Fixes (#105)

* Fix for 90960

* Fix for 90993

* Fix references in 90832

* Fix for 90465

README.md

@@ -601,6 +601,27 @@ This xsl fixes the capture of reference number 70, which has been mistagged and
 
 This xsl fixes an incorrect orcid in 92083.
 
+### [/src/2022.10.04.510784/title-fix.xsl](/src/2022.10.04.510784/title-fix.xsl)
+
+This xsl changes the caseing of the title of this preprint from all caps to sentence case.
+
+### [/src/2023.06.26.546606/various-fixes.xsl](/src/2023.06.26.546606/various-fixes.xsl)
+
+This xsl carries out three fixes:
+1. It removes the corresponding author status from one of the authors
+2. It corrects a title for one of the reference (no. 6)
+3. It fixes the DOIs which have been included incorrectly (in the incorrect URI format) by the authors.
+
+### [/src/2023.08.03.551564/fix-refs.xsl](/src/2023.08.03.551564/fix-refs.xsl)
+
+This xsl fixes numerous references which are missing key information and as a result rendering poorly on EPP.
+
+### [/src/arXiv.2211.16879/equation-fix.xsl](/src/arXiv.2211.16879/equation-fix.xsl)
+
+This xsl accounts for a bug in Encoda. In this preprint some text that precedes a display equation is pulled in as if it is a caption for that equation which it treats as a figure.
+
+The xsl adds an empty `disp-quote` element between the paragraph and display equation in order for the two to be adequately separated in the JSON.
+
 # Modify bioRxiv XML in preparation for Encoda
 
 Prerequisites:

src/2022.10.04.510784/title-fix.xsl

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+    xmlns:xs="http://www.w3.org/2001/XMLSchema"
+    xmlns:xlink="http://www.w3.org/1999/xlink"
+    exclude-result-prefixes="xs"
+    version="3.0">
+
+    <xsl:output method="xml" encoding="UTF-8"/>
+
+    <xsl:template match="*|@*|text()">
+        <xsl:copy>
+            <xsl:apply-templates select="*|@*|text()"/>
+        </xsl:copy>
+    </xsl:template>
+
+    <xsl:template match="article[//article-meta/article-version='1.2']//article-meta//article-title">
+        <article-title>Equivalent excitability through different sodium channels and implications for the analgesic efficacy of selective drugs</article-title>
+    </xsl:template>
+
+</xsl:stylesheet>

src/2023.06.26.546606/various-fixes.xsl

@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+    xmlns:xs="http://www.w3.org/2001/XMLSchema"
+    xmlns:xlink="http://www.w3.org/1999/xlink"
+    exclude-result-prefixes="xs"
+    version="3.0">
+
+    <xsl:output method="xml" encoding="UTF-8"/>
+
+    <xsl:template match="*|@*|text()">
+        <xsl:copy>
+            <xsl:apply-templates select="*|@*|text()"/>
+        </xsl:copy>
+    </xsl:template>
+
+    <xsl:template match="article[//article-meta/article-version='1.1']//article-meta//contrib[@contrib-type='author' and name[1]/surname[1]='Peng']">
+        <xsl:copy>
+            <xsl:apply-templates select="@*[name()!='corresp']|text()|*[not(@ref-type='corresp')]"/>
+        </xsl:copy>
+    </xsl:template>
+
+    <xsl:template match="article[//article-meta/article-version='1.1']//ref[@id='c6']">
+        <ref id="c6"><label>6</label><mixed-citation publication-type="journal"><string-name><surname>Stine</surname>, <given-names>Z. E.</given-names></string-name>, <string-name><surname>Walton</surname>, <given-names>Z. E.</given-names></string-name>, <string-name><surname>Altman</surname>, <given-names>B. J.</given-names></string-name>, <string-name><surname>Hsieh</surname>, <given-names>A. L.</given-names></string-name> &#x0026; <string-name><surname>Dang</surname>, <given-names>C. V.</given-names></string-name> <article-title>MYC, Metabolism, and Cancer</article-title>. <source>Cancer Discov</source> <volume>5</volume>, <fpage>1024</fpage>&#x2013;<lpage>1039</lpage> (<year>2015</year>). <pub-id pub-id-type="doi">10.1158/2159-8290.CD-15-0507</pub-id></mixed-citation></ref>
+    </xsl:template>
+
+    <xsl:template match="article[//article-meta/article-version='1.1']//ref[@id!='c6']//ext-link[matches(.,'doi\.org:')]">
+        <pub-id pub-id-type="doi"><xsl:value-of select="substring-after(.,'doi.org:')"/></pub-id>
+    </xsl:template>
+
+</xsl:stylesheet>

src/2023.08.03.551564/fix-refs.xsl

@@ -0,0 +1,51 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+    xmlns:xs="http://www.w3.org/2001/XMLSchema"
+    xmlns:xlink="http://www.w3.org/1999/xlink"
+    exclude-result-prefixes="xs"
+    version="3.0">
+
+    <xsl:output method="xml" encoding="UTF-8"/>
+
+    <xsl:template match="*|@*|text()">
+        <xsl:copy>
+            <xsl:apply-templates select="*|@*|text()"/>
+        </xsl:copy>
+    </xsl:template>
+
+    <xsl:template match="article[//article-meta/article-version='1.1']//ref[mixed-citation[@publication-type='journal' and not(article-title)]]">
+        <xsl:choose>
+            <xsl:when test="@id='c4'">
+                <ref id="c4"><mixed-citation publication-type="journal"><string-name><surname>Bolton</surname> <given-names>AD</given-names></string-name>, <string-name><surname>Murata</surname> <given-names>Y</given-names></string-name>, <string-name><surname>Kirchner</surname> <given-names>R</given-names></string-name>, <string-name><surname>Kim</surname> <given-names>S-Y</given-names></string-name>, <string-name><surname>Young</surname> <given-names>A</given-names></string-name>, <string-name><surname>Dang</surname> <given-names>T</given-names></string-name>, <string-name><surname>Yanagawa</surname> <given-names>Y</given-names></string-name>, <string-name><surname>Constantine-Paton</surname> <given-names>M</given-names></string-name>. <year>2015</year>. <article-title>A Diencephalic Dopamine Source Provides Input to the Superior Colliculus, where D1 and D2 Receptors Segregate to Distinct Functional Zones</article-title>. <source>Cell Rep</source> <volume>13</volume>:<elocation-id>1003&#x2013;1015</elocation-id>.</mixed-citation></ref>
+            </xsl:when>
+            <xsl:when test="@id='c12'">
+                <ref id="c12"><mixed-citation publication-type="journal"><string-name><surname>Chen</surname> <given-names>F</given-names></string-name>, <string-name><surname>Qian</surname> <given-names>J</given-names></string-name>, <string-name><surname>Cao</surname> <given-names>Z</given-names></string-name>, <string-name><surname>Li</surname> <given-names>A</given-names></string-name>, <string-name><surname>Cui</surname> <given-names>J</given-names></string-name>, <string-name><surname>Shi</surname> <given-names>L</given-names></string-name>, <string-name><surname>Xie</surname> <given-names>J.</given-names></string-name> <year>2023</year>. <article-title>Chemogenetic and optogenetic stimulation of zona incerta GABAergic neurons ameliorates motor impairment in Parkinson&#x2019;s disease</article-title>. <source>iScience</source> <volume>26</volume>:<elocation-id>107149</elocation-id>.</mixed-citation></ref>
+            </xsl:when>
+            <xsl:when test="@id='c14'">
+                <ref id="c14"><mixed-citation publication-type="book"><string-name><surname>Cohen</surname> <given-names>J.</given-names></string-name> <year>1988</year>. <source>Statistical power analysis for the behavioral sciences</source> <publisher-loc>New York</publisher-loc>. <publisher-name>NY: Academic</publisher-name> <fpage>54</fpage>.</mixed-citation></ref>
+            </xsl:when>
+            <xsl:when test="@id='c36'">
+                <ref id="c36"><mixed-citation publication-type="journal"><string-name><surname>Kim</surname> <given-names>L</given-names></string-name>, <string-name><surname>Chomiak</surname> <given-names>T</given-names></string-name>, <string-name><surname>Tran</surname> <given-names>MA</given-names></string-name>, <string-name><surname>Tam</surname> <given-names>S</given-names></string-name>, <string-name><surname>McPherson</surname> <given-names>C</given-names></string-name>, <string-name><surname>Eaton</surname> <given-names>SEA</given-names></string-name>, <string-name><surname>Ou</surname> <given-names>Y</given-names></string-name>, <string-name><surname>Kiss</surname> <given-names>ZHT</given-names></string-name>, <string-name><surname>Whelan</surname> <given-names>PJ.</given-names></string-name> <year>2021</year>. <article-title>Global remodelling of afferent and efferent projections of the A13 region following unilateral nigrostriatal degeneration using 6-hydroxydopamineNeuroscience Meeting Planner</article-title>. <source>Presented at the Society for Neuroscience</source>.</mixed-citation></ref>
+            </xsl:when>
+            <xsl:when test="@id='c37'">
+                <ref id="c37"><mixed-citation publication-type="journal"><string-name><surname>Kim</surname> <given-names>LH</given-names></string-name>, <string-name><surname>Chomiak</surname> <given-names>T</given-names></string-name>, <string-name><surname>Tran</surname> <given-names>M</given-names></string-name>, <string-name><surname>Tam</surname> <given-names>S</given-names></string-name>, <string-name><surname>McPherson</surname> <given-names>C</given-names></string-name>, <string-name><surname>Eaton</surname> <given-names>SEA</given-names></string-name>, <string-name><surname>Ou</surname> <given-names>Y</given-names></string-name>, <string-name><surname>Resch</surname> <given-names>L</given-names></string-name>, <string-name><surname>Kiss</surname> <given-names>ZHT</given-names></string-name>, <string-name><surname>Whelan</surname> <given-names>PJ.</given-names></string-name> <year>2021</year>. <article-title>Substantia nigra degradation results in widespread changes in medial zona incerta afferent and efferent connectomics</article-title>. <source>bioRxiv</source>.</mixed-citation></ref>
+            </xsl:when>
+            <xsl:when test="@id='c41'">
+                <ref id="c41"><mixed-citation publication-type="journal"><string-name><surname>Konnova</surname> <given-names>EA</given-names></string-name>, <string-name><given-names>Translational Neurogenetics</given-names> <surname>Unit</surname></string-name>, <string-name><given-names>Wallenberg Neuroscience</given-names> <surname>Center</surname></string-name>, <string-name><surname>Lund University</surname>, <given-names>Lund</given-names></string-name>, <string-name><surname>Sweden</surname>, <given-names>Swanberg M</given-names></string-name>, <string-name><given-names>Translational Neurogenetics</given-names> <surname>Unit</surname></string-name>, <string-name><given-names>Wallenberg Neuroscience</given-names> <surname>Center</surname></string-name>, <string-name><surname>Lund University</surname>, <given-names>Lund</given-names></string-name>, Sweden. <year>2018</year>. <article-title>Animal models of Parkinson&#x2019;s diseaseParkinson&#x2019;s Disease: Pathogenesis and Clinical Aspects</article-title>. <source>Codon Publications</source>. pp. <fpage>83</fpage>&#x2013;<lpage>106</lpage>.</mixed-citation></ref>
+            </xsl:when>
+            <xsl:when test="@id='c47'">
+                <ref id="c47"><mixed-citation publication-type="journal"><string-name><surname>Li</surname> <given-names>S</given-names></string-name>, <string-name><surname>Shi</surname> <given-names>Y</given-names></string-name>, <string-name><surname>Kirouac</surname> <given-names>GJ</given-names></string-name>. <year>2014</year>. <article-title>The hypothalamus and periaqueductal gray are the sources of dopamine fibers in the paraventricular nucleus of the thalamus in the rat</article-title>. <source>Front. Neuroanat</source> <volume>8</volume>:<elocation-id>136</elocation-id>. <pub-id pub-id-type="doi">10.3389/fnana.2014.00136</pub-id></mixed-citation></ref>
+            </xsl:when>
+            <xsl:when test="@id='c92'">
+                <ref id="c92"><mixed-citation publication-type="journal"><string-name><surname>Sita</surname> <given-names>LV</given-names></string-name>, <string-name><surname>Elias</surname> <given-names>CF</given-names></string-name>, <string-name><surname>Bittencourt</surname> <given-names>JC</given-names></string-name>. <year>2007</year>. <article-title>Connectivity pattern suggests that incerto-hypothalamic area belongs to the medial hypothalamic system</article-title>. <source>Neuroscience</source> <volume>148</volume>:<fpage>949</fpage>&#x2013;<lpage>969</lpage>.</mixed-citation></ref>
+            </xsl:when>
+            <xsl:when test="@id='c93a'">
+                <ref id="c93a"><mixed-citation publication-type="journal"><string-name><surname>Stefani</surname> <given-names>A</given-names></string-name>, <string-name><surname>Lozano</surname> <given-names>AM</given-names></string-name>, <string-name><surname>Peppe</surname> <given-names>A</given-names></string-name>, <string-name><surname>Stanzione</surname> <given-names>P</given-names></string-name>, <string-name><surname>Galati</surname> <given-names>S</given-names></string-name>, <string-name><surname>Tropepi</surname> <given-names>D</given-names></string-name>, <string-name><surname>Pierantozzi</surname> <given-names>M</given-names></string-name>, <string-name><surname>Brusa</surname> <given-names>L</given-names></string-name>, <string-name><surname>Scarnati</surname> <given-names>E</given-names></string-name>, <string-name><surname>Mazzone</surname> <given-names>P</given-names></string-name>. <year>2007</year>. <article-title>Bilateral deep brain stimulation of the pedunculopontine and subthalamic nuclei in severe Parkinson&#x2019;s disease</article-title>. <source>Brain</source> <volume>130</volume>:<elocation-id>1596&#x2013;1607</elocation-id>.</mixed-citation></ref>
+            </xsl:when>
+            <xsl:when test="@id='c97'">
+                <ref id="c97"><mixed-citation publication-type="journal"><string-name><surname>Tsang</surname> <given-names>E</given-names></string-name>, <string-name><surname>Orlandini</surname> <given-names>C</given-names></string-name>, <string-name><surname>Sureka</surname> <given-names>R</given-names></string-name>, <string-name><surname>Crevenna</surname> <given-names>AH</given-names></string-name>, <string-name><surname>Perlas</surname> <given-names>E</given-names></string-name>, <string-name><surname>Prankerd</surname> <given-names>I</given-names></string-name>, <string-name><surname>Masferrer</surname> <given-names>ME</given-names></string-name>, <string-name><surname>Gross</surname> <given-names>CT.</given-names></string-name> <year>2021</year>. <article-title>Induction of flight via midbrain projections to the cuneiform nucleus</article-title>. <source>bioRxiv</source>. doi:<pub-id pub-id-type="doi">10.1101/2021.12.21.473683</pub-id></mixed-citation></ref>
+            </xsl:when>
+        </xsl:choose>
+    </xsl:template>
+
+</xsl:stylesheet>

src/arXiv.2211.16879/equation-fix.xsl

@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+    xmlns:xs="http://www.w3.org/2001/XMLSchema"
+    xmlns:xlink="http://www.w3.org/1999/xlink"
+    exclude-result-prefixes="xs"
+    version="3.0">
+
+    <xsl:output method="xml" encoding="UTF-8"/>
+
+    <xsl:template match="*|@*|text()">
+        <xsl:copy>
+            <xsl:apply-templates select="*|@*|text()"/>
+        </xsl:copy>
+    </xsl:template>
+
+    <xsl:template match="article[//article-meta/article-version='1.2']//disp-formula[@id='FD7']">
+        <disp-quote/>
+        <xsl:text>&#xA;</xsl:text>
+        <xsl:copy>
+            <xsl:apply-templates select="*|@*|text()"/>
+        </xsl:copy>
+        <xsl:text>&#xA;</xsl:text>
+        <disp-quote/>
+    </xsl:template>
+
+</xsl:stylesheet>