentary','editorial','discussion')"/>
+  <let name="research-subj" value="('Research Article', 'Short Report', 'Tools and Resources', 'Research Advance', 'Registered Report', 'Replication Study', 'Research Communication', 'Correction', 'Retraction', 'Scientific Correspondence', 'Review Article')"/>
+  <let name="notice-article-types" value="('correction','retraction','expression-of-concern')"/>
+  <let name="notice-display-types" value="('Correction','Retraction','Expression of Concern')"/>
+  <let name="allowed-article-types" value="('research-article','review-article',$features-article-types, $notice-article-types)"/>
+  <let name="allowed-disp-subj" value="($research-subj, $features-subj)"/>
+  <let name="MSAs" value="('Biochemistry and Chemical Biology', 'Cancer Biology', 'Cell Biology', 'Chromosomes and Gene Expression', 'Computational and Systems Biology', 'Developmental Biology', 'Ecology', 'Epidemiology and Global Health', 'Evolutionary Biology', 'Genetics and Genomics', 'Medicine', 'Immunology and Inflammation', 'Microbiology and Infectious Disease', 'Neuroscience', 'Physics of Living Systems', 'Plant Biology', 'Stem Cells and Regenerative Medicine', 'Structural Biology and Molecular Biophysics')"/>
+  <let name="funders" value="'../../../../../src/funders.xml'"/>
+  <let name="wellcome-fundref-ids" value="('http://dx.doi.org/10.13039/100010269','http://dx.doi.org/10.13039/100004440')"/>
+  <xsl:function name="e:is-prc" as="xs:boolean">
+    <xsl:param name="elem" as="node()"/>
+    <xsl:choose>
+      <xsl:when test="$elem/name()='article'">
+        <xsl:value-of select="e:is-prc-helper($elem)"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="e:is-prc-helper($elem/ancestor::article[1])"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:is-prc-helper" as="xs:boolean">
+    <xsl:param name="article" as="node()"/>
+    <xsl:choose>
+      <xsl:when test="$article//article-meta/custom-meta-group/custom-meta[meta-name='publishing-route']/meta-value='prc'">
+        <xsl:value-of select="true()"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="false()"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-version" as="xs:string">
+    <xsl:param name="elem" as="node()"/>
+    <xsl:choose>
+      <xsl:when test="$elem/name()='article'">
+        <xsl:value-of select="e:get-version-helper($elem)"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="e:get-version-helper($elem/ancestor::article[1])"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-version-helper" as="xs:string">
+    <xsl:param name="article" as="node()"/>
+    <xsl:choose>
+      <xsl:when test="$article//article-meta/custom-meta-group/custom-meta[meta-name='schema-version']/meta-value">
+        <xsl:value-of select="$article//article-meta/custom-meta-group/custom-meta[meta-name='schema-version']/meta-value"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'1'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:titleCaseToken" as="xs:string">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="contains($s,'-')">
+        <xsl:value-of select="concat(           upper-case(substring(substring-before($s,'-'), 1, 1)),           lower-case(substring(substring-before($s,'-'),2)),           '-',           upper-case(substring(substring-after($s,'-'), 1, 1)),           lower-case(substring(substring-after($s,'-'),2)))"/>
+      </xsl:when>
+      <xsl:when test="lower-case($s)='elife'">
+        <xsl:value-of select="'eLife'"/>
+      </xsl:when>
+      <xsl:when test="lower-case($s)=('and','or','the','an','of','in','as','at','by','for','a','to','up','but','yet')">
+        <xsl:value-of select="lower-case($s)"/>
+      </xsl:when>
+      <xsl:when test="matches(lower-case($s),'^rna$|^dna$|^mri$|^hiv$|^tor$|^aids$|^covid-19$|^covid$')">
+        <xsl:value-of select="upper-case($s)"/>
+      </xsl:when>
+      <xsl:when test="matches(lower-case($s),'[1-4]d')">
+        <xsl:value-of select="upper-case($s)"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="concat(upper-case(substring($s, 1, 1)), lower-case(substring($s, 2)))"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:titleCase" as="xs:string">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      
+      <xsl:when test="lower-case($s)='protein kinase a'">
+        <xsl:value-of select="'Protein Kinase A'"/>
+      </xsl:when>
+      <xsl:when test="contains($s,' ')">
+        <xsl:variable name="token1" select="substring-before($s,' ')"/>
+        <xsl:variable name="token2" select="substring-after($s,$token1)"/>
+        <xsl:choose>
+          <xsl:when test="lower-case($token1)='elife'">
+            <xsl:value-of select="concat('eLife',               ' ',               string-join(for $x in tokenize(substring-after($token2,' '),'\p{Zs}') return e:titleCaseToken($x),' ')               )"/>
+          </xsl:when>
+          <xsl:when test="matches(lower-case($token1),'^rna$|^dna$|^mri$|^hiv$|^tor$|^aids$|^covid-19$|^covid$')">
+            <xsl:value-of select="concat(upper-case($token1),               ' ',               string-join(for $x in tokenize(substring-after($token2,' '),'\p{Zs}') return e:titleCaseToken($x),' ')               )"/>
+          </xsl:when>
+          <xsl:when test="matches(lower-case($token1),'[1-4]d')">
+            <xsl:value-of select="concat(upper-case($token1),               ' ',               string-join(for $x in tokenize(substring-after($token2,' '),'\p{Zs}') return e:titleCaseToken($x),' ')               )"/>
+          </xsl:when>
+          <xsl:when test="contains($token1,'-')">
+            <xsl:value-of select="string-join(for $x in tokenize($s,'\p{Zs}') return e:titleCaseToken($x),' ')"/>
+          </xsl:when>
+          <xsl:otherwise>
+            <xsl:value-of select="concat(               concat(upper-case(substring($token1, 1, 1)), lower-case(substring($token1, 2))),               ' ',               string-join(for $x in tokenize(substring-after($token2,' '),'\p{Zs}') return e:titleCaseToken($x),' ')               )"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:when>
+      <xsl:when test="lower-case($s)='elife'">
+        <xsl:value-of select="'eLife'"/>
+      </xsl:when>
+      <xsl:when test="lower-case($s)=('and','or','the','an','of')">
+        <xsl:value-of select="lower-case($s)"/>
+      </xsl:when>
+      <xsl:when test="matches(lower-case($s),'^rna$|^dna$|^mri$|^hiv$|^tor$|^aids$|^covid-19$|^covid$')">
+        <xsl:value-of select="upper-case($s)"/>
+      </xsl:when>
+      <xsl:when test="matches(lower-case($s),'[1-4]d')">
+        <xsl:value-of select="upper-case($s)"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="e:titleCaseToken($s)"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:article-type2title" as="xs:string">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="$s = 'Replication Study'">
+        <xsl:value-of select="'Replication Study:'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'Registered Report'">
+        <xsl:value-of select="'Registered report:'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'Correction'">
+        <xsl:value-of select="'Correction:'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'Retraction'">
+        <xsl:value-of select="'Retraction:'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'Expression of Concern'">
+        <xsl:value-of select="'Expression of Concern:'"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'undefined'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:sec-type2title" as="xs:string">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="$s = 'intro'">
+        <xsl:value-of select="'Introduction'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'results'">
+        <xsl:value-of select="'Results'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'discussion'">
+        <xsl:value-of select="'Discussion'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'materials|methods'">
+        <xsl:value-of select="'Materials and methods'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'results|discussion'">
+        <xsl:value-of select="'Results and discussion'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'methods'">
+        <xsl:value-of select="'Methods'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'model'">
+        <xsl:value-of select="'Model'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'additional-information'">
+        <xsl:value-of select="'Additional information'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'supplementary-material'">
+        <xsl:value-of select="'Additional files'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'data-availability'">
+        <xsl:value-of select="'Data availability'"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'undefined'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:fig-id-type" as="xs:string">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="matches($s,'^fig[0-9]{1,3}$')">
+        <xsl:value-of select="'Figure'"/>
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+      <xsl:when test="matches($s,'^fig[0-9]{1,3}s[0-9]{1,3}$')">
+        <xsl:value-of select="'Figure supplement'"/>
+      </xsl:when>
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+        <xsl:value-of select="'Box figure'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^app[0-9]{1,3}fig[0-9]{1,3}$')">
+        <xsl:value-of select="'Appendix figure'"/>
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+        <xsl:value-of select="'Appendix figure supplement'"/>
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+        <xsl:value-of select="'Author response figure'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^C[0-9]{1,3}$|^chem[0-9]{1,3}$')">
+        <xsl:value-of select="'Chemical structure'"/>
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+      <xsl:when test="matches($s,'^app[0-9]{1,3}C[0-9]{1,3}$|^app[0-9]{1,3}chem[0-9]{1,3}$')">
+        <xsl:value-of select="'Appendix chemical structure'"/>
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+      <xsl:when test="matches($s,'^S[0-9]{1,3}$|^scheme[0-9]{1,3}$')">
+        <xsl:value-of select="'Scheme'"/>
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+      <xsl:when test="matches($s,'^app[0-9]{1,3}S[0-9]{1,3}$|^app[0-9]{1,3}scheme[0-9]{1,3}$')">
+        <xsl:value-of select="'Appendix scheme'"/>
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+      <xsl:otherwise>
+        <xsl:value-of select="'undefined'"/>
+      </xsl:otherwise>
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+  <xsl:function name="e:stripDiacritics" as="xs:string">
+    <xsl:param name="string" as="xs:string"/>
+    <xsl:value-of select="replace(replace(replace(translate(normalize-unicode($string,'NFD'),'ƀȼđɇǥħɨıɉꝁłøɍŧɏƶ','bcdeghiijklortyz'),'[\p{M}’]',''),'æ','ae'),'ß','ss')"/>
+  </xsl:function>
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+    <xsl:param name="ref"/>
+    <xsl:choose>
+      <xsl:when test="$ref/element-citation[1]/person-group[1]/* and $ref/element-citation[1]/year">
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+      </xsl:when>
+      <xsl:when test="$ref/element-citation/person-group[1]/*">
+        <xsl:value-of select="concat(           replace(e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[1]),'\p{Zs}',''),           ' 9999 ',           string-join(for $x in $ref/element-citation[1]/person-group[1]/*[position()=(2,3)]           return replace(e:get-collab-or-surname($x),'\p{Zs}',''),' ')           )"/>
+      </xsl:when>
+      <xsl:when test="$ref/element-citation/year">
+        <xsl:value-of select="concat(' ',$ref/element-citation[1]/year[1])"/>
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+      <xsl:otherwise>
+        <xsl:value-of select="'zzzzz 9999'"/>
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+  <xsl:function name="e:ref-list-string2" as="xs:string">
+    <xsl:param name="ref"/>
+    <xsl:choose>
+      <xsl:when test="$ref/element-citation[1]/year and count($ref/element-citation[1]/person-group[1]/*) = 2">
+        <xsl:value-of select="concat(           e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[1]),           ' ',           e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[2]),           ' ',           $ref/element-citation[1]/year[1])"/>
+      </xsl:when>
+      <xsl:when test="$ref/element-citation/person-group[1]/* and $ref/element-citation[1]/year">
+        <xsl:value-of select="concat(           e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[1]),           ' ',           $ref/element-citation[1]/year[1])"/>
+      </xsl:when>
+      <xsl:when test="$ref/element-citation/person-group[1]/*">
+        <xsl:value-of select="concat(           e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[1]),           ' 9999 ')"/>
+      </xsl:when>
+      <xsl:when test="$ref/element-citation/year">
+        <xsl:value-of select="concat(' ',$ref/element-citation[1]/year[1])"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'zzzzz 9999'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-collab-or-surname" as="xs:string?">
+    <xsl:param name="collab-or-name"/>
+    <xsl:choose>
+      <xsl:when test="$collab-or-name/name()='collab'">
+        <xsl:value-of select="e:stripDiacritics(replace(lower-case($collab-or-name),'\.',''))"/>
+      </xsl:when>
+      <xsl:when test="$collab-or-name/surname">
+        <xsl:value-of select="e:stripDiacritics(lower-case($collab-or-name/surname[1]))"/>
+      </xsl:when>
+      <xsl:otherwise/>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:cite-name-text" as="xs:string">
+    <xsl:param name="person-group"/>
+    <xsl:choose>
+      <xsl:when test="(count($person-group/*) = 1) and $person-group/name">
+        <xsl:value-of select="$person-group/name/surname[1]"/>
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+      <xsl:when test="(count($person-group/*) = 1) and $person-group/collab">
+        <xsl:value-of select="$person-group/collab"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) = 2) and (count($person-group/name) = 1) and $person-group/*[1]/local-name() = 'collab'">
+        <xsl:value-of select="concat($person-group/collab,' and ',$person-group/name/surname[1])"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) = 2) and (count($person-group/name) = 1) and $person-group/*[1]/local-name() = 'name'">
+        <xsl:value-of select="concat($person-group/name/surname[1],' and ',$person-group/collab)"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) = 2) and (count($person-group/name) = 2)">
+        <xsl:value-of select="concat($person-group/name[1]/surname[1],' and ',$person-group/name[2]/surname[1])"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) = 2) and (count($person-group/collab) = 2)">
+        <xsl:value-of select="concat($person-group/collab[1],' and ',$person-group/collab[2])"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) ge 2) and $person-group/*[1]/local-name() = 'collab'">
+        <xsl:value-of select="concat($person-group/collab[1], ' et al.')"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) ge 2) and $person-group/*[1]/local-name() = 'name'">
+        <xsl:value-of select="concat($person-group/name[1]/surname[1], ' et al.')"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'undetermined'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:citation-format1" as="xs:string">
+    <xsl:param name="element-citation"/>
+    <xsl:choose>
+      <xsl:when test="$element-citation/person-group and $element-citation//year">
+        <xsl:value-of select="concat(e:cite-name-text($element-citation/person-group[1]),', ',$element-citation/descendant::year[1])"/>
+      </xsl:when>
+      <xsl:when test="$element-citation/person-group and not($element-citation//year)">
+        <xsl:value-of select="concat(e:cite-name-text($element-citation/person-group[1]),', ')"/>
+      </xsl:when>
+      <xsl:when test="not($element-citation/person-group) and $element-citation//year">
+        <xsl:value-of select="concat('et al., ',$element-citation/descendant::year[1])"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="', '"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:citation-format2" as="xs:string">
+    <xsl:param name="element-citation"/>
+    <xsl:choose>
+      <xsl:when test="$element-citation/person-group and $element-citation//year">
+        <xsl:value-of select="concat(e:cite-name-text($element-citation/person-group[1]),' (',$element-citation/descendant::year[1],')')"/>
+      </xsl:when>
+      <xsl:when test="$element-citation/person-group and not($element-citation//year)">
+        <xsl:value-of select="concat(e:cite-name-text($element-citation/person-group[1]),' ()')"/>
+      </xsl:when>
+      <xsl:when test="not($element-citation/person-group) and $element-citation//year">
+        <xsl:value-of select="concat('et al. (',$element-citation/descendant::year[1],')')"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="', '"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:ref-cite-list">
+    <xsl:param name="ref-list" as="node()"/>
+    <xsl:element name="list">
+      <xsl:for-each select="$ref-list/ref[element-citation[year]]">
+        <xsl:variable name="cite" select="e:citation-format1(./element-citation[1])"/>
+        <xsl:element name="item">
+          <xsl:attribute name="id">
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+          <xsl:value-of select="$cite"/>
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+      </xsl:for-each>
+    </xsl:element>
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+  <xsl:function name="e:non-distinct-citations">
+    <xsl:param name="cite-list" as="node()"/>
+    <xsl:element name="list">
+    <xsl:for-each select="$cite-list//*:item">
+      <xsl:variable name="cite" select="./string()"/>
+      <xsl:choose>
+        <xsl:when test="./preceding::*:item/string() = $cite">
+          <xsl:element name="item">
+            <xsl:attribute name="id">
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+            <xsl:value-of select="$cite"/>
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+        </xsl:when>
+        <xsl:when test="not(matches($cite,'[A-Za-z]$')) and (./preceding::*:item/@no-suffix/string() = $cite)">
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+            <xsl:attribute name="id">
+              <xsl:value-of select="./@id"/>
+            </xsl:attribute>
+          <xsl:value-of select="$cite"/>
+          </xsl:element>
+        </xsl:when>
+        <xsl:when test="not(matches($cite,'[A-Za-z]$')) and ./following::*:item/@no-suffix/string() = $cite">
+          <xsl:element name="item">
+            <xsl:attribute name="id">
+              <xsl:value-of select="./@id"/>
+            </xsl:attribute>
+          <xsl:value-of select="$cite"/>
+          </xsl:element>
+        </xsl:when>
+        <xsl:otherwise/>
+      </xsl:choose>
+    </xsl:for-each>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:get-name" as="xs:string">
+    <xsl:param name="name"/>
+    <xsl:choose>
+      <xsl:when test="$name/given-names[1] and $name/surname[1] and $name/suffix[1]">
+        <xsl:value-of select="concat($name/given-names[1],' ',$name/surname[1],' ',$name/suffix[1])"/>
+      </xsl:when>
+      <xsl:when test="not($name/given-names[1]) and $name/surname[1] and $name/suffix[1]">
+        <xsl:value-of select="concat($name/surname[1],' ',$name/suffix[1])"/>
+      </xsl:when>
+      <xsl:when test="$name/given-names[1] and $name/surname[1] and not($name/suffix[1])">
+        <xsl:value-of select="concat($name/given-names[1],' ',$name/surname[1])"/>
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+      <xsl:when test="not($name/given-names[1]) and $name/surname[1] and not($name/suffix[1])">
+        <xsl:value-of select="$name/surname[1]"/>
+      </xsl:when>
+      <xsl:otherwise>
+        
+        <xsl:value-of select="'No elements present'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-collab">
+    <xsl:param name="collab"/>
+    <xsl:for-each select="$collab/(*|text())">
+      <xsl:choose>
+        <xsl:when test="./name()='contrib-group'"/>
+        <xsl:otherwise>
+          <xsl:value-of select="."/>
+        </xsl:otherwise>
+      </xsl:choose>
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+  <xsl:function name="e:isbn-sum" as="xs:integer">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="string-length($s) = 10">
+        <xsl:variable name="d1" select="number(substring($s,1,1)) * 10"/>
+        <xsl:variable name="d2" select="number(substring($s,2,1)) * 9"/>
+        <xsl:variable name="d3" select="number(substring($s,3,1)) * 8"/>
+        <xsl:variable name="d4" select="number(substring($s,4,1)) * 7"/>
+        <xsl:variable name="d5" select="number(substring($s,5,1)) * 6"/>
+        <xsl:variable name="d6" select="number(substring($s,6,1)) * 5"/>
+        <xsl:variable name="d7" select="number(substring($s,7,1)) * 4"/>
+        <xsl:variable name="d8" select="number(substring($s,8,1)) * 3"/>
+        <xsl:variable name="d9" select="number(substring($s,9,1)) * 2"/>
+        <xsl:variable name="d10" select="number(substring($s,10,1)) * 1"/>
+        <xsl:value-of select="number($d1 + $d2 + $d3 + $d4 + $d5 + $d6 + $d7 + $d8 + $d9 + $d10) mod 11"/>
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+      <xsl:when test="string-length($s) = 13">
+        <xsl:variable name="d1" select="number(substring($s,1,1))"/>
+        <xsl:variable name="d2" select="number(substring($s,2,1)) * 3"/>
+        <xsl:variable name="d3" select="number(substring($s,3,1))"/>
+        <xsl:variable name="d4" select="number(substring($s,4,1)) * 3"/>
+        <xsl:variable name="d5" select="number(substring($s,5,1))"/>
+        <xsl:variable name="d6" select="number(substring($s,6,1)) * 3"/>
+        <xsl:variable name="d7" select="number(substring($s,7,1))"/>
+        <xsl:variable name="d8" select="number(substring($s,8,1)) * 3"/>
+        <xsl:variable name="d9" select="number(substring($s,9,1))"/>
+        <xsl:variable name="d10" select="number(substring($s,10,1)) * 3"/>
+        <xsl:variable name="d11" select="number(substring($s,11,1))"/>
+        <xsl:variable name="d12" select="number(substring($s,12,1)) * 3"/>
+        <xsl:variable name="d13" select="number(substring($s,13,1))"/>
+        <xsl:value-of select="number($d1 + $d2 + $d3 + $d4 + $d5 + $d6 + $d7 + $d8 + $d9 + $d10 + $d11 + $d12 + $d13) mod 10"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="number('1')"/>
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+    </xsl:choose>
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+  <xsl:function name="e:escape-for-regex" as="xs:string">
+    <xsl:param name="arg" as="xs:string?"/>
+    <xsl:sequence select="replace($arg,'(\.|\[|\]|\\|\||\-|\^|\$|\?|\*|\+|\{|\}|\(|\))','\\$1')"/>
+  </xsl:function>
+  <xsl:function name="e:get-ordinal" as="xs:string">
+    <xsl:param name="value" as="xs:integer?"/>
+    <xsl:if test="translate(string($value), '0123456789', '') = '' and number($value) &gt; 0">
+      <xsl:variable name="mod100" select="$value mod 100"/>
+      <xsl:variable name="mod10" select="$value mod 10"/>
+      <xsl:choose>
+        <xsl:when test="$mod100 = 11 or $mod100 = 12 or $mod100 = 13">
+          <xsl:value-of select="concat($value,'th')"/>
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+        <xsl:when test="$mod10 = 1">
+          <xsl:value-of select="concat($value,'st')"/>
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+        <xsl:when test="$mod10 = 2">
+          <xsl:value-of select="concat($value,'nd')"/>
+        </xsl:when>
+        <xsl:when test="$mod10 = 3">
+          <xsl:value-of select="concat($value,'rd')"/>
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+        <xsl:otherwise>
+          <xsl:value-of select="concat($value,'th')"/>
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+      </xsl:choose>
+    </xsl:if>
+  </xsl:function>
+  <let name="org-regex" value="'b\.\p{Zs}?subtilis|bacillus\p{Zs}?subtilis|d\.\p{Zs}?melanogaster|drosophila\p{Zs}?melanogaster|e\.\p{Zs}?coli|escherichia\p{Zs}?coli|s\.\p{Zs}?pombe|schizosaccharomyces\p{Zs}?pombe|s\.\p{Zs}?cerevisiae|saccharomyces\p{Zs}?cerevisiae|c\.\p{Zs}?elegans|caenorhabditis\p{Zs}?elegans|a\.\p{Zs}?thaliana|arabidopsis\p{Zs}?thaliana|m\.\p{Zs}?thermophila|myceliophthora\p{Zs}?thermophila|dictyostelium|p\.\p{Zs}?falciparum|plasmodium\p{Zs}?falciparum|s\.\p{Zs}?enterica|salmonella\p{Zs}?enterica|s\.\p{Zs}?pyogenes|streptococcus\p{Zs}?pyogenes|p\.\p{Zs}?dumerilii|platynereis\p{Zs}?dumerilii|p\.\p{Zs}?cynocephalus|papio\p{Zs}?cynocephalus|o\.\p{Zs}?fasciatus|oncopeltus\p{Zs}?fasciatus|n\.\p{Zs}?crassa|neurospora\p{Zs}?crassa|c\.\p{Zs}?intestinalis|ciona\p{Zs}?intestinalis|e\.\p{Zs}?cuniculi|encephalitozoon\p{Zs}?cuniculi|h\.\p{Zs}?salinarum|halobacterium\p{Zs}?salinarum|s\.\p{Zs}?solfataricus|sulfolobus\p{Zs}?solfataricus|s\.\p{Zs}?mediterranea|schmidtea\p{Zs}?mediterranea|s\.\p{Zs}?rosetta|salpingoeca\p{Zs}?rosetta|n\.\p{Zs}?vectensis|nematostella\p{Zs}?vectensis|s\.\p{Zs}?aureus|staphylococcus\p{Zs}?aureus|v\.\p{Zs}?cholerae|vibrio\p{Zs}?cholerae|t\.\p{Zs}?thermophila|tetrahymena\p{Zs}?thermophila|c\.\p{Zs}?reinhardtii|chlamydomonas\p{Zs}?reinhardtii|n\.\p{Zs}?attenuata|nicotiana\p{Zs}?attenuata|e\.\p{Zs}?carotovora|erwinia\p{Zs}?carotovora|e\.\p{Zs}?faecalis|h\.\p{Zs}?sapiens|homo\p{Zs}?sapiens|c\.\p{Zs}?trachomatis|chlamydia\p{Zs}?trachomatis|enterococcus\p{Zs}?faecalis|x\.\p{Zs}?laevis|xenopus\p{Zs}?laevis|x\.\p{Zs}?tropicalis|xenopus\p{Zs}?tropicalis|m\.\p{Zs}?musculus|mus\p{Zs}?musculus|d\.\p{Zs}?immigrans|drosophila\p{Zs}?immigrans|d\.\p{Zs}?subobscura|drosophila\p{Zs}?subobscura|d\.\p{Zs}?affinis|drosophila\p{Zs}?affinis|d\.\p{Zs}?obscura|drosophila\p{Zs}?obscura|f\.\p{Zs}?tularensis|francisella\p{Zs}?tularensis|p\.\p{Zs}?plantaginis|podosphaera\p{Zs}?plantaginis|p\.\p{Zs}?lanceolata|plantago\p{Zs}?lanceolata|m\.\p{Zs}?trossulus|mytilus\p{Zs}?trossulus|m\.\p{Zs}?edulis|mytilus\p{Zs}?edulis|m\.\p{Zs}?chilensis|mytilus\p{Zs}?chilensis|u\.\p{Zs}?maydis|ustilago\p{Zs}?maydis|p\.\p{Zs}?knowlesi|plasmodium\p{Zs}?knowlesi|p\.\p{Zs}?aeruginosa|pseudomonas\p{Zs}?aeruginosa|t\.\p{Zs}?brucei|trypanosoma\p{Zs}?brucei|t\.\p{Zs}?gondii|toxoplasma\p{Zs}?gondii|d\.\p{Zs}?rerio|danio\p{Zs}?rerio|yimenosaurus|lesothosaurus\p{Zs}?diagnosticus|l\.\p{Zs}?diagnosticus|scelidosaurus\p{Zs}?harrisonii|s\.\p{Zs}?harrisonii|haya\p{Zs}?griva|h\.\p{Zs}?griva|polacanthus\p{Zs}?foxii|p\.\p{Zs}?foxii|scutellosaurus\p{Zs}?lawleri|s\.\p{Zs}?lawleri|saichania\p{Zs}?chulsanensis|s\.\p{Zs}?chulsanensis|gargoyleosaurus\p{Zs}?parkpinorum|g\.\p{Zs}?parkpinorum|europelta\p{Zs}?carbonensis|e\.\p{Zs}?carbonensis|stegosaurus\p{Zs}?stenops|s\.\p{Zs}?stenops|pinacosaurus\p{Zs}?grangeri|p\.\p{Zs}?grangeri|tatisaurus\p{Zs}?oehleri|t\.\p{Zs}?oehleri|hungarosaurus\p{Zs}?tormai|h\.\p{Zs}?tormai|bienosaurus\p{Zs}?lufengensis|b\.\p{Zs}?lufengensis|fabrosaurus\p{Zs}?australis|f\.\p{Zs}?australis|chinshakiangosaurus\p{Zs}?chunghoensis|c\.\p{Zs}?chunghoensis|euoplocephalus\p{Zs}?tutus|e\.\p{Zs}?tutus|drosophila|xenopus|salmonella|g\.\p{Zs}?beringei|gorilla\p{Zs}?beringei|m\.\p{Zs}?assamensis|macaca\p{Zs}?assamensis|m\.\p{Zs}?fuscata|macaca\p{Zs}?fuscata|m\.\p{Zs}?mulatta|macaca\p{Zs}?mulatta|m\.\p{Zs}?nemestrina|macaca\p{Zs}?nemestrina|m\.\p{Zs}?sphinx|mandrillus\p{Zs}?sphinx|p\.\p{Zs}?anubis|papio\p{Zs}?anubis|p\.\p{Zs}?hamadryas|papio\p{Zs}?hamadryas|p\.\p{Zs}?paniscus|pan\p{Zs}?paniscus|p\.\p{Zs}?troglodytes|pan\p{Zs}?troglodytes'"/>
+  <let name="sec-title-regex" value="string-join(     for $x in tokenize($org-regex,'\|')     return concat('^',$x,'$')     ,'|')"/>
+  <xsl:function name="e:org-conform" as="xs:string">
+  <xsl:param name="s" as="xs:string"/>
+  <xsl:choose>
+    <xsl:when test="matches($s,'b\.\p{Zs}?subtilis')">
+      <xsl:value-of select="'B. subtilis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'bacillus\p{Zs}?subtilis')">
+      <xsl:value-of select="'Bacillus subtilis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?melanogaster')">
+      <xsl:value-of select="'D. melanogaster'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila\p{Zs}?melanogaster')">
+      <xsl:value-of select="'Drosophila melanogaster'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e\.\p{Zs}?coli')">
+      <xsl:value-of select="'E. coli'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'escherichia\p{Zs}?coli')">
+      <xsl:value-of select="'Escherichia coli'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?pombe')">
+      <xsl:value-of select="'S. pombe'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'schizosaccharomyces\p{Zs}?pombe')">
+      <xsl:value-of select="'Schizosaccharomyces pombe'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?cerevisiae')">
+      <xsl:value-of select="'S. cerevisiae'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'saccharomyces\p{Zs}?cerevisiae')">
+      <xsl:value-of select="'Saccharomyces cerevisiae'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c\.\p{Zs}?elegans')">
+      <xsl:value-of select="'C. elegans'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'caenorhabditis\p{Zs}?elegans')">
+      <xsl:value-of select="'Caenorhabditis elegans'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'a\.\p{Zs}?thaliana')">
+      <xsl:value-of select="'A. thaliana'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'arabidopsis\p{Zs}?thaliana')">
+      <xsl:value-of select="'Arabidopsis thaliana'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?thermophila')">
+      <xsl:value-of select="'M. thermophila'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'myceliophthora\p{Zs}?thermophila')">
+      <xsl:value-of select="'Myceliophthora thermophila'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'dictyostelium')">
+      <xsl:value-of select="'Dictyostelium'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?falciparum')">
+      <xsl:value-of select="'P. falciparum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'plasmodium\p{Zs}?falciparum')">
+      <xsl:value-of select="'Plasmodium falciparum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?enterica')">
+      <xsl:value-of select="'S. enterica'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'salmonella\p{Zs}?enterica')">
+      <xsl:value-of select="'Salmonella enterica'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?pyogenes')">
+      <xsl:value-of select="'S. pyogenes'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'streptococcus\p{Zs}?pyogenes')">
+      <xsl:value-of select="'Streptococcus pyogenes'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?dumerilii')">
+      <xsl:value-of select="'P. dumerilii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'platynereis\p{Zs}?dumerilii')">
+      <xsl:value-of select="'Platynereis dumerilii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?cynocephalus')">
+      <xsl:value-of select="'P. cynocephalus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'papio\p{Zs}?cynocephalus')">
+      <xsl:value-of select="'Papio cynocephalus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'o\.\p{Zs}?fasciatus')">
+      <xsl:value-of select="'O. fasciatus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'oncopeltus\p{Zs}?fasciatus')">
+      <xsl:value-of select="'Oncopeltus fasciatus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'n\.\p{Zs}?crassa')">
+      <xsl:value-of select="'N. crassa'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'neurospora\p{Zs}?crassa')">
+      <xsl:value-of select="'Neurospora crassa'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c\.\p{Zs}?intestinalis')">
+      <xsl:value-of select="'C. intestinalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'ciona\p{Zs}?intestinalis')">
+      <xsl:value-of select="'Ciona intestinalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e\.\p{Zs}?cuniculi')">
+      <xsl:value-of select="'E. cuniculi'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'encephalitozoon\p{Zs}?cuniculi')">
+      <xsl:value-of select="'Encephalitozoon cuniculi'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'h\.\p{Zs}?salinarum')">
+      <xsl:value-of select="'H. salinarum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'halobacterium\p{Zs}?salinarum')">
+      <xsl:value-of select="'Halobacterium salinarum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?solfataricus')">
+      <xsl:value-of select="'S. solfataricus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'sulfolobus\p{Zs}?solfataricus')">
+      <xsl:value-of select="'Sulfolobus solfataricus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?mediterranea')">
+      <xsl:value-of select="'S. mediterranea'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'schmidtea\p{Zs}?mediterranea')">
+      <xsl:value-of select="'Schmidtea mediterranea'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?rosetta')">
+      <xsl:value-of select="'S. rosetta'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'salpingoeca\p{Zs}?rosetta')">
+      <xsl:value-of select="'Salpingoeca rosetta'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'n\.\p{Zs}?vectensis')">
+      <xsl:value-of select="'N. vectensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'nematostella\p{Zs}?vectensis')">
+      <xsl:value-of select="'Nematostella vectensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?aureus')">
+      <xsl:value-of select="'S. aureus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'staphylococcus\p{Zs}?aureus')">
+      <xsl:value-of select="'Staphylococcus aureus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'v\.\p{Zs}?cholerae')">
+      <xsl:value-of select="'V. cholerae'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'vibrio\p{Zs}?cholerae')">
+      <xsl:value-of select="'Vibrio cholerae'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'t\.\p{Zs}?thermophila')">
+      <xsl:value-of select="'T. thermophila'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'tetrahymena\p{Zs}?thermophila')">
+      <xsl:value-of select="'Tetrahymena thermophila'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c\.\p{Zs}?reinhardtii')">
+      <xsl:value-of select="'C. reinhardtii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'chlamydomonas\p{Zs}?reinhardtii')">
+      <xsl:value-of select="'Chlamydomonas reinhardtii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'n\.\p{Zs}?attenuata')">
+      <xsl:value-of select="'N. attenuata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'nicotiana\p{Zs}?attenuata')">
+      <xsl:value-of select="'Nicotiana attenuata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e\.\p{Zs}?carotovora')">
+      <xsl:value-of select="'E. carotovora'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'erwinia\p{Zs}?carotovora')">
+      <xsl:value-of select="'Erwinia carotovora'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e\.\p{Zs}?faecalis')">
+      <xsl:value-of select="'E. faecalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'h\.\p{Zs}?sapiens')">
+      <xsl:value-of select="'H. sapiens'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'homo\p{Zs}?sapiens')">
+      <xsl:value-of select="'Homo sapiens'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c\.\p{Zs}?trachomatis')">
+      <xsl:value-of select="'C. trachomatis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'chlamydia\p{Zs}?trachomatis')">
+      <xsl:value-of select="'Chlamydia trachomatis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'enterococcus\p{Zs}?faecalis')">
+      <xsl:value-of select="'Enterococcus faecalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'x\.\p{Zs}?laevis')">
+      <xsl:value-of select="'X. laevis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'xenopus\p{Zs}?laevis')">
+      <xsl:value-of select="'Xenopus laevis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'x\.\p{Zs}?tropicalis')">
+      <xsl:value-of select="'X. tropicalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'xenopus\p{Zs}?tropicalis')">
+      <xsl:value-of select="'Xenopus tropicalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?musculus')">
+      <xsl:value-of select="'M. musculus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'mus\p{Zs}?musculus')">
+      <xsl:value-of select="'Mus musculus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?immigrans')">
+      <xsl:value-of select="'D. immigrans'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila\p{Zs}?immigrans')">
+      <xsl:value-of select="'Drosophila immigrans'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?subobscura')">
+      <xsl:value-of select="'D. subobscura'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila\p{Zs}?subobscura')">
+      <xsl:value-of select="'Drosophila subobscura'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?affinis')">
+      <xsl:value-of select="'D. affinis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila\p{Zs}?affinis')">
+      <xsl:value-of select="'Drosophila affinis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?obscura')">
+      <xsl:value-of select="'D. obscura'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila\p{Zs}?obscura')">
+      <xsl:value-of select="'Drosophila obscura'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'f\.\p{Zs}?tularensis')">
+      <xsl:value-of select="'F. tularensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'francisella\p{Zs}?tularensis')">
+      <xsl:value-of select="'Francisella tularensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?plantaginis')">
+      <xsl:value-of select="'P. plantaginis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'podosphaera\p{Zs}?plantaginis')">
+      <xsl:value-of select="'Podosphaera plantaginis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?lanceolata')">
+      <xsl:value-of select="'P. lanceolata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'plantago\p{Zs}?lanceolata')">
+      <xsl:value-of select="'Plantago lanceolata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?trossulus')">
+      <xsl:value-of select="'M. trossulus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'mytilus\p{Zs}?trossulus')">
+      <xsl:value-of select="'Mytilus trossulus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?edulis')">
+      <xsl:value-of select="'M. edulis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'mytilus\p{Zs}?edulis')">
+      <xsl:value-of select="'Mytilus edulis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?chilensis')">
+      <xsl:value-of select="'M. chilensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'mytilus\p{Zs}?chilensis')">
+      <xsl:value-of select="'Mytilus chilensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'u\.\p{Zs}?maydis')">
+      <xsl:value-of select="'U. maydis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'ustilago\p{Zs}?maydis')">
+      <xsl:value-of select="'Ustilago maydis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?knowlesi')">
+      <xsl:value-of select="'P. knowlesi'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'plasmodium\p{Zs}?knowlesi')">
+      <xsl:value-of select="'Plasmodium knowlesi'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?aeruginosa')">
+      <xsl:value-of select="'P. aeruginosa'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'pseudomonas\p{Zs}?aeruginosa')">
+      <xsl:value-of select="'Pseudomonas aeruginosa'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'t\.\p{Zs}?brucei')">
+      <xsl:value-of select="'T. brucei'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'trypanosoma\p{Zs}?brucei')">
+      <xsl:value-of select="'Trypanosoma brucei'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'caulobacter\p{Zs}?crescentus')">
+      <xsl:value-of select="'Caulobacter crescentus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c\.\p{Zs}?crescentus')">
+      <xsl:value-of select="'C. crescentus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'agrobacterium\p{Zs}?tumefaciens')">
+      <xsl:value-of select="'Agrobacterium tumefaciens'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'a\.\p{Zs}?tumefaciens')">
+      <xsl:value-of select="'A. tumefaciens'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'t\.\p{Zs}?gondii')">
+      <xsl:value-of select="'T. gondii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'toxoplasma\p{Zs}?gondii')">
+      <xsl:value-of select="'Toxoplasma gondii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?rerio')">
+      <xsl:value-of select="'D. rerio'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'danio\p{Zs}?rerio')">
+      <xsl:value-of select="'Danio rerio'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila')">
+      <xsl:value-of select="'Drosophila'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'yimenosaurus')">
+      <xsl:value-of select="'Yimenosaurus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'lesothosaurus\p{Zs}?diagnosticus')">
+      <xsl:value-of select="'Lesothosaurus diagnosticus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'l.\p{Zs}?diagnosticus')">
+      <xsl:value-of select="'L. diagnosticus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'scelidosaurus\p{Zs}?harrisonii')">
+      <xsl:value-of select="'Scelidosaurus harrisonii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s.\p{Zs}?harrisonii')">
+      <xsl:value-of select="'S. harrisonii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'haya\p{Zs}?griva')">
+      <xsl:value-of select="'Haya griva'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'h.\p{Zs}?griva')">
+      <xsl:value-of select="'H. griva'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'polacanthus\p{Zs}?foxii')">
+      <xsl:value-of select="'Polacanthus foxii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p.\p{Zs}?foxii')">
+      <xsl:value-of select="'P. foxii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'scutellosaurus\p{Zs}?lawleri')">
+      <xsl:value-of select="'Scutellosaurus lawleri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s.\p{Zs}?lawleri')">
+      <xsl:value-of select="'S. lawleri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'saichania\p{Zs}?chulsanensis')">
+      <xsl:value-of select="'Saichania chulsanensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s.\p{Zs}?chulsanensis')">
+      <xsl:value-of select="'S. chulsanensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'gargoyleosaurus\p{Zs}?parkpinorum')">
+      <xsl:value-of select="'Gargoyleosaurus parkpinorum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'g.\p{Zs}?parkpinorum')">
+      <xsl:value-of select="'G. parkpinorum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'europelta\p{Zs}?carbonensis')">
+      <xsl:value-of select="'Europelta carbonensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e.\p{Zs}?carbonensis')">
+      <xsl:value-of select="'E. carbonensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'stegosaurus\p{Zs}?stenops')">
+      <xsl:value-of select="'Stegosaurus stenops'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s.\p{Zs}?stenops')">
+      <xsl:value-of select="'S. stenops'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'pinacosaurus\p{Zs}?grangeri')">
+      <xsl:value-of select="'Pinacosaurus grangeri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p.\p{Zs}?grangeri')">
+      <xsl:value-of select="'P. grangeri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'tatisaurus\p{Zs}?oehleri')">
+      <xsl:value-of select="'Tatisaurus oehleri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'t.\p{Zs}?oehleri')">
+      <xsl:value-of select="'T. oehleri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'hungarosaurus\p{Zs}?tormai')">
+      <xsl:value-of select="'Hungarosaurus tormai'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'h.\p{Zs}?tormai')">
+      <xsl:value-of select="'H. tormai'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'lesothosaurus\p{Zs}?diagnosticus')">
+      <xsl:value-of select="'Lesothosaurus diagnosticus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'l.\p{Zs}?diagnosticus')">
+      <xsl:value-of select="'L. diagnosticus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'bienosaurus\p{Zs}?lufengensis')">
+      <xsl:value-of select="'Bienosaurus lufengensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'b.\p{Zs}?lufengensis')">
+      <xsl:value-of select="'B. lufengensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'fabrosaurus\p{Zs}?australis')">
+      <xsl:value-of select="'Fabrosaurus australis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'f.\p{Zs}?australis')">
+      <xsl:value-of select="'F. australis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'chinshakiangosaurus\p{Zs}?chunghoensis')">
+      <xsl:value-of select="'Chinshakiangosaurus chunghoensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c.\p{Zs}?chunghoensis')">
+      <xsl:value-of select="'C. chunghoensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'euoplocephalus\p{Zs}?tutus')">
+      <xsl:value-of select="'Euoplocephalus tutus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e.\p{Zs}?tutus')">
+      <xsl:value-of select="'E. tutus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'g\.\p{Zs}?beringei')">
+      <xsl:value-of select="'G. beringei'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'gorilla\p{Zs}?beringei')">
+      <xsl:value-of select="'Gorilla beringei'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?assamensis')">
+      <xsl:value-of select="'M. assamensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'macaca\p{Zs}?assamensis')">
+      <xsl:value-of select="'Macaca assamensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?fuscata')">
+      <xsl:value-of select="'M. fuscata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'macaca\p{Zs}?fuscata')">
+      <xsl:value-of select="'Macaca fuscata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?mulatta')">
+      <xsl:value-of select="'M. mulatta'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'macaca\p{Zs}?mulatta')">
+      <xsl:value-of select="'Macaca mulatta'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?nemestrina')">
+      <xsl:value-of select="'M. nemestrina'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'macaca\p{Zs}?nemestrina')">
+      <xsl:value-of select="'Macaca nemestrina'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?sphinx')">
+      <xsl:value-of select="'M. sphinx'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'mandrillus\p{Zs}?sphinx')">
+      <xsl:value-of select="'Mandrillus sphinx'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?anubis')">
+      <xsl:value-of select="'P. anubis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'papio\p{Zs}?anubis')">
+      <xsl:value-of select="'Papio anubis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?hamadryas')">
+      <xsl:value-of select="'P. hamadryas'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'papio\p{Zs}?hamadryas')">
+      <xsl:value-of select="'Papio hamadryas'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?paniscus')">
+      <xsl:value-of select="'P. paniscus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'pan\p{Zs}?paniscus')">
+      <xsl:value-of select="'Pan paniscus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?troglodytes')">
+      <xsl:value-of select="'P. troglodytes'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'pan\p{Zs}?troglodytes')">
+      <xsl:value-of select="'Pan troglodytes'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'xenopus')">
+      <xsl:value-of select="'Xenopus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'salmonella')">
+      <xsl:value-of select="'Salmonella'"/>
+    </xsl:when>
+    <xsl:otherwise>
+      <xsl:value-of select="'undefined'"/>
+    </xsl:otherwise>
+  </xsl:choose>
+</xsl:function>
+  <xsl:function name="e:code-check">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:element name="code">
+      <xsl:if test="contains($s,'github')">
+        <xsl:element name="match">
+        <xsl:value-of select="'github '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'gitlab')">
+        <xsl:element name="match">
+        <xsl:value-of select="'gitlab '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'git.exeter.ac.uk')">
+        <xsl:element name="match">
+          <xsl:value-of select="'git.exeter.ac.uk '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'codeplex')">
+        <xsl:element name="match">
+        <xsl:value-of select="'codeplex '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'sourceforge')">
+        <xsl:element name="match">
+        <xsl:value-of select="'sourceforge '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'bitbucket')">
+        <xsl:element name="match">
+        <xsl:value-of select="'bitbucket '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'assembla ')">
+        <xsl:element name="match">
+        <xsl:value-of select="'assembla '"/>
+        </xsl:element>
+      </xsl:if>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:get-xrefs">
+    <xsl:param name="article"/>
+    <xsl:param name="object-id"/>
+    <xsl:param name="object-type"/>
+    <xsl:variable name="object-no" select="replace($object-id,'[^0-9]','')"/>
+    <xsl:element name="matches">
+      <xsl:for-each select="$article//xref[(@ref-type=$object-type) and not(ancestor::caption)]">
+        <xsl:variable name="rid-no" select="replace(./@rid,'[^0-9]','')"/>
+        <xsl:variable name="text-no" select="tokenize(normalize-space(replace(.,'[^0-9]',' ')),'\p{Zs}')[last()]"/>
+        <xsl:choose>
+          <xsl:when test="./@rid = $object-id">
+            <xsl:element name="match">
+              <xsl:attribute name="sec-id">
+                <xsl:value-of select="./ancestor::sec[1]/@id"/>
+              </xsl:attribute>
+              <xsl:value-of select="self::*"/>
+            </xsl:element>
+          </xsl:when>
+          <xsl:when test="contains(./@rid,'app')"/>
+          <xsl:when test="($rid-no lt $object-no) and (./following-sibling::text()[1] = '–') and (./following-sibling::*[1]/name()='xref') and (number(replace(replace(./following-sibling::xref[1]/@rid,'\-','.'),'[a-z]','')) gt number($object-no))">
+            <xsl:element name="match">
+              <xsl:attribute name="sec-id">
+                <xsl:value-of select="./ancestor::sec[1]/@id"/>
+              </xsl:attribute>
+              <xsl:value-of select="self::*"/>
+            </xsl:element>
+          </xsl:when>
+          <xsl:when test="($rid-no lt $object-no) and contains(.,$object-no) and (contains(.,'Videos') or contains(.,'videos') and contains(.,'–'))">
+            <xsl:element name="match">
+              <xsl:attribute name="sec-id">
+                <xsl:value-of select="./ancestor::sec[1]/@id"/>
+              </xsl:attribute>
+              <xsl:value-of select="self::*"/>
+            </xsl:element>
+          </xsl:when>
+          <xsl:when test="($rid-no lt $object-no) and (contains(.,'Videos') or contains(.,'videos') and contains(.,'—')) and ($text-no gt $object-no)">
+            <xsl:element name="match">
+              <xsl:attribute name="sec-id">
+                <xsl:value-of select="./ancestor::sec[1]/@id"/>
+              </xsl:attribute>
+              <xsl:value-of select="self::*"/>
+            </xsl:element>
+          </xsl:when>
+          <xsl:otherwise/>
+        </xsl:choose>
+      </xsl:for-each>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:get-iso-pub-date">
+    <xsl:param name="element"/>
+    <xsl:choose>
+      <xsl:when test="$element/ancestor-or-self::article//article-meta/pub-date[(@date-type='publication') or (@date-type='pub')]/month">
+        <xsl:variable name="pub-date" select="$element/ancestor-or-self::article//article-meta/pub-date[(@date-type='publication') or (@date-type='pub')]"/>
+        <xsl:value-of select="concat($pub-date/year,'-',$pub-date/month,'-',$pub-date/day)"/>
+      </xsl:when>
+      <xsl:otherwise/>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-copyright-holder">
+    <xsl:param name="contrib-group"/>
+    <xsl:variable name="author-count" select="count($contrib-group/contrib[@contrib-type='author'])"/>
+    <xsl:choose>
+      <xsl:when test="$author-count lt 1"/>
+      <xsl:when test="$author-count = 1">
+        <xsl:choose>
+          <xsl:when test="$contrib-group/contrib[@contrib-type='author']/collab">
+            <xsl:value-of select="$contrib-group/contrib[@contrib-type='author']/collab[1]/text()[1]"/>
+          </xsl:when>
+          <xsl:otherwise>
+            <xsl:value-of select="$contrib-group/contrib[@contrib-type='author']/name[1]/surname[1]"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:when>
+      <xsl:when test="$author-count = 2">
+        <xsl:choose>
+          <xsl:when test="$contrib-group/contrib[@contrib-type='author']/collab">
+            <xsl:choose>
+              <xsl:when test="$contrib-group/contrib[@contrib-type='author'][1]/collab and $contrib-group/contrib[@contrib-type='author'][2]/collab">
+                <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author']/collab[1]/text()[1],' and ',$contrib-group/contrib[@contrib-type='author']/collab[2]/text()[1])"/>
+              </xsl:when>
+              <xsl:when test="$contrib-group/contrib[@contrib-type='author'][1]/collab">
+                <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author'][1]/collab[1]/text()[1],' and ',$contrib-group/contrib[@contrib-type='author'][2]/name[1]/surname[1])"/>
+              </xsl:when>
+              <xsl:otherwise>
+                <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author'][1]/name[1]/surname[1],' and ',$contrib-group/contrib[@contrib-type='author'][2]/collab[1]/text()[1])"/>
+              </xsl:otherwise>
+            </xsl:choose>
+          </xsl:when>
+          <xsl:otherwise>
+            <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author'][1]/name[1]/surname[1],' and ',$contrib-group/contrib[@contrib-type='author'][2]/name[1]/surname[1])"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:when>
+      
+      <xsl:otherwise>
+        <xsl:variable name="is-equal-contrib" select="if ($contrib-group/contrib[@contrib-type='author'][1]/@equal-contrib='yes') then true() else false()"/>
+        <xsl:choose>
+          <xsl:when test="$is-equal-contrib">
+            
+            <xsl:variable name="equal-contrib-rid" select="$contrib-group/contrib[@contrib-type='author'][1]/xref[starts-with(@rid,'equal-contrib')]/@rid"/>
+            <xsl:variable name="first-authors" select="$contrib-group/contrib[@contrib-type='author' and @equal-contrib='yes' and xref[@rid=$equal-contrib-rid] and not(preceding-sibling::contrib[not(xref[@rid=$equal-contrib-rid])])]"/>
+            <xsl:choose>
+              
+              <xsl:when test="$author-count = 3 and count($first-authors) = 3">
+                <xsl:value-of select="concat(e:get-surname($contrib-group/contrib[@contrib-type='author'][1]),                   ', ',                   e:get-surname($contrib-group/contrib[@contrib-type='author'][2]),                   ' and ',                   e:get-surname($contrib-group/contrib[@contrib-type='author'][3]))"/>
+              </xsl:when>
+              
+              <xsl:when test="count($first-authors) gt 3">
+                <xsl:variable name="first-auth-string" select="string-join(for $auth in $contrib-group/contrib[@contrib-type='author'][position() lt 4] return e:get-surname($auth),', ')"/>
+                <xsl:value-of select="concat($first-auth-string,' et al')"/>
+              </xsl:when>
+              
+              <xsl:otherwise>
+                <xsl:variable name="first-auth-string" select="string-join(for $auth in $first-authors return e:get-surname($auth),', ')"/>
+                <xsl:value-of select="concat($first-auth-string,' et al')"/>
+              </xsl:otherwise>
+            </xsl:choose>
+          </xsl:when>
+          
+          <xsl:otherwise>
+            <xsl:value-of select="concat(e:get-surname($contrib-group/contrib[@contrib-type='author'][1]),' et al')"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-surname" as="text()">
+    <xsl:param name="contrib"/>
+    <xsl:choose>
+      <xsl:when test="$contrib/collab">
+        <xsl:value-of select="$contrib/collab[1]/text()[1]"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="$contrib//name[1]/surname[1]"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:insight-box" as="element()">
+    <xsl:param name="box" as="xs:string"/>
+    <xsl:param name="cite-text" as="xs:string"/>
+    <xsl:variable name="box-text" select="substring-after(substring-after($box,'article'),' ')"/> 
+    
+    <xsl:element name="list">
+      <xsl:for-each select="tokenize($cite-text,'\p{Zs}')">
+        <xsl:choose>
+          <xsl:when test="contains($box-text,.)"/>
+          <xsl:otherwise>
+            <xsl:element name="item">
+              <xsl:attribute name="type">cite</xsl:attribute>
+              <xsl:value-of select="."/>
+            </xsl:element>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:for-each>
+      <xsl:for-each select="tokenize($box-text,'\p{Zs}')">
+        <xsl:choose>
+          <xsl:when test="contains($cite-text,.)"/>
+          <xsl:otherwise>
+            <xsl:element name="item">
+              <xsl:attribute name="type">box</xsl:attribute>
+              <xsl:value-of select="."/>
+            </xsl:element>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:for-each>
+    </xsl:element>
+  </xsl:function>
+  <let name="latin-regex" value="'in\p{Zs}+vitro|ex\p{Zs}+vitro|in\p{Zs}+vivo|ex\p{Zs}+vivo|a\p{Zs}+priori|a\p{Zs}+posteriori|de\p{Zs}+novo|in\p{Zs}+utero|in\p{Zs}+natura|in\p{Zs}+situ|in\p{Zs}+planta|in\p{Zs}+cellulo|rete\p{Zs}+mirabile|nomen\p{Zs}+novum| sensu |ad\p{Zs}+libitum|in\p{Zs}+ovo'"/>
+  <xsl:function name="e:get-latin-terms" as="element()">
+    <xsl:param name="article" as="element()"/>
+    <xsl:param name="regex" as="xs:string"/>
+    
+    <xsl:variable name="roman-text" select="lower-case(       string-join(for $x in $article/*[local-name() = 'body' or local-name() = 'back']//*       return       if ($x/ancestor-or-self::sec[@sec-type='additional-information']) then ()       else if ($x/ancestor-or-self::ref-list) then ()       else if ($x/local-name() = 'italic') then ()       else $x/text(),' '))"/>
+    <xsl:variable name="italic-text" select="lower-case(string-join($article//*:italic[not(ancestor::ref-list) and not(ancestor::sec[@sec-type='additional-information'])],' '))"/>
+    
+    
+    <xsl:element name="result">
+      <xsl:choose>
+        <xsl:when test="matches($roman-text,$regex)">
+          <xsl:element name="list">
+            <xsl:attribute name="list-type">roman</xsl:attribute>
+            <xsl:for-each select="tokenize($regex,'\|')">
+              <xsl:variable name="display" select="replace(replace(.,'\\p\{Zs\}\+',' '),'^ | $','')"/>
+              <xsl:element name="match">
+                <xsl:attribute name="count">
+                  <xsl:value-of select="count(tokenize($roman-text,.)) - 1"/>
+                </xsl:attribute>
+                <xsl:value-of select="$display"/>
+              </xsl:element>
+            </xsl:for-each>
+          </xsl:element>
+        </xsl:when>
+        <xsl:otherwise>
+          <xsl:element name="list">
+            <xsl:attribute name="list-type">roman</xsl:attribute>
+          </xsl:element>
+        </xsl:otherwise>
+      </xsl:choose>
+      <xsl:choose>
+        <xsl:when test="matches($italic-text,$regex)">
+          <xsl:element name="list">
+            <xsl:attribute name="list-type">italic</xsl:attribute>
+            <xsl:for-each select="tokenize($regex,'\|')">
+              <xsl:variable name="display" select="replace(.,'\\p\{Zs\}\+',' ')"/>
+              <xsl:element name="match">
+                <xsl:attribute name="count">
+                  <xsl:value-of select="count(tokenize($italic-text,.)) - 1"/>
+                </xsl:attribute>
+                <xsl:value-of select="$display"/>
+              </xsl:element>
+            </xsl:for-each>
+          </xsl:element>
+        </xsl:when>
+        <xsl:otherwise>
+          <xsl:element name="list">
+            <xsl:attribute name="list-type">italic</xsl:attribute>
+          </xsl:element>
+        </xsl:otherwise>
+      </xsl:choose>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:print-latin-terms" as="xs:string">
+    <xsl:param name="list" as="element()"/>
+    <xsl:value-of select="string-join(       for $term in $list//*:match[@count != '0']        return if (number($term/@count) gt 1) then concat($term/@count,' instances of ',$term)       else concat($term/@count,' instance of ',$term)       ,', ')"/>
+  </xsl:function>
+  <xsl:function name="e:list-panels">
+    <xsl:param name="caption" as="xs:string"/>
+    <xsl:element name="list">
+      <xsl:for-each select="tokenize($caption,'\.\p{Zs}+')">
+        <xsl:if test="matches(.,'^[B-K]\p{P}?[A-K]?\.?\p{Zs}+')">
+          <xsl:element name="item">
+            <xsl:attribute name="token">
+              <xsl:value-of select="substring-before(.,' ')"/>
+            </xsl:attribute>
+            <xsl:value-of select="."/>
+          </xsl:element>
+        </xsl:if>
+      </xsl:for-each>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:get-weekday" as="xs:integer?">
+    <xsl:param name="date" as="xs:anyAtomicType?"/>
+    <xsl:sequence select="       if (empty($date)) then ()       else xs:integer((xs:date($date) - xs:date('1901-01-06')) div xs:dayTimeDuration('P1D')) mod 7       "/>
+  </xsl:function>
+  <xsl:function name="e:line-count" as="xs:integer">
+    <xsl:param name="arg" as="xs:string?"/>
+    
+    <xsl:sequence select="count(tokenize($arg,'(\r\n?|\n\r?)'))"/>
+    
+  </xsl:function>
+  <pattern id="article-metadata">
+    <rule context="abstract[not(@abstract-type)]/sec" id="abstract-sec-titles">
+      <let name="pos" value="count(ancestor::abstract/sec) - count(following-sibling::sec)"/>
+      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="error" id="final-clintrial-conformance-9">A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
+    </rule>
+  </pattern>
+  <pattern id="root-pattern">
+    <rule context="root" id="root-rule">
+      <assert test="descendant::abstract[not(@abstract-type)]/sec" role="error" id="abstract-sec-titles-xspec-assert">abstract[not(@abstract-type)]/sec must be present.</assert>
+    </rule>
+  </pattern>
+</schema>
\ No newline at end of file
diff --git a/test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/pass.xml b/test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/pass.xml
new file mode 100644
index 0000000000..06169dea0c
--- /dev/null
+++ b/test/tests/gen/abstract-sec-titles/final-clintrial-conformance-9/pass.xml
@@ -0,0 +1,29 @@
+<?oxygen SCHSchema="final-clintrial-conformance-9.sch"?>
+<!--Context: abstract[not(@abstract-type)]/sec
+Test: report    starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])
+Message: A section with the title  in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not. -->
+<root xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:ali="http://www.niso.org/schemas/ali/1.0/">
+  <article>
+    <abstract>
+      <sec id="abs1">
+        <title>Background:</title>
+      </sec>
+      <sec id="abs2">
+        <title>Methods:</title>
+      </sec>
+      <sec id="abs3">
+        <title>Results:</title>
+      </sec>
+      <sec id="abs4">
+        <title>Conclusions:</title>
+      </sec>
+      <sec id="abs5">
+        <title>Funding:</title>
+      </sec>
+      <sec id="abs6">
+        <title>Clinical trial number:</title>
+        <p><related-object document-id-type="clinical-trial-number" xlink:href="https://clinicaltrials.gov/">CTN1234567890</related-object>.</p>
+      </sec>
+    </abstract>
+  </article>
+</root>
\ No newline at end of file
diff --git a/test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/fail.xml b/test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/fail.xml
new file mode 100644
index 0000000000..4b6da7a84a
--- /dev/null
+++ b/test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/fail.xml
@@ -0,0 +1,29 @@
+<?oxygen SCHSchema="pre-clintrial-conformance-9.sch"?>
+<!--Context: abstract[not(@abstract-type)]/sec
+Test: report    starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])
+Message: A section with the title  in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not. -->
+<root xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:ali="http://www.niso.org/schemas/ali/1.0/">
+  <article>
+    <abstract>
+      <sec id="abs1">
+        <title>Background:</title>
+      </sec>
+      <sec id="abs2">
+        <title>Methods:</title>
+      </sec>
+      <sec id="abs3">
+        <title>Results:</title>
+      </sec>
+      <sec id="abs4">
+        <title>Conclusions:</title>
+      </sec>
+      <sec id="abs5">
+        <title>Funding:</title>
+      </sec>
+      <sec id="abs6">
+        <title>Clinical trial number:</title>
+        <p><ext-link ext-link-type="uri" xlink:href="https://clinicaltrials.gov/">https://clinicaltrials.gov/</ext-link> (CTN1234567890).</p>
+      </sec>
+    </abstract>
+  </article>
+</root>
\ No newline at end of file
diff --git a/test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/pass.xml b/test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/pass.xml
new file mode 100644
index 0000000000..5397769d6c
--- /dev/null
+++ b/test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/pass.xml
@@ -0,0 +1,29 @@
+<?oxygen SCHSchema="pre-clintrial-conformance-9.sch"?>
+<!--Context: abstract[not(@abstract-type)]/sec
+Test: report    starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])
+Message: A section with the title  in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not. -->
+<root xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:ali="http://www.niso.org/schemas/ali/1.0/">
+  <article>
+    <abstract>
+      <sec id="abs1">
+        <title>Background:</title>
+      </sec>
+      <sec id="abs2">
+        <title>Methods:</title>
+      </sec>
+      <sec id="abs3">
+        <title>Results:</title>
+      </sec>
+      <sec id="abs4">
+        <title>Conclusions:</title>
+      </sec>
+      <sec id="abs5">
+        <title>Funding:</title>
+      </sec>
+      <sec id="abs6">
+        <title>Clinical trial number:</title>
+        <p><related-object document-id-type="clinical-trial-number" xlink:href="https://clinicaltrials.gov/">CTN1234567890</related-object>.</p>
+      </sec>
+    </abstract>
+  </article>
+</root>
diff --git a/test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/pre-clintrial-conformance-9.sch b/test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/pre-clintrial-conformance-9.sch
new file mode 100644
index 0000000000..fcc3f67fbb
--- /dev/null
+++ b/test/tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/pre-clintrial-conformance-9.sch
@@ -0,0 +1,1303 @@
+<schema xmlns="http://purl.oclc.org/dsdl/schematron" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:java="http://www.java.com/" xmlns:file="java.io.File" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:mml="http://www.w3.org/1998/Math/MathML" queryBinding="xslt2">
+  <title>eLife Schematron</title>
+  <ns uri="http://www.niso.org/schemas/ali/1.0/" prefix="ali"/>
+  <ns uri="http://www.w3.org/XML/1998/namespace" prefix="xml"/>
+  <ns uri="http://www.w3.org/1999/xlink" prefix="xlink"/>
+  <ns uri="http://www.w3.org/2001/XInclude" prefix="xi"/>
+  <ns uri="http://www.w3.org/1998/Math/MathML" prefix="mml"/>
+  <ns uri="http://saxon.sf.net/" prefix="saxon"/>
+  <ns uri="http://purl.org/dc/terms/" prefix="dc"/>
+  <ns uri="http://www.w3.org/2001/XMLSchema" prefix="xs"/>
+  <ns uri="https://elifesciences.org/namespace" prefix="e"/>
+  <ns uri="java.io.File" prefix="file"/>
+  <ns uri="http://www.java.com/" prefix="java"/>
+  <let name="features-subj" value="('Feature Article', 'Insight', 'Editorial')"/>
+  <let name="features-article-types" value="('article-commentary','editorial','discussion')"/>
+  <let name="research-subj" value="('Research Article', 'Short Report', 'Tools and Resources', 'Research Advance', 'Registered Report', 'Replication Study', 'Research Communication', 'Correction', 'Retraction', 'Scientific Correspondence', 'Review Article')"/>
+  <let name="notice-article-types" value="('correction','retraction','expression-of-concern')"/>
+  <let name="notice-display-types" value="('Correction','Retraction','Expression of Concern')"/>
+  <let name="allowed-article-types" value="('research-article','review-article',$features-article-types, $notice-article-types)"/>
+  <let name="allowed-disp-subj" value="($research-subj, $features-subj)"/>
+  <let name="MSAs" value="('Biochemistry and Chemical Biology', 'Cancer Biology', 'Cell Biology', 'Chromosomes and Gene Expression', 'Computational and Systems Biology', 'Developmental Biology', 'Ecology', 'Epidemiology and Global Health', 'Evolutionary Biology', 'Genetics and Genomics', 'Medicine', 'Immunology and Inflammation', 'Microbiology and Infectious Disease', 'Neuroscience', 'Physics of Living Systems', 'Plant Biology', 'Stem Cells and Regenerative Medicine', 'Structural Biology and Molecular Biophysics')"/>
+  <let name="funders" value="'../../../../../src/funders.xml'"/>
+  <let name="wellcome-fundref-ids" value="('http://dx.doi.org/10.13039/100010269','http://dx.doi.org/10.13039/100004440')"/>
+  <xsl:function name="e:is-prc" as="xs:boolean">
+    <xsl:param name="elem" as="node()"/>
+    <xsl:choose>
+      <xsl:when test="$elem/name()='article'">
+        <xsl:value-of select="e:is-prc-helper($elem)"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="e:is-prc-helper($elem/ancestor::article[1])"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:is-prc-helper" as="xs:boolean">
+    <xsl:param name="article" as="node()"/>
+    <xsl:choose>
+      <xsl:when test="$article//article-meta/custom-meta-group/custom-meta[meta-name='publishing-route']/meta-value='prc'">
+        <xsl:value-of select="true()"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="false()"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-version" as="xs:string">
+    <xsl:param name="elem" as="node()"/>
+    <xsl:choose>
+      <xsl:when test="$elem/name()='article'">
+        <xsl:value-of select="e:get-version-helper($elem)"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="e:get-version-helper($elem/ancestor::article[1])"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-version-helper" as="xs:string">
+    <xsl:param name="article" as="node()"/>
+    <xsl:choose>
+      <xsl:when test="$article//article-meta/custom-meta-group/custom-meta[meta-name='schema-version']/meta-value">
+        <xsl:value-of select="$article//article-meta/custom-meta-group/custom-meta[meta-name='schema-version']/meta-value"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'1'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:titleCaseToken" as="xs:string">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="contains($s,'-')">
+        <xsl:value-of select="concat(           upper-case(substring(substring-before($s,'-'), 1, 1)),           lower-case(substring(substring-before($s,'-'),2)),           '-',           upper-case(substring(substring-after($s,'-'), 1, 1)),           lower-case(substring(substring-after($s,'-'),2)))"/>
+      </xsl:when>
+      <xsl:when test="lower-case($s)='elife'">
+        <xsl:value-of select="'eLife'"/>
+      </xsl:when>
+      <xsl:when test="lower-case($s)=('and','or','the','an','of','in','as','at','by','for','a','to','up','but','yet')">
+        <xsl:value-of select="lower-case($s)"/>
+      </xsl:when>
+      <xsl:when test="matches(lower-case($s),'^rna$|^dna$|^mri$|^hiv$|^tor$|^aids$|^covid-19$|^covid$')">
+        <xsl:value-of select="upper-case($s)"/>
+      </xsl:when>
+      <xsl:when test="matches(lower-case($s),'[1-4]d')">
+        <xsl:value-of select="upper-case($s)"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="concat(upper-case(substring($s, 1, 1)), lower-case(substring($s, 2)))"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:titleCase" as="xs:string">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      
+      <xsl:when test="lower-case($s)='protein kinase a'">
+        <xsl:value-of select="'Protein Kinase A'"/>
+      </xsl:when>
+      <xsl:when test="contains($s,' ')">
+        <xsl:variable name="token1" select="substring-before($s,' ')"/>
+        <xsl:variable name="token2" select="substring-after($s,$token1)"/>
+        <xsl:choose>
+          <xsl:when test="lower-case($token1)='elife'">
+            <xsl:value-of select="concat('eLife',               ' ',               string-join(for $x in tokenize(substring-after($token2,' '),'\p{Zs}') return e:titleCaseToken($x),' ')               )"/>
+          </xsl:when>
+          <xsl:when test="matches(lower-case($token1),'^rna$|^dna$|^mri$|^hiv$|^tor$|^aids$|^covid-19$|^covid$')">
+            <xsl:value-of select="concat(upper-case($token1),               ' ',               string-join(for $x in tokenize(substring-after($token2,' '),'\p{Zs}') return e:titleCaseToken($x),' ')               )"/>
+          </xsl:when>
+          <xsl:when test="matches(lower-case($token1),'[1-4]d')">
+            <xsl:value-of select="concat(upper-case($token1),               ' ',               string-join(for $x in tokenize(substring-after($token2,' '),'\p{Zs}') return e:titleCaseToken($x),' ')               )"/>
+          </xsl:when>
+          <xsl:when test="contains($token1,'-')">
+            <xsl:value-of select="string-join(for $x in tokenize($s,'\p{Zs}') return e:titleCaseToken($x),' ')"/>
+          </xsl:when>
+          <xsl:otherwise>
+            <xsl:value-of select="concat(               concat(upper-case(substring($token1, 1, 1)), lower-case(substring($token1, 2))),               ' ',               string-join(for $x in tokenize(substring-after($token2,' '),'\p{Zs}') return e:titleCaseToken($x),' ')               )"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:when>
+      <xsl:when test="lower-case($s)='elife'">
+        <xsl:value-of select="'eLife'"/>
+      </xsl:when>
+      <xsl:when test="lower-case($s)=('and','or','the','an','of')">
+        <xsl:value-of select="lower-case($s)"/>
+      </xsl:when>
+      <xsl:when test="matches(lower-case($s),'^rna$|^dna$|^mri$|^hiv$|^tor$|^aids$|^covid-19$|^covid$')">
+        <xsl:value-of select="upper-case($s)"/>
+      </xsl:when>
+      <xsl:when test="matches(lower-case($s),'[1-4]d')">
+        <xsl:value-of select="upper-case($s)"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="e:titleCaseToken($s)"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:article-type2title" as="xs:string">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="$s = 'Replication Study'">
+        <xsl:value-of select="'Replication Study:'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'Registered Report'">
+        <xsl:value-of select="'Registered report:'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'Correction'">
+        <xsl:value-of select="'Correction:'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'Retraction'">
+        <xsl:value-of select="'Retraction:'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'Expression of Concern'">
+        <xsl:value-of select="'Expression of Concern:'"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'undefined'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:sec-type2title" as="xs:string">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="$s = 'intro'">
+        <xsl:value-of select="'Introduction'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'results'">
+        <xsl:value-of select="'Results'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'discussion'">
+        <xsl:value-of select="'Discussion'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'materials|methods'">
+        <xsl:value-of select="'Materials and methods'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'results|discussion'">
+        <xsl:value-of select="'Results and discussion'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'methods'">
+        <xsl:value-of select="'Methods'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'model'">
+        <xsl:value-of select="'Model'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'additional-information'">
+        <xsl:value-of select="'Additional information'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'supplementary-material'">
+        <xsl:value-of select="'Additional files'"/>
+      </xsl:when>
+      <xsl:when test="$s = 'data-availability'">
+        <xsl:value-of select="'Data availability'"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'undefined'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:fig-id-type" as="xs:string">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="matches($s,'^fig[0-9]{1,3}$')">
+        <xsl:value-of select="'Figure'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^fig[0-9]{1,3}s[0-9]{1,3}$')">
+        <xsl:value-of select="'Figure supplement'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^box[0-9]{1,3}fig[0-9]{1,3}$')">
+        <xsl:value-of select="'Box figure'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^app[0-9]{1,3}fig[0-9]{1,3}$')">
+        <xsl:value-of select="'Appendix figure'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^app[0-9]{1,3}fig[0-9]{1,3}s[0-9]{1,3}$')">
+        <xsl:value-of select="'Appendix figure supplement'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^respfig[0-9]{1,3}$|^sa[0-9]fig[0-9]{1,3}$')">
+        <xsl:value-of select="'Author response figure'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^C[0-9]{1,3}$|^chem[0-9]{1,3}$')">
+        <xsl:value-of select="'Chemical structure'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^app[0-9]{1,3}C[0-9]{1,3}$|^app[0-9]{1,3}chem[0-9]{1,3}$')">
+        <xsl:value-of select="'Appendix chemical structure'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^S[0-9]{1,3}$|^scheme[0-9]{1,3}$')">
+        <xsl:value-of select="'Scheme'"/>
+      </xsl:when>
+      <xsl:when test="matches($s,'^app[0-9]{1,3}S[0-9]{1,3}$|^app[0-9]{1,3}scheme[0-9]{1,3}$')">
+        <xsl:value-of select="'Appendix scheme'"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'undefined'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:stripDiacritics" as="xs:string">
+    <xsl:param name="string" as="xs:string"/>
+    <xsl:value-of select="replace(replace(replace(translate(normalize-unicode($string,'NFD'),'ƀȼđɇǥħɨıɉꝁłøɍŧɏƶ','bcdeghiijklortyz'),'[\p{M}’]',''),'æ','ae'),'ß','ss')"/>
+  </xsl:function>
+  <xsl:function name="e:ref-list-string" as="xs:string">
+    <xsl:param name="ref"/>
+    <xsl:choose>
+      <xsl:when test="$ref/element-citation[1]/person-group[1]/* and $ref/element-citation[1]/year">
+        <xsl:value-of select="concat(           replace(e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[1]),'\p{Zs}',''),           ' ',           $ref/element-citation[1]/year[1],           ' ',           string-join(for $x in $ref/element-citation[1]/person-group[1]/*[position()=(2,3)]           return replace(e:get-collab-or-surname($x),'\p{Zs}',''),' ')           )"/>
+      </xsl:when>
+      <xsl:when test="$ref/element-citation/person-group[1]/*">
+        <xsl:value-of select="concat(           replace(e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[1]),'\p{Zs}',''),           ' 9999 ',           string-join(for $x in $ref/element-citation[1]/person-group[1]/*[position()=(2,3)]           return replace(e:get-collab-or-surname($x),'\p{Zs}',''),' ')           )"/>
+      </xsl:when>
+      <xsl:when test="$ref/element-citation/year">
+        <xsl:value-of select="concat(' ',$ref/element-citation[1]/year[1])"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'zzzzz 9999'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:ref-list-string2" as="xs:string">
+    <xsl:param name="ref"/>
+    <xsl:choose>
+      <xsl:when test="$ref/element-citation[1]/year and count($ref/element-citation[1]/person-group[1]/*) = 2">
+        <xsl:value-of select="concat(           e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[1]),           ' ',           e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[2]),           ' ',           $ref/element-citation[1]/year[1])"/>
+      </xsl:when>
+      <xsl:when test="$ref/element-citation/person-group[1]/* and $ref/element-citation[1]/year">
+        <xsl:value-of select="concat(           e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[1]),           ' ',           $ref/element-citation[1]/year[1])"/>
+      </xsl:when>
+      <xsl:when test="$ref/element-citation/person-group[1]/*">
+        <xsl:value-of select="concat(           e:get-collab-or-surname($ref/element-citation[1]/person-group[1]/*[1]),           ' 9999 ')"/>
+      </xsl:when>
+      <xsl:when test="$ref/element-citation/year">
+        <xsl:value-of select="concat(' ',$ref/element-citation[1]/year[1])"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'zzzzz 9999'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-collab-or-surname" as="xs:string?">
+    <xsl:param name="collab-or-name"/>
+    <xsl:choose>
+      <xsl:when test="$collab-or-name/name()='collab'">
+        <xsl:value-of select="e:stripDiacritics(replace(lower-case($collab-or-name),'\.',''))"/>
+      </xsl:when>
+      <xsl:when test="$collab-or-name/surname">
+        <xsl:value-of select="e:stripDiacritics(lower-case($collab-or-name/surname[1]))"/>
+      </xsl:when>
+      <xsl:otherwise/>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:cite-name-text" as="xs:string">
+    <xsl:param name="person-group"/>
+    <xsl:choose>
+      <xsl:when test="(count($person-group/*) = 1) and $person-group/name">
+        <xsl:value-of select="$person-group/name/surname[1]"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) = 1) and $person-group/collab">
+        <xsl:value-of select="$person-group/collab"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) = 2) and (count($person-group/name) = 1) and $person-group/*[1]/local-name() = 'collab'">
+        <xsl:value-of select="concat($person-group/collab,' and ',$person-group/name/surname[1])"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) = 2) and (count($person-group/name) = 1) and $person-group/*[1]/local-name() = 'name'">
+        <xsl:value-of select="concat($person-group/name/surname[1],' and ',$person-group/collab)"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) = 2) and (count($person-group/name) = 2)">
+        <xsl:value-of select="concat($person-group/name[1]/surname[1],' and ',$person-group/name[2]/surname[1])"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) = 2) and (count($person-group/collab) = 2)">
+        <xsl:value-of select="concat($person-group/collab[1],' and ',$person-group/collab[2])"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) ge 2) and $person-group/*[1]/local-name() = 'collab'">
+        <xsl:value-of select="concat($person-group/collab[1], ' et al.')"/>
+      </xsl:when>
+      <xsl:when test="(count($person-group/*) ge 2) and $person-group/*[1]/local-name() = 'name'">
+        <xsl:value-of select="concat($person-group/name[1]/surname[1], ' et al.')"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'undetermined'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:citation-format1" as="xs:string">
+    <xsl:param name="element-citation"/>
+    <xsl:choose>
+      <xsl:when test="$element-citation/person-group and $element-citation//year">
+        <xsl:value-of select="concat(e:cite-name-text($element-citation/person-group[1]),', ',$element-citation/descendant::year[1])"/>
+      </xsl:when>
+      <xsl:when test="$element-citation/person-group and not($element-citation//year)">
+        <xsl:value-of select="concat(e:cite-name-text($element-citation/person-group[1]),', ')"/>
+      </xsl:when>
+      <xsl:when test="not($element-citation/person-group) and $element-citation//year">
+        <xsl:value-of select="concat('et al., ',$element-citation/descendant::year[1])"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="', '"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:citation-format2" as="xs:string">
+    <xsl:param name="element-citation"/>
+    <xsl:choose>
+      <xsl:when test="$element-citation/person-group and $element-citation//year">
+        <xsl:value-of select="concat(e:cite-name-text($element-citation/person-group[1]),' (',$element-citation/descendant::year[1],')')"/>
+      </xsl:when>
+      <xsl:when test="$element-citation/person-group and not($element-citation//year)">
+        <xsl:value-of select="concat(e:cite-name-text($element-citation/person-group[1]),' ()')"/>
+      </xsl:when>
+      <xsl:when test="not($element-citation/person-group) and $element-citation//year">
+        <xsl:value-of select="concat('et al. (',$element-citation/descendant::year[1],')')"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="', '"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:ref-cite-list">
+    <xsl:param name="ref-list" as="node()"/>
+    <xsl:element name="list">
+      <xsl:for-each select="$ref-list/ref[element-citation[year]]">
+        <xsl:variable name="cite" select="e:citation-format1(./element-citation[1])"/>
+        <xsl:element name="item">
+          <xsl:attribute name="id">
+            <xsl:value-of select="./@id"/>
+          </xsl:attribute>
+          <xsl:attribute name="no-suffix">
+            <xsl:value-of select="replace($cite,'[A-Za-z]$','')"/>
+          </xsl:attribute>
+          <xsl:value-of select="$cite"/>
+        </xsl:element>
+      </xsl:for-each>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:non-distinct-citations">
+    <xsl:param name="cite-list" as="node()"/>
+    <xsl:element name="list">
+    <xsl:for-each select="$cite-list//*:item">
+      <xsl:variable name="cite" select="./string()"/>
+      <xsl:choose>
+        <xsl:when test="./preceding::*:item/string() = $cite">
+          <xsl:element name="item">
+            <xsl:attribute name="id">
+              <xsl:value-of select="./@id"/>
+            </xsl:attribute>
+            <xsl:value-of select="$cite"/>
+          </xsl:element>
+        </xsl:when>
+        <xsl:when test="not(matches($cite,'[A-Za-z]$')) and (./preceding::*:item/@no-suffix/string() = $cite)">
+          <xsl:element name="item">
+            <xsl:attribute name="id">
+              <xsl:value-of select="./@id"/>
+            </xsl:attribute>
+          <xsl:value-of select="$cite"/>
+          </xsl:element>
+        </xsl:when>
+        <xsl:when test="not(matches($cite,'[A-Za-z]$')) and ./following::*:item/@no-suffix/string() = $cite">
+          <xsl:element name="item">
+            <xsl:attribute name="id">
+              <xsl:value-of select="./@id"/>
+            </xsl:attribute>
+          <xsl:value-of select="$cite"/>
+          </xsl:element>
+        </xsl:when>
+        <xsl:otherwise/>
+      </xsl:choose>
+    </xsl:for-each>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:get-name" as="xs:string">
+    <xsl:param name="name"/>
+    <xsl:choose>
+      <xsl:when test="$name/given-names[1] and $name/surname[1] and $name/suffix[1]">
+        <xsl:value-of select="concat($name/given-names[1],' ',$name/surname[1],' ',$name/suffix[1])"/>
+      </xsl:when>
+      <xsl:when test="not($name/given-names[1]) and $name/surname[1] and $name/suffix[1]">
+        <xsl:value-of select="concat($name/surname[1],' ',$name/suffix[1])"/>
+      </xsl:when>
+      <xsl:when test="$name/given-names[1] and $name/surname[1] and not($name/suffix[1])">
+        <xsl:value-of select="concat($name/given-names[1],' ',$name/surname[1])"/>
+      </xsl:when>
+      <xsl:when test="not($name/given-names[1]) and $name/surname[1] and not($name/suffix[1])">
+        <xsl:value-of select="$name/surname[1]"/>
+      </xsl:when>
+      <xsl:otherwise>
+        
+        <xsl:value-of select="'No elements present'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-collab">
+    <xsl:param name="collab"/>
+    <xsl:for-each select="$collab/(*|text())">
+      <xsl:choose>
+        <xsl:when test="./name()='contrib-group'"/>
+        <xsl:otherwise>
+          <xsl:value-of select="."/>
+        </xsl:otherwise>
+      </xsl:choose>
+    </xsl:for-each>
+  </xsl:function>
+  <xsl:function name="e:isbn-sum" as="xs:integer">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="string-length($s) = 10">
+        <xsl:variable name="d1" select="number(substring($s,1,1)) * 10"/>
+        <xsl:variable name="d2" select="number(substring($s,2,1)) * 9"/>
+        <xsl:variable name="d3" select="number(substring($s,3,1)) * 8"/>
+        <xsl:variable name="d4" select="number(substring($s,4,1)) * 7"/>
+        <xsl:variable name="d5" select="number(substring($s,5,1)) * 6"/>
+        <xsl:variable name="d6" select="number(substring($s,6,1)) * 5"/>
+        <xsl:variable name="d7" select="number(substring($s,7,1)) * 4"/>
+        <xsl:variable name="d8" select="number(substring($s,8,1)) * 3"/>
+        <xsl:variable name="d9" select="number(substring($s,9,1)) * 2"/>
+        <xsl:variable name="d10" select="number(substring($s,10,1)) * 1"/>
+        <xsl:value-of select="number($d1 + $d2 + $d3 + $d4 + $d5 + $d6 + $d7 + $d8 + $d9 + $d10) mod 11"/>
+      </xsl:when>
+      <xsl:when test="string-length($s) = 13">
+        <xsl:variable name="d1" select="number(substring($s,1,1))"/>
+        <xsl:variable name="d2" select="number(substring($s,2,1)) * 3"/>
+        <xsl:variable name="d3" select="number(substring($s,3,1))"/>
+        <xsl:variable name="d4" select="number(substring($s,4,1)) * 3"/>
+        <xsl:variable name="d5" select="number(substring($s,5,1))"/>
+        <xsl:variable name="d6" select="number(substring($s,6,1)) * 3"/>
+        <xsl:variable name="d7" select="number(substring($s,7,1))"/>
+        <xsl:variable name="d8" select="number(substring($s,8,1)) * 3"/>
+        <xsl:variable name="d9" select="number(substring($s,9,1))"/>
+        <xsl:variable name="d10" select="number(substring($s,10,1)) * 3"/>
+        <xsl:variable name="d11" select="number(substring($s,11,1))"/>
+        <xsl:variable name="d12" select="number(substring($s,12,1)) * 3"/>
+        <xsl:variable name="d13" select="number(substring($s,13,1))"/>
+        <xsl:value-of select="number($d1 + $d2 + $d3 + $d4 + $d5 + $d6 + $d7 + $d8 + $d9 + $d10 + $d11 + $d12 + $d13) mod 10"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="number('1')"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:escape-for-regex" as="xs:string">
+    <xsl:param name="arg" as="xs:string?"/>
+    <xsl:sequence select="replace($arg,'(\.|\[|\]|\\|\||\-|\^|\$|\?|\*|\+|\{|\}|\(|\))','\\$1')"/>
+  </xsl:function>
+  <xsl:function name="e:get-ordinal" as="xs:string">
+    <xsl:param name="value" as="xs:integer?"/>
+    <xsl:if test="translate(string($value), '0123456789', '') = '' and number($value) &gt; 0">
+      <xsl:variable name="mod100" select="$value mod 100"/>
+      <xsl:variable name="mod10" select="$value mod 10"/>
+      <xsl:choose>
+        <xsl:when test="$mod100 = 11 or $mod100 = 12 or $mod100 = 13">
+          <xsl:value-of select="concat($value,'th')"/>
+        </xsl:when>
+        <xsl:when test="$mod10 = 1">
+          <xsl:value-of select="concat($value,'st')"/>
+        </xsl:when>
+        <xsl:when test="$mod10 = 2">
+          <xsl:value-of select="concat($value,'nd')"/>
+        </xsl:when>
+        <xsl:when test="$mod10 = 3">
+          <xsl:value-of select="concat($value,'rd')"/>
+        </xsl:when>
+        <xsl:otherwise>
+          <xsl:value-of select="concat($value,'th')"/>
+        </xsl:otherwise>
+      </xsl:choose>
+    </xsl:if>
+  </xsl:function>
+  <let name="org-regex" value="'b\.\p{Zs}?subtilis|bacillus\p{Zs}?subtilis|d\.\p{Zs}?melanogaster|drosophila\p{Zs}?melanogaster|e\.\p{Zs}?coli|escherichia\p{Zs}?coli|s\.\p{Zs}?pombe|schizosaccharomyces\p{Zs}?pombe|s\.\p{Zs}?cerevisiae|saccharomyces\p{Zs}?cerevisiae|c\.\p{Zs}?elegans|caenorhabditis\p{Zs}?elegans|a\.\p{Zs}?thaliana|arabidopsis\p{Zs}?thaliana|m\.\p{Zs}?thermophila|myceliophthora\p{Zs}?thermophila|dictyostelium|p\.\p{Zs}?falciparum|plasmodium\p{Zs}?falciparum|s\.\p{Zs}?enterica|salmonella\p{Zs}?enterica|s\.\p{Zs}?pyogenes|streptococcus\p{Zs}?pyogenes|p\.\p{Zs}?dumerilii|platynereis\p{Zs}?dumerilii|p\.\p{Zs}?cynocephalus|papio\p{Zs}?cynocephalus|o\.\p{Zs}?fasciatus|oncopeltus\p{Zs}?fasciatus|n\.\p{Zs}?crassa|neurospora\p{Zs}?crassa|c\.\p{Zs}?intestinalis|ciona\p{Zs}?intestinalis|e\.\p{Zs}?cuniculi|encephalitozoon\p{Zs}?cuniculi|h\.\p{Zs}?salinarum|halobacterium\p{Zs}?salinarum|s\.\p{Zs}?solfataricus|sulfolobus\p{Zs}?solfataricus|s\.\p{Zs}?mediterranea|schmidtea\p{Zs}?mediterranea|s\.\p{Zs}?rosetta|salpingoeca\p{Zs}?rosetta|n\.\p{Zs}?vectensis|nematostella\p{Zs}?vectensis|s\.\p{Zs}?aureus|staphylococcus\p{Zs}?aureus|v\.\p{Zs}?cholerae|vibrio\p{Zs}?cholerae|t\.\p{Zs}?thermophila|tetrahymena\p{Zs}?thermophila|c\.\p{Zs}?reinhardtii|chlamydomonas\p{Zs}?reinhardtii|n\.\p{Zs}?attenuata|nicotiana\p{Zs}?attenuata|e\.\p{Zs}?carotovora|erwinia\p{Zs}?carotovora|e\.\p{Zs}?faecalis|h\.\p{Zs}?sapiens|homo\p{Zs}?sapiens|c\.\p{Zs}?trachomatis|chlamydia\p{Zs}?trachomatis|enterococcus\p{Zs}?faecalis|x\.\p{Zs}?laevis|xenopus\p{Zs}?laevis|x\.\p{Zs}?tropicalis|xenopus\p{Zs}?tropicalis|m\.\p{Zs}?musculus|mus\p{Zs}?musculus|d\.\p{Zs}?immigrans|drosophila\p{Zs}?immigrans|d\.\p{Zs}?subobscura|drosophila\p{Zs}?subobscura|d\.\p{Zs}?affinis|drosophila\p{Zs}?affinis|d\.\p{Zs}?obscura|drosophila\p{Zs}?obscura|f\.\p{Zs}?tularensis|francisella\p{Zs}?tularensis|p\.\p{Zs}?plantaginis|podosphaera\p{Zs}?plantaginis|p\.\p{Zs}?lanceolata|plantago\p{Zs}?lanceolata|m\.\p{Zs}?trossulus|mytilus\p{Zs}?trossulus|m\.\p{Zs}?edulis|mytilus\p{Zs}?edulis|m\.\p{Zs}?chilensis|mytilus\p{Zs}?chilensis|u\.\p{Zs}?maydis|ustilago\p{Zs}?maydis|p\.\p{Zs}?knowlesi|plasmodium\p{Zs}?knowlesi|p\.\p{Zs}?aeruginosa|pseudomonas\p{Zs}?aeruginosa|t\.\p{Zs}?brucei|trypanosoma\p{Zs}?brucei|t\.\p{Zs}?gondii|toxoplasma\p{Zs}?gondii|d\.\p{Zs}?rerio|danio\p{Zs}?rerio|yimenosaurus|lesothosaurus\p{Zs}?diagnosticus|l\.\p{Zs}?diagnosticus|scelidosaurus\p{Zs}?harrisonii|s\.\p{Zs}?harrisonii|haya\p{Zs}?griva|h\.\p{Zs}?griva|polacanthus\p{Zs}?foxii|p\.\p{Zs}?foxii|scutellosaurus\p{Zs}?lawleri|s\.\p{Zs}?lawleri|saichania\p{Zs}?chulsanensis|s\.\p{Zs}?chulsanensis|gargoyleosaurus\p{Zs}?parkpinorum|g\.\p{Zs}?parkpinorum|europelta\p{Zs}?carbonensis|e\.\p{Zs}?carbonensis|stegosaurus\p{Zs}?stenops|s\.\p{Zs}?stenops|pinacosaurus\p{Zs}?grangeri|p\.\p{Zs}?grangeri|tatisaurus\p{Zs}?oehleri|t\.\p{Zs}?oehleri|hungarosaurus\p{Zs}?tormai|h\.\p{Zs}?tormai|bienosaurus\p{Zs}?lufengensis|b\.\p{Zs}?lufengensis|fabrosaurus\p{Zs}?australis|f\.\p{Zs}?australis|chinshakiangosaurus\p{Zs}?chunghoensis|c\.\p{Zs}?chunghoensis|euoplocephalus\p{Zs}?tutus|e\.\p{Zs}?tutus|drosophila|xenopus|salmonella|g\.\p{Zs}?beringei|gorilla\p{Zs}?beringei|m\.\p{Zs}?assamensis|macaca\p{Zs}?assamensis|m\.\p{Zs}?fuscata|macaca\p{Zs}?fuscata|m\.\p{Zs}?mulatta|macaca\p{Zs}?mulatta|m\.\p{Zs}?nemestrina|macaca\p{Zs}?nemestrina|m\.\p{Zs}?sphinx|mandrillus\p{Zs}?sphinx|p\.\p{Zs}?anubis|papio\p{Zs}?anubis|p\.\p{Zs}?hamadryas|papio\p{Zs}?hamadryas|p\.\p{Zs}?paniscus|pan\p{Zs}?paniscus|p\.\p{Zs}?troglodytes|pan\p{Zs}?troglodytes'"/>
+  <let name="sec-title-regex" value="string-join(     for $x in tokenize($org-regex,'\|')     return concat('^',$x,'$')     ,'|')"/>
+  <xsl:function name="e:org-conform" as="xs:string">
+  <xsl:param name="s" as="xs:string"/>
+  <xsl:choose>
+    <xsl:when test="matches($s,'b\.\p{Zs}?subtilis')">
+      <xsl:value-of select="'B. subtilis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'bacillus\p{Zs}?subtilis')">
+      <xsl:value-of select="'Bacillus subtilis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?melanogaster')">
+      <xsl:value-of select="'D. melanogaster'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila\p{Zs}?melanogaster')">
+      <xsl:value-of select="'Drosophila melanogaster'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e\.\p{Zs}?coli')">
+      <xsl:value-of select="'E. coli'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'escherichia\p{Zs}?coli')">
+      <xsl:value-of select="'Escherichia coli'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?pombe')">
+      <xsl:value-of select="'S. pombe'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'schizosaccharomyces\p{Zs}?pombe')">
+      <xsl:value-of select="'Schizosaccharomyces pombe'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?cerevisiae')">
+      <xsl:value-of select="'S. cerevisiae'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'saccharomyces\p{Zs}?cerevisiae')">
+      <xsl:value-of select="'Saccharomyces cerevisiae'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c\.\p{Zs}?elegans')">
+      <xsl:value-of select="'C. elegans'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'caenorhabditis\p{Zs}?elegans')">
+      <xsl:value-of select="'Caenorhabditis elegans'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'a\.\p{Zs}?thaliana')">
+      <xsl:value-of select="'A. thaliana'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'arabidopsis\p{Zs}?thaliana')">
+      <xsl:value-of select="'Arabidopsis thaliana'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?thermophila')">
+      <xsl:value-of select="'M. thermophila'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'myceliophthora\p{Zs}?thermophila')">
+      <xsl:value-of select="'Myceliophthora thermophila'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'dictyostelium')">
+      <xsl:value-of select="'Dictyostelium'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?falciparum')">
+      <xsl:value-of select="'P. falciparum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'plasmodium\p{Zs}?falciparum')">
+      <xsl:value-of select="'Plasmodium falciparum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?enterica')">
+      <xsl:value-of select="'S. enterica'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'salmonella\p{Zs}?enterica')">
+      <xsl:value-of select="'Salmonella enterica'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?pyogenes')">
+      <xsl:value-of select="'S. pyogenes'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'streptococcus\p{Zs}?pyogenes')">
+      <xsl:value-of select="'Streptococcus pyogenes'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?dumerilii')">
+      <xsl:value-of select="'P. dumerilii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'platynereis\p{Zs}?dumerilii')">
+      <xsl:value-of select="'Platynereis dumerilii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?cynocephalus')">
+      <xsl:value-of select="'P. cynocephalus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'papio\p{Zs}?cynocephalus')">
+      <xsl:value-of select="'Papio cynocephalus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'o\.\p{Zs}?fasciatus')">
+      <xsl:value-of select="'O. fasciatus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'oncopeltus\p{Zs}?fasciatus')">
+      <xsl:value-of select="'Oncopeltus fasciatus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'n\.\p{Zs}?crassa')">
+      <xsl:value-of select="'N. crassa'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'neurospora\p{Zs}?crassa')">
+      <xsl:value-of select="'Neurospora crassa'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c\.\p{Zs}?intestinalis')">
+      <xsl:value-of select="'C. intestinalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'ciona\p{Zs}?intestinalis')">
+      <xsl:value-of select="'Ciona intestinalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e\.\p{Zs}?cuniculi')">
+      <xsl:value-of select="'E. cuniculi'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'encephalitozoon\p{Zs}?cuniculi')">
+      <xsl:value-of select="'Encephalitozoon cuniculi'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'h\.\p{Zs}?salinarum')">
+      <xsl:value-of select="'H. salinarum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'halobacterium\p{Zs}?salinarum')">
+      <xsl:value-of select="'Halobacterium salinarum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?solfataricus')">
+      <xsl:value-of select="'S. solfataricus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'sulfolobus\p{Zs}?solfataricus')">
+      <xsl:value-of select="'Sulfolobus solfataricus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?mediterranea')">
+      <xsl:value-of select="'S. mediterranea'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'schmidtea\p{Zs}?mediterranea')">
+      <xsl:value-of select="'Schmidtea mediterranea'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?rosetta')">
+      <xsl:value-of select="'S. rosetta'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'salpingoeca\p{Zs}?rosetta')">
+      <xsl:value-of select="'Salpingoeca rosetta'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'n\.\p{Zs}?vectensis')">
+      <xsl:value-of select="'N. vectensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'nematostella\p{Zs}?vectensis')">
+      <xsl:value-of select="'Nematostella vectensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s\.\p{Zs}?aureus')">
+      <xsl:value-of select="'S. aureus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'staphylococcus\p{Zs}?aureus')">
+      <xsl:value-of select="'Staphylococcus aureus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'v\.\p{Zs}?cholerae')">
+      <xsl:value-of select="'V. cholerae'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'vibrio\p{Zs}?cholerae')">
+      <xsl:value-of select="'Vibrio cholerae'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'t\.\p{Zs}?thermophila')">
+      <xsl:value-of select="'T. thermophila'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'tetrahymena\p{Zs}?thermophila')">
+      <xsl:value-of select="'Tetrahymena thermophila'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c\.\p{Zs}?reinhardtii')">
+      <xsl:value-of select="'C. reinhardtii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'chlamydomonas\p{Zs}?reinhardtii')">
+      <xsl:value-of select="'Chlamydomonas reinhardtii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'n\.\p{Zs}?attenuata')">
+      <xsl:value-of select="'N. attenuata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'nicotiana\p{Zs}?attenuata')">
+      <xsl:value-of select="'Nicotiana attenuata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e\.\p{Zs}?carotovora')">
+      <xsl:value-of select="'E. carotovora'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'erwinia\p{Zs}?carotovora')">
+      <xsl:value-of select="'Erwinia carotovora'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e\.\p{Zs}?faecalis')">
+      <xsl:value-of select="'E. faecalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'h\.\p{Zs}?sapiens')">
+      <xsl:value-of select="'H. sapiens'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'homo\p{Zs}?sapiens')">
+      <xsl:value-of select="'Homo sapiens'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c\.\p{Zs}?trachomatis')">
+      <xsl:value-of select="'C. trachomatis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'chlamydia\p{Zs}?trachomatis')">
+      <xsl:value-of select="'Chlamydia trachomatis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'enterococcus\p{Zs}?faecalis')">
+      <xsl:value-of select="'Enterococcus faecalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'x\.\p{Zs}?laevis')">
+      <xsl:value-of select="'X. laevis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'xenopus\p{Zs}?laevis')">
+      <xsl:value-of select="'Xenopus laevis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'x\.\p{Zs}?tropicalis')">
+      <xsl:value-of select="'X. tropicalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'xenopus\p{Zs}?tropicalis')">
+      <xsl:value-of select="'Xenopus tropicalis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?musculus')">
+      <xsl:value-of select="'M. musculus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'mus\p{Zs}?musculus')">
+      <xsl:value-of select="'Mus musculus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?immigrans')">
+      <xsl:value-of select="'D. immigrans'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila\p{Zs}?immigrans')">
+      <xsl:value-of select="'Drosophila immigrans'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?subobscura')">
+      <xsl:value-of select="'D. subobscura'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila\p{Zs}?subobscura')">
+      <xsl:value-of select="'Drosophila subobscura'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?affinis')">
+      <xsl:value-of select="'D. affinis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila\p{Zs}?affinis')">
+      <xsl:value-of select="'Drosophila affinis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?obscura')">
+      <xsl:value-of select="'D. obscura'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila\p{Zs}?obscura')">
+      <xsl:value-of select="'Drosophila obscura'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'f\.\p{Zs}?tularensis')">
+      <xsl:value-of select="'F. tularensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'francisella\p{Zs}?tularensis')">
+      <xsl:value-of select="'Francisella tularensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?plantaginis')">
+      <xsl:value-of select="'P. plantaginis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'podosphaera\p{Zs}?plantaginis')">
+      <xsl:value-of select="'Podosphaera plantaginis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?lanceolata')">
+      <xsl:value-of select="'P. lanceolata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'plantago\p{Zs}?lanceolata')">
+      <xsl:value-of select="'Plantago lanceolata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?trossulus')">
+      <xsl:value-of select="'M. trossulus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'mytilus\p{Zs}?trossulus')">
+      <xsl:value-of select="'Mytilus trossulus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?edulis')">
+      <xsl:value-of select="'M. edulis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'mytilus\p{Zs}?edulis')">
+      <xsl:value-of select="'Mytilus edulis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?chilensis')">
+      <xsl:value-of select="'M. chilensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'mytilus\p{Zs}?chilensis')">
+      <xsl:value-of select="'Mytilus chilensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'u\.\p{Zs}?maydis')">
+      <xsl:value-of select="'U. maydis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'ustilago\p{Zs}?maydis')">
+      <xsl:value-of select="'Ustilago maydis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?knowlesi')">
+      <xsl:value-of select="'P. knowlesi'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'plasmodium\p{Zs}?knowlesi')">
+      <xsl:value-of select="'Plasmodium knowlesi'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?aeruginosa')">
+      <xsl:value-of select="'P. aeruginosa'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'pseudomonas\p{Zs}?aeruginosa')">
+      <xsl:value-of select="'Pseudomonas aeruginosa'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'t\.\p{Zs}?brucei')">
+      <xsl:value-of select="'T. brucei'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'trypanosoma\p{Zs}?brucei')">
+      <xsl:value-of select="'Trypanosoma brucei'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'caulobacter\p{Zs}?crescentus')">
+      <xsl:value-of select="'Caulobacter crescentus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c\.\p{Zs}?crescentus')">
+      <xsl:value-of select="'C. crescentus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'agrobacterium\p{Zs}?tumefaciens')">
+      <xsl:value-of select="'Agrobacterium tumefaciens'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'a\.\p{Zs}?tumefaciens')">
+      <xsl:value-of select="'A. tumefaciens'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'t\.\p{Zs}?gondii')">
+      <xsl:value-of select="'T. gondii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'toxoplasma\p{Zs}?gondii')">
+      <xsl:value-of select="'Toxoplasma gondii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'d\.\p{Zs}?rerio')">
+      <xsl:value-of select="'D. rerio'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'danio\p{Zs}?rerio')">
+      <xsl:value-of select="'Danio rerio'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'drosophila')">
+      <xsl:value-of select="'Drosophila'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'yimenosaurus')">
+      <xsl:value-of select="'Yimenosaurus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'lesothosaurus\p{Zs}?diagnosticus')">
+      <xsl:value-of select="'Lesothosaurus diagnosticus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'l.\p{Zs}?diagnosticus')">
+      <xsl:value-of select="'L. diagnosticus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'scelidosaurus\p{Zs}?harrisonii')">
+      <xsl:value-of select="'Scelidosaurus harrisonii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s.\p{Zs}?harrisonii')">
+      <xsl:value-of select="'S. harrisonii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'haya\p{Zs}?griva')">
+      <xsl:value-of select="'Haya griva'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'h.\p{Zs}?griva')">
+      <xsl:value-of select="'H. griva'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'polacanthus\p{Zs}?foxii')">
+      <xsl:value-of select="'Polacanthus foxii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p.\p{Zs}?foxii')">
+      <xsl:value-of select="'P. foxii'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'scutellosaurus\p{Zs}?lawleri')">
+      <xsl:value-of select="'Scutellosaurus lawleri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s.\p{Zs}?lawleri')">
+      <xsl:value-of select="'S. lawleri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'saichania\p{Zs}?chulsanensis')">
+      <xsl:value-of select="'Saichania chulsanensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s.\p{Zs}?chulsanensis')">
+      <xsl:value-of select="'S. chulsanensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'gargoyleosaurus\p{Zs}?parkpinorum')">
+      <xsl:value-of select="'Gargoyleosaurus parkpinorum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'g.\p{Zs}?parkpinorum')">
+      <xsl:value-of select="'G. parkpinorum'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'europelta\p{Zs}?carbonensis')">
+      <xsl:value-of select="'Europelta carbonensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e.\p{Zs}?carbonensis')">
+      <xsl:value-of select="'E. carbonensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'stegosaurus\p{Zs}?stenops')">
+      <xsl:value-of select="'Stegosaurus stenops'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'s.\p{Zs}?stenops')">
+      <xsl:value-of select="'S. stenops'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'pinacosaurus\p{Zs}?grangeri')">
+      <xsl:value-of select="'Pinacosaurus grangeri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p.\p{Zs}?grangeri')">
+      <xsl:value-of select="'P. grangeri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'tatisaurus\p{Zs}?oehleri')">
+      <xsl:value-of select="'Tatisaurus oehleri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'t.\p{Zs}?oehleri')">
+      <xsl:value-of select="'T. oehleri'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'hungarosaurus\p{Zs}?tormai')">
+      <xsl:value-of select="'Hungarosaurus tormai'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'h.\p{Zs}?tormai')">
+      <xsl:value-of select="'H. tormai'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'lesothosaurus\p{Zs}?diagnosticus')">
+      <xsl:value-of select="'Lesothosaurus diagnosticus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'l.\p{Zs}?diagnosticus')">
+      <xsl:value-of select="'L. diagnosticus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'bienosaurus\p{Zs}?lufengensis')">
+      <xsl:value-of select="'Bienosaurus lufengensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'b.\p{Zs}?lufengensis')">
+      <xsl:value-of select="'B. lufengensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'fabrosaurus\p{Zs}?australis')">
+      <xsl:value-of select="'Fabrosaurus australis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'f.\p{Zs}?australis')">
+      <xsl:value-of select="'F. australis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'chinshakiangosaurus\p{Zs}?chunghoensis')">
+      <xsl:value-of select="'Chinshakiangosaurus chunghoensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'c.\p{Zs}?chunghoensis')">
+      <xsl:value-of select="'C. chunghoensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'euoplocephalus\p{Zs}?tutus')">
+      <xsl:value-of select="'Euoplocephalus tutus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'e.\p{Zs}?tutus')">
+      <xsl:value-of select="'E. tutus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'g\.\p{Zs}?beringei')">
+      <xsl:value-of select="'G. beringei'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'gorilla\p{Zs}?beringei')">
+      <xsl:value-of select="'Gorilla beringei'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?assamensis')">
+      <xsl:value-of select="'M. assamensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'macaca\p{Zs}?assamensis')">
+      <xsl:value-of select="'Macaca assamensis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?fuscata')">
+      <xsl:value-of select="'M. fuscata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'macaca\p{Zs}?fuscata')">
+      <xsl:value-of select="'Macaca fuscata'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?mulatta')">
+      <xsl:value-of select="'M. mulatta'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'macaca\p{Zs}?mulatta')">
+      <xsl:value-of select="'Macaca mulatta'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?nemestrina')">
+      <xsl:value-of select="'M. nemestrina'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'macaca\p{Zs}?nemestrina')">
+      <xsl:value-of select="'Macaca nemestrina'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'m\.\p{Zs}?sphinx')">
+      <xsl:value-of select="'M. sphinx'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'mandrillus\p{Zs}?sphinx')">
+      <xsl:value-of select="'Mandrillus sphinx'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?anubis')">
+      <xsl:value-of select="'P. anubis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'papio\p{Zs}?anubis')">
+      <xsl:value-of select="'Papio anubis'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?hamadryas')">
+      <xsl:value-of select="'P. hamadryas'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'papio\p{Zs}?hamadryas')">
+      <xsl:value-of select="'Papio hamadryas'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?paniscus')">
+      <xsl:value-of select="'P. paniscus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'pan\p{Zs}?paniscus')">
+      <xsl:value-of select="'Pan paniscus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'p\.\p{Zs}?troglodytes')">
+      <xsl:value-of select="'P. troglodytes'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'pan\p{Zs}?troglodytes')">
+      <xsl:value-of select="'Pan troglodytes'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'xenopus')">
+      <xsl:value-of select="'Xenopus'"/>
+    </xsl:when>
+    <xsl:when test="matches($s,'salmonella')">
+      <xsl:value-of select="'Salmonella'"/>
+    </xsl:when>
+    <xsl:otherwise>
+      <xsl:value-of select="'undefined'"/>
+    </xsl:otherwise>
+  </xsl:choose>
+</xsl:function>
+  <xsl:function name="e:code-check">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:element name="code">
+      <xsl:if test="contains($s,'github')">
+        <xsl:element name="match">
+        <xsl:value-of select="'github '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'gitlab')">
+        <xsl:element name="match">
+        <xsl:value-of select="'gitlab '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'git.exeter.ac.uk')">
+        <xsl:element name="match">
+          <xsl:value-of select="'git.exeter.ac.uk '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'codeplex')">
+        <xsl:element name="match">
+        <xsl:value-of select="'codeplex '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'sourceforge')">
+        <xsl:element name="match">
+        <xsl:value-of select="'sourceforge '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'bitbucket')">
+        <xsl:element name="match">
+        <xsl:value-of select="'bitbucket '"/>
+        </xsl:element>
+      </xsl:if>
+      <xsl:if test="contains($s,'assembla ')">
+        <xsl:element name="match">
+        <xsl:value-of select="'assembla '"/>
+        </xsl:element>
+      </xsl:if>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:get-xrefs">
+    <xsl:param name="article"/>
+    <xsl:param name="object-id"/>
+    <xsl:param name="object-type"/>
+    <xsl:variable name="object-no" select="replace($object-id,'[^0-9]','')"/>
+    <xsl:element name="matches">
+      <xsl:for-each select="$article//xref[(@ref-type=$object-type) and not(ancestor::caption)]">
+        <xsl:variable name="rid-no" select="replace(./@rid,'[^0-9]','')"/>
+        <xsl:variable name="text-no" select="tokenize(normalize-space(replace(.,'[^0-9]',' ')),'\p{Zs}')[last()]"/>
+        <xsl:choose>
+          <xsl:when test="./@rid = $object-id">
+            <xsl:element name="match">
+              <xsl:attribute name="sec-id">
+                <xsl:value-of select="./ancestor::sec[1]/@id"/>
+              </xsl:attribute>
+              <xsl:value-of select="self::*"/>
+            </xsl:element>
+          </xsl:when>
+          <xsl:when test="contains(./@rid,'app')"/>
+          <xsl:when test="($rid-no lt $object-no) and (./following-sibling::text()[1] = '–') and (./following-sibling::*[1]/name()='xref') and (number(replace(replace(./following-sibling::xref[1]/@rid,'\-','.'),'[a-z]','')) gt number($object-no))">
+            <xsl:element name="match">
+              <xsl:attribute name="sec-id">
+                <xsl:value-of select="./ancestor::sec[1]/@id"/>
+              </xsl:attribute>
+              <xsl:value-of select="self::*"/>
+            </xsl:element>
+          </xsl:when>
+          <xsl:when test="($rid-no lt $object-no) and contains(.,$object-no) and (contains(.,'Videos') or contains(.,'videos') and contains(.,'–'))">
+            <xsl:element name="match">
+              <xsl:attribute name="sec-id">
+                <xsl:value-of select="./ancestor::sec[1]/@id"/>
+              </xsl:attribute>
+              <xsl:value-of select="self::*"/>
+            </xsl:element>
+          </xsl:when>
+          <xsl:when test="($rid-no lt $object-no) and (contains(.,'Videos') or contains(.,'videos') and contains(.,'—')) and ($text-no gt $object-no)">
+            <xsl:element name="match">
+              <xsl:attribute name="sec-id">
+                <xsl:value-of select="./ancestor::sec[1]/@id"/>
+              </xsl:attribute>
+              <xsl:value-of select="self::*"/>
+            </xsl:element>
+          </xsl:when>
+          <xsl:otherwise/>
+        </xsl:choose>
+      </xsl:for-each>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:get-iso-pub-date">
+    <xsl:param name="element"/>
+    <xsl:choose>
+      <xsl:when test="$element/ancestor-or-self::article//article-meta/pub-date[(@date-type='publication') or (@date-type='pub')]/month">
+        <xsl:variable name="pub-date" select="$element/ancestor-or-self::article//article-meta/pub-date[(@date-type='publication') or (@date-type='pub')]"/>
+        <xsl:value-of select="concat($pub-date/year,'-',$pub-date/month,'-',$pub-date/day)"/>
+      </xsl:when>
+      <xsl:otherwise/>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-copyright-holder">
+    <xsl:param name="contrib-group"/>
+    <xsl:variable name="author-count" select="count($contrib-group/contrib[@contrib-type='author'])"/>
+    <xsl:choose>
+      <xsl:when test="$author-count lt 1"/>
+      <xsl:when test="$author-count = 1">
+        <xsl:choose>
+          <xsl:when test="$contrib-group/contrib[@contrib-type='author']/collab">
+            <xsl:value-of select="$contrib-group/contrib[@contrib-type='author']/collab[1]/text()[1]"/>
+          </xsl:when>
+          <xsl:otherwise>
+            <xsl:value-of select="$contrib-group/contrib[@contrib-type='author']/name[1]/surname[1]"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:when>
+      <xsl:when test="$author-count = 2">
+        <xsl:choose>
+          <xsl:when test="$contrib-group/contrib[@contrib-type='author']/collab">
+            <xsl:choose>
+              <xsl:when test="$contrib-group/contrib[@contrib-type='author'][1]/collab and $contrib-group/contrib[@contrib-type='author'][2]/collab">
+                <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author']/collab[1]/text()[1],' and ',$contrib-group/contrib[@contrib-type='author']/collab[2]/text()[1])"/>
+              </xsl:when>
+              <xsl:when test="$contrib-group/contrib[@contrib-type='author'][1]/collab">
+                <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author'][1]/collab[1]/text()[1],' and ',$contrib-group/contrib[@contrib-type='author'][2]/name[1]/surname[1])"/>
+              </xsl:when>
+              <xsl:otherwise>
+                <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author'][1]/name[1]/surname[1],' and ',$contrib-group/contrib[@contrib-type='author'][2]/collab[1]/text()[1])"/>
+              </xsl:otherwise>
+            </xsl:choose>
+          </xsl:when>
+          <xsl:otherwise>
+            <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author'][1]/name[1]/surname[1],' and ',$contrib-group/contrib[@contrib-type='author'][2]/name[1]/surname[1])"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:when>
+      
+      <xsl:otherwise>
+        <xsl:variable name="is-equal-contrib" select="if ($contrib-group/contrib[@contrib-type='author'][1]/@equal-contrib='yes') then true() else false()"/>
+        <xsl:choose>
+          <xsl:when test="$is-equal-contrib">
+            
+            <xsl:variable name="equal-contrib-rid" select="$contrib-group/contrib[@contrib-type='author'][1]/xref[starts-with(@rid,'equal-contrib')]/@rid"/>
+            <xsl:variable name="first-authors" select="$contrib-group/contrib[@contrib-type='author' and @equal-contrib='yes' and xref[@rid=$equal-contrib-rid] and not(preceding-sibling::contrib[not(xref[@rid=$equal-contrib-rid])])]"/>
+            <xsl:choose>
+              
+              <xsl:when test="$author-count = 3 and count($first-authors) = 3">
+                <xsl:value-of select="concat(e:get-surname($contrib-group/contrib[@contrib-type='author'][1]),                   ', ',                   e:get-surname($contrib-group/contrib[@contrib-type='author'][2]),                   ' and ',                   e:get-surname($contrib-group/contrib[@contrib-type='author'][3]))"/>
+              </xsl:when>
+              
+              <xsl:when test="count($first-authors) gt 3">
+                <xsl:variable name="first-auth-string" select="string-join(for $auth in $contrib-group/contrib[@contrib-type='author'][position() lt 4] return e:get-surname($auth),', ')"/>
+                <xsl:value-of select="concat($first-auth-string,' et al')"/>
+              </xsl:when>
+              
+              <xsl:otherwise>
+                <xsl:variable name="first-auth-string" select="string-join(for $auth in $first-authors return e:get-surname($auth),', ')"/>
+                <xsl:value-of select="concat($first-auth-string,' et al')"/>
+              </xsl:otherwise>
+            </xsl:choose>
+          </xsl:when>
+          
+          <xsl:otherwise>
+            <xsl:value-of select="concat(e:get-surname($contrib-group/contrib[@contrib-type='author'][1]),' et al')"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-surname" as="text()">
+    <xsl:param name="contrib"/>
+    <xsl:choose>
+      <xsl:when test="$contrib/collab">
+        <xsl:value-of select="$contrib/collab[1]/text()[1]"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="$contrib//name[1]/surname[1]"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:insight-box" as="element()">
+    <xsl:param name="box" as="xs:string"/>
+    <xsl:param name="cite-text" as="xs:string"/>
+    <xsl:variable name="box-text" select="substring-after(substring-after($box,'article'),' ')"/> 
+    
+    <xsl:element name="list">
+      <xsl:for-each select="tokenize($cite-text,'\p{Zs}')">
+        <xsl:choose>
+          <xsl:when test="contains($box-text,.)"/>
+          <xsl:otherwise>
+            <xsl:element name="item">
+              <xsl:attribute name="type">cite</xsl:attribute>
+              <xsl:value-of select="."/>
+            </xsl:element>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:for-each>
+      <xsl:for-each select="tokenize($box-text,'\p{Zs}')">
+        <xsl:choose>
+          <xsl:when test="contains($cite-text,.)"/>
+          <xsl:otherwise>
+            <xsl:element name="item">
+              <xsl:attribute name="type">box</xsl:attribute>
+              <xsl:value-of select="."/>
+            </xsl:element>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:for-each>
+    </xsl:element>
+  </xsl:function>
+  <let name="latin-regex" value="'in\p{Zs}+vitro|ex\p{Zs}+vitro|in\p{Zs}+vivo|ex\p{Zs}+vivo|a\p{Zs}+priori|a\p{Zs}+posteriori|de\p{Zs}+novo|in\p{Zs}+utero|in\p{Zs}+natura|in\p{Zs}+situ|in\p{Zs}+planta|in\p{Zs}+cellulo|rete\p{Zs}+mirabile|nomen\p{Zs}+novum| sensu |ad\p{Zs}+libitum|in\p{Zs}+ovo'"/>
+  <xsl:function name="e:get-latin-terms" as="element()">
+    <xsl:param name="article" as="element()"/>
+    <xsl:param name="regex" as="xs:string"/>
+    
+    <xsl:variable name="roman-text" select="lower-case(       string-join(for $x in $article/*[local-name() = 'body' or local-name() = 'back']//*       return       if ($x/ancestor-or-self::sec[@sec-type='additional-information']) then ()       else if ($x/ancestor-or-self::ref-list) then ()       else if ($x/local-name() = 'italic') then ()       else $x/text(),' '))"/>
+    <xsl:variable name="italic-text" select="lower-case(string-join($article//*:italic[not(ancestor::ref-list) and not(ancestor::sec[@sec-type='additional-information'])],' '))"/>
+    
+    
+    <xsl:element name="result">
+      <xsl:choose>
+        <xsl:when test="matches($roman-text,$regex)">
+          <xsl:element name="list">
+            <xsl:attribute name="list-type">roman</xsl:attribute>
+            <xsl:for-each select="tokenize($regex,'\|')">
+              <xsl:variable name="display" select="replace(replace(.,'\\p\{Zs\}\+',' '),'^ | $','')"/>
+              <xsl:element name="match">
+                <xsl:attribute name="count">
+                  <xsl:value-of select="count(tokenize($roman-text,.)) - 1"/>
+                </xsl:attribute>
+                <xsl:value-of select="$display"/>
+              </xsl:element>
+            </xsl:for-each>
+          </xsl:element>
+        </xsl:when>
+        <xsl:otherwise>
+          <xsl:element name="list">
+            <xsl:attribute name="list-type">roman</xsl:attribute>
+          </xsl:element>
+        </xsl:otherwise>
+      </xsl:choose>
+      <xsl:choose>
+        <xsl:when test="matches($italic-text,$regex)">
+          <xsl:element name="list">
+            <xsl:attribute name="list-type">italic</xsl:attribute>
+            <xsl:for-each select="tokenize($regex,'\|')">
+              <xsl:variable name="display" select="replace(.,'\\p\{Zs\}\+',' ')"/>
+              <xsl:element name="match">
+                <xsl:attribute name="count">
+                  <xsl:value-of select="count(tokenize($italic-text,.)) - 1"/>
+                </xsl:attribute>
+                <xsl:value-of select="$display"/>
+              </xsl:element>
+            </xsl:for-each>
+          </xsl:element>
+        </xsl:when>
+        <xsl:otherwise>
+          <xsl:element name="list">
+            <xsl:attribute name="list-type">italic</xsl:attribute>
+          </xsl:element>
+        </xsl:otherwise>
+      </xsl:choose>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:print-latin-terms" as="xs:string">
+    <xsl:param name="list" as="element()"/>
+    <xsl:value-of select="string-join(       for $term in $list//*:match[@count != '0']        return if (number($term/@count) gt 1) then concat($term/@count,' instances of ',$term)       else concat($term/@count,' instance of ',$term)       ,', ')"/>
+  </xsl:function>
+  <xsl:function name="e:list-panels">
+    <xsl:param name="caption" as="xs:string"/>
+    <xsl:element name="list">
+      <xsl:for-each select="tokenize($caption,'\.\p{Zs}+')">
+        <xsl:if test="matches(.,'^[B-K]\p{P}?[A-K]?\.?\p{Zs}+')">
+          <xsl:element name="item">
+            <xsl:attribute name="token">
+              <xsl:value-of select="substring-before(.,' ')"/>
+            </xsl:attribute>
+            <xsl:value-of select="."/>
+          </xsl:element>
+        </xsl:if>
+      </xsl:for-each>
+    </xsl:element>
+  </xsl:function>
+  <xsl:function name="e:get-weekday" as="xs:integer?">
+    <xsl:param name="date" as="xs:anyAtomicType?"/>
+    <xsl:sequence select="       if (empty($date)) then ()       else xs:integer((xs:date($date) - xs:date('1901-01-06')) div xs:dayTimeDuration('P1D')) mod 7       "/>
+  </xsl:function>
+  <xsl:function name="e:line-count" as="xs:integer">
+    <xsl:param name="arg" as="xs:string?"/>
+    
+    <xsl:sequence select="count(tokenize($arg,'(\r\n?|\n\r?)'))"/>
+    
+  </xsl:function>
+  <pattern id="article-metadata">
+    <rule context="abstract[not(@abstract-type)]/sec" id="abstract-sec-titles">
+      <let name="pos" value="count(ancestor::abstract/sec) - count(following-sibling::sec)"/>
+      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="warning" id="pre-clintrial-conformance-9">A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
+    </rule>
+  </pattern>
+  <pattern id="root-pattern">
+    <rule context="root" id="root-rule">
+      <assert test="descendant::abstract[not(@abstract-type)]/sec" role="error" id="abstract-sec-titles-xspec-assert">abstract[not(@abstract-type)]/sec must be present.</assert>
+    </rule>
+  </pattern>
+</schema>
\ No newline at end of file
diff --git a/test/xspec/schematron.sch b/test/xspec/schematron.sch
index 48a58ecaff..02d96e6f82 100644
--- a/test/xspec/schematron.sch
+++ b/test/xspec/schematron.sch
@@ -2433,7 +2433,10 @@
       <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-8" test="matches(@id,'^abs[1-9]$')" role="error" id="clintrial-conformance-8">
         <name/> must have an @id in the format 'abs1'. <value-of select="@id"/> does not conform to this convention.</assert>
       
-      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="error" id="clintrial-conformance-9">A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
+      <!-- temporarily doing pre and final versions -->
+      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="warning" id="pre-clintrial-conformance-9">A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
+
+      <report see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-conformance-5" test="starts-with(lower-case(title),'clinical trial number') and not(descendant::related-object[@document-id-type='clinical-trial-number'])" role="error" id="final-clintrial-conformance-9">A section with the title <value-of select="title"/> in the abstract must have at least one related-object element that contains all the information related to the clinical trial. This one does not.</report>
     </rule>
   </pattern>
   <pattern id="abstract-sec-title-content-pattern">
diff --git a/test/xspec/schematron.xspec b/test/xspec/schematron.xspec
index 3789e99ae7..1265ce7d46 100644
--- a/test/xspec/schematron.xspec
+++ b/test/xspec/schematron.xspec
@@ -2757,14 +2757,24 @@
         <x:expect-assert id="clintrial-conformance-8" role="error"/>
         <x:expect-not-assert id="abstract-sec-titles-xspec-assert" role="error"/>
       </x:scenario>
-      <x:scenario label="clintrial-conformance-9-pass">
-        <x:context href="../tests/gen/abstract-sec-titles/clintrial-conformance-9/pass.xml"/>
-        <x:expect-not-report id="clintrial-conformance-9" role="error"/>
+      <x:scenario label="pre-clintrial-conformance-9-pass">
+        <x:context href="../tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/pass.xml"/>
+        <x:expect-not-report id="pre-clintrial-conformance-9" role="warning"/>
         <x:expect-not-assert id="abstract-sec-titles-xspec-assert" role="error"/>
       </x:scenario>
-      <x:scenario label="clintrial-conformance-9-fail">
-        <x:context href="../tests/gen/abstract-sec-titles/clintrial-conformance-9/fail.xml"/>
-        <x:expect-report id="clintrial-conformance-9" role="error"/>
+      <x:scenario label="pre-clintrial-conformance-9-fail">
+        <x:context href="../tests/gen/abstract-sec-titles/pre-clintrial-conformance-9/fail.xml"/>
+        <x:expect-report id="pre-clintrial-conformance-9" role="warning"/>
+        <x:expect-not-assert id="abstract-sec-titles-xspec-assert" role="error"/>
+      </x:scenario>
+      <x:scenario label="final-clintrial-conformance-9-pass">
+        <x:context href="../tests/gen/abstract-sec-titles/final-clintrial-conformance-9/pass.xml"/>
+        <x:expect-not-report id="final-clintrial-conformance-9" role="error"/>
+        <x:expect-not-assert id="abstract-sec-titles-xspec-assert" role="error"/>
+      </x:scenario>
+      <x:scenario label="final-clintrial-conformance-9-fail">
+        <x:context href="../tests/gen/abstract-sec-titles/final-clintrial-conformance-9/fail.xml"/>
+        <x:expect-report id="final-clintrial-conformance-9" role="error"/>
         <x:expect-not-assert id="abstract-sec-titles-xspec-assert" role="error"/>
       </x:scenario>
     </x:scenario>