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Update examples and specs
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70 changes: 33 additions & 37 deletions doc/content/specs/nidm-results_dev.html
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Expand Up @@ -1105,7 +1105,7 @@ <h1 label="NIDM_0000144">nidm:'Resels Per Voxel Map'</h1>
<td><a title="NIDM_0000002">nidm:'Contrast Map'</a>
</td>

<td rowspan="4" style="text-align: center;">NIDM-Results Types<br/> (PROV Entity)</td>
<td rowspan="3" style="text-align: center;">NIDM-Results Types<br/> (PROV Entity)</td>

<td><a title="NIDM_0000002">nidm:'Contrast Map'</a></td>
</tr>
Expand All @@ -1117,13 +1117,6 @@ <h1 label="NIDM_0000144">nidm:'Resels Per Voxel Map'</h1>
<td><a title="NIDM_0000013">nidm:'Contrast Standard Error Map'</a></td>
</tr>

<tr>
<td><a title="NIDM_0000014">nidm:'Contrast Weights'</a>
</td>

<td><a title="NIDM_0000014">nidm:'Contrast Weights'</a></td>
</tr>

<tr>
<td><a title="NIDM_0000076">nidm:'Statistic Map'</a>
</td>
Expand All @@ -1138,7 +1131,7 @@ <h1 label="NIDM_0000144">nidm:'Resels Per Voxel Map'</h1>
<section id="section-nidm:'Contrast Estimation'">
<h1 label="NIDM_0000001">nidm:'Contrast Estimation'</h1>
<div class="glossary-ref">
A <a title="NIDM_0000001"><dfn title="NIDM_0000001">nidm:'Contrast Estimation'</dfn></a> is the process of performing a <a href="http://purl.obolibrary.org/obo/STATO_0000383) at each element (e.g., pixel, voxel, vertex, or face">obo:contrast estimation</a> of a map. <a title="NIDM_0000001">nidm:'Contrast Estimation'</a> is a prov:Activity that uses <a title="NIDM_0000014">nidm:'Contrast Weights'</a>, <a title="NIDM_0000019">nidm:'Design Matrix'</a>, <a title="NIDM_0000054">nidm:'Mask Map'</a>, <a title="NIDM_0000061">nidm:'Parameter Estimate Map'</a>, <a title="NIDM_0000066">nidm:'Residual Mean Squares Map'</a> entities. This activity generates <a title="NIDM_0000002">nidm:'Contrast Map'</a>, <a title="NIDM_0000013">nidm:'Contrast Standard Error Map'</a>, <a title="NIDM_0000076">nidm:'Statistic Map'</a> entities.
A <a title="NIDM_0000001"><dfn title="NIDM_0000001">nidm:'Contrast Estimation'</dfn></a> is the process of performing a <a href="http://purl.obolibrary.org/obo/STATO_0000383) at each element (e.g., pixel, voxel, vertex, or face">obo:contrast estimation</a> of a map. <a title="NIDM_0000001">nidm:'Contrast Estimation'</a> is a prov:Activity that uses <a title="NIDM_0000019">nidm:'Design Matrix'</a>, <a title="NIDM_0000054">nidm:'Mask Map'</a>, <a title="NIDM_0000061">nidm:'Parameter Estimate Map'</a>, <a title="NIDM_0000066">nidm:'Residual Mean Squares Map'</a>, <a title="STATO_0000323" href ="http://purl.obolibrary.org/obo/STATO_0000323">obo:'contrast weight matrix'</a> entities. This activity generates <a title="NIDM_0000002">nidm:'Contrast Map'</a>, <a title="NIDM_0000013">nidm:'Contrast Standard Error Map'</a>, <a title="NIDM_0000076">nidm:'Statistic Map'</a> entities.
</div>
<p></p>
<div class="attributes" id="attributes-nidm:'Contrast Estimation'"> A <a title="NIDM_0000001">nidm:'Contrast Estimation'</a> has attributes:
Expand Down Expand Up @@ -1214,33 +1207,6 @@ <h1 label="NIDM_0000013">nidm:'Contrast Standard Error Map'</h1>
nidm_inCoordinateSpace: niiri:coordinate_space_id_1 ;
crypto:sha512 "e43b6e01b0463fe7d40782137867a..."^^xsd:string ;
prov:wasGeneratedBy niiri:contrast_estimation_id .</pre>
</section>
<!-- nidm:'Contrast Weights' (NIDM_0000014) -->
<section id="section-nidm:'Contrast Weights'">
<h1 label="NIDM_0000014">nidm:'Contrast Weights'</h1>
<div class="glossary-ref">
A <a title="NIDM_0000014"><dfn title="NIDM_0000014">nidm:'Contrast Weights'</dfn></a> is vector defining the linear combination associated with a particular contrast. . <a title="NIDM_0000014">nidm:'Contrast Weights'</a> is a prov:Entity used by <a title="NIDM_0000001">nidm:'Contrast Estimation'</a>.
</div>
<p></p>
<div class="attributes" id="attributes-nidm:'Contrast Weights'"> A <a title="NIDM_0000014">nidm:'Contrast Weights'</a> has attributes:
<ul>
<li><span class="attribute" id="nidm:'Contrast Weights'.label">rdfs:label</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> human readable description of the nidm:'Contrast Weights'.</li>

<li><a title="NIDM_0000085">nidm:'contrast Name'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> name of the contrast.(range <a title="string" href ="http://www.w3.org/2001/XMLSchema#string">xsd:string</a>)</li>
<li><a title="NIDM_0000123"><dfn title="NIDM_0000123">nidm:'statistic Type'</dfn></a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property that associates a <a href="http://purl.obolibrary.org/obo/STATO_0000039">stato:"statistic"</a> with a StatisticMap or a ContrastWeights entity.(range <a title="STATO_0000039" href ="http://purl.obolibrary.org/obo/STATO_0000039">obo:'statistic'</a> such as <a title="STATO_0000030" href ="http://purl.obolibrary.org/obo/STATO_0000030">obo:'Chi-Squared statistic'</a>, <a title="STATO_0000282" href ="http://purl.obolibrary.org/obo/STATO_0000282">obo:'F-statistic'</a>, <a title="STATO_0000376" href ="http://purl.obolibrary.org/obo/STATO_0000376">obo:'Z-statistic'</a>, <a title="STATO_0000176" href ="http://purl.obolibrary.org/obo/STATO_0000176">obo:'t-statistic'</a>)</li>
</ul>
</div>
<pre class='example highlight'>@prefix nidm_ContrastWeights: &lt;http://purl.org/nidash/nidm#NIDM_0000014&gt; .
@prefix nidm_statisticType: &lt;http://purl.org/nidash/nidm#NIDM_0000123&gt; .
@prefix nidm_contrastName: &lt;http://purl.org/nidash/nidm#NIDM_0000085&gt; .
@prefix obo_tstatistic: &lt;http://purl.obolibrary.org/obo/STATO_0000176&gt; .


niiri:contrast_id a prov:Entity , nidm_ContrastWeights: ;
rdfs:label "Contrast: Listening &gt; Rest" ;
prov:value "[1, 0, 0]"^^xsd:string ;
nidm_statisticType: obo_tstatistic: ; # obo:'t-statistic'
nidm_contrastName: "listening &gt; rest"^^xsd:string .</pre>
</section>
<!-- nidm:'Statistic Map' (NIDM_0000076) -->
<section id="section-nidm:'Statistic Map'">
Expand All @@ -1258,7 +1224,7 @@ <h1 label="NIDM_0000076">nidm:'Statistic Map'</h1>
<li><a title="NIDM_0000093"><dfn title="NIDM_0000093">nidm:'error Degrees Of Freedom'</dfn></a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> degrees of freedom of the error.(range <a title="float" href ="http://www.w3.org/2001/XMLSchema#float">xsd:float</a>)</li>
<li><a title="NIDM_0000103">nidm:'has Map Header'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> a Property that associates an additional file containing the map header with a map.(range <a title="NIDM_0000053">nidm:'Map Header'</a>)</li>
<li><a title="NIDM_0000104">nidm:'in Coordinate Space'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property of a DataArray to associate a CoordinateSpace with a physical file.(range <a title="NIDM_0000016">nidm:'Coordinate Space'</a>)</li>
<li><a title="NIDM_0000123">nidm:'statistic Type'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property that associates a <a href="http://purl.obolibrary.org/obo/STATO_0000039">stato:"statistic"</a> with a StatisticMap or a ContrastWeights entity.(range <a title="STATO_0000039" href ="http://purl.obolibrary.org/obo/STATO_0000039">obo:'statistic'</a> such as <a title="STATO_0000030" href ="http://purl.obolibrary.org/obo/STATO_0000030">obo:'Chi-Squared statistic'</a>, <a title="STATO_0000282" href ="http://purl.obolibrary.org/obo/STATO_0000282">obo:'F-statistic'</a>, <a title="STATO_0000376" href ="http://purl.obolibrary.org/obo/STATO_0000376">obo:'Z-statistic'</a>, <a title="STATO_0000176" href ="http://purl.obolibrary.org/obo/STATO_0000176">obo:'t-statistic'</a>)</li>
<li><a title="NIDM_0000123"><dfn title="NIDM_0000123">nidm:'statistic Type'</dfn></a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property that associates a <a href="http://purl.obolibrary.org/obo/STATO_0000039">stato:"statistic"</a> with a StatisticMap or a ContrastWeights entity.(range <a title="STATO_0000039" href ="http://purl.obolibrary.org/obo/STATO_0000039">obo:'statistic'</a> such as <a title="STATO_0000030" href ="http://purl.obolibrary.org/obo/STATO_0000030">obo:'Chi-Squared statistic'</a>, <a title="STATO_0000282" href ="http://purl.obolibrary.org/obo/STATO_0000282">obo:'F-statistic'</a>, <a title="STATO_0000376" href ="http://purl.obolibrary.org/obo/STATO_0000376">obo:'Z-statistic'</a>, <a title="STATO_0000176" href ="http://purl.obolibrary.org/obo/STATO_0000176">obo:'t-statistic'</a>)</li>
</ul>
</div>
<pre class='example highlight'>@prefix nidm_StatisticMap: &lt;http://purl.org/nidash/nidm#NIDM_0000076&gt; .
Expand All @@ -1282,6 +1248,36 @@ <h1 label="NIDM_0000076">nidm:'Statistic Map'</h1>
crypto:sha512 "e43b6e01b0463fe7d40782137867a..."^^xsd:string ;
prov:wasGeneratedBy niiri:contrast_estimation_id;
nidm_errorDegreesOfFreedom: "72.9999999990787"^^xsd:float .</pre>
</section>
<!-- obo:'contrast weight matrix' (STATO_0000323) -->
<section id="section-obo:'contrast weight matrix'">
<h1 label="STATO_0000323">obo:'contrast weight matrix'</h1>
<div class="glossary-ref">
A <a title="STATO_0000323" href ="http://purl.obolibrary.org/obo/STATO_0000323"><dfn title="STATO_0000323" href ="http://purl.obolibrary.org/obo/STATO_0000323">obo:'contrast weight matrix'</dfn></a> is a contrast weight matrix is a information content entity which holds a set of contrast weight, coefficient used in a weighting sum of means defining a contrast. <a title="STATO_0000323" href ="http://purl.obolibrary.org/obo/STATO_0000323">obo:'contrast weight matrix'</a> is used by <a title="NIDM_0000001">nidm:'Contrast Estimation'</a>.
</div>
<p></p>
<div class="attributes" id="attributes-obo:'contrast weight matrix'"> A <a title="STATO_0000323" href ="http://purl.obolibrary.org/obo/STATO_0000323">obo:'contrast weight matrix'</a> has attributes:
<ul>
<li><span class="attribute" id="obo:'contrast weight matrix'.label">rdfs:label</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> human readable description of the obo:'contrast weight matrix'.</li>

<li><a title="NIDM_0000085">nidm:'contrast Name'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> name of the contrast.(range <a title="string" href ="http://www.w3.org/2001/XMLSchema#string">xsd:string</a>)</li>
<li><a title="NIDM_0000123">nidm:'statistic Type'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property that associates a <a href="http://purl.obolibrary.org/obo/STATO_0000039">stato:"statistic"</a> with a StatisticMap or a ContrastWeights entity.(range <a title="STATO_0000039" href ="http://purl.obolibrary.org/obo/STATO_0000039">obo:'statistic'</a> such as <a title="STATO_0000030" href ="http://purl.obolibrary.org/obo/STATO_0000030">obo:'Chi-Squared statistic'</a>, <a title="STATO_0000282" href ="http://purl.obolibrary.org/obo/STATO_0000282">obo:'F-statistic'</a>, <a title="STATO_0000376" href ="http://purl.obolibrary.org/obo/STATO_0000376">obo:'Z-statistic'</a>, <a title="STATO_0000176" href ="http://purl.obolibrary.org/obo/STATO_0000176">obo:'t-statistic'</a>)</li>
</ul>
</div>
<pre class='example highlight'>[1,0,0]</pre>
</ul>
</div>
<pre class='example highlight'>@prefix nidm_statisticType: &lt;http://purl.org/nidash/nidm#NIDM_0000123&gt; .
@prefix nidm_contrastName: &lt;http://purl.org/nidash/nidm#NIDM_0000085&gt; .
@prefix obo_contrastweightmatrix: &lt;http://purl.obolibrary.org/obo/STATO_0000323&gt; .
@prefix obo_tstatistic: &lt;http://purl.obolibrary.org/obo/STATO_0000176&gt; .


niiri:contrast_id a prov:Entity , obo_contrastweightmatrix: ;
rdfs:label "Contrast: Listening &gt; Rest" ;
prov:value "[1, 0, 0]"^^xsd:string ;
nidm_statisticType: obo_tstatistic: ; # obo:'t-statistic'
nidm_contrastName: "listening &gt; rest"^^xsd:string .</pre>
</section>
</section>
<section><h1>Inference</h1>
Expand Down
8 changes: 4 additions & 4 deletions nidm/nidm-results/fsl/README.md
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@@ -1,9 +1,9 @@

Prov store: https://provenance.ecs.soton.ac.uk/store/documents/77387/
Prov store: https://provenance.ecs.soton.ac.uk/store/documents/77421/

Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/77387.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/77387.ttl),
Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/77387.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/77387.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/77387.png)
Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/77421.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/77421.ttl),
Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/77421.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/77421.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/77421.png)

![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/77387.png)
![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/77421.png)

8 changes: 4 additions & 4 deletions nidm/nidm-results/fsl/example001/README.md
View file
@@ -1,9 +1,9 @@

Prov store: https://provenance.ecs.soton.ac.uk/store/documents/77687/
Prov store: https://provenance.ecs.soton.ac.uk/store/documents/77691/

Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/77687.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/77687.ttl),
Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/77687.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/77687.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/77687.png)
Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/77691.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/77691.ttl),
Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/77691.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/77691.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/77691.png)

![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/77687.png)
![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/77691.png)

4 changes: 2 additions & 2 deletions nidm/nidm-results/fsl/example001/fsl_nidm.provn
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Expand Up @@ -74,6 +74,7 @@ prefix nidm_ContrastMap <http://purl.org/nidash/nidm#NIDM_0000002>
prefix nidm_pValueFWER <http://purl.org/nidash/nidm#NIDM_0000115>
prefix nidm_coordinate <http://purl.org/nidash/nidm#NIDM_0000086>
prefix nidm_hasErrorDependence <http://purl.org/nidash/nidm#NIDM_0000100>
prefix obo_contrastweightmatrix <http://purl.obolibrary.org/obo/STATO_0000323>
prefix nidm_clusterLabelId <http://purl.org/nidash/nidm#NIDM_0000082>
prefix nidm_ContrastVarianceMap <http://purl.org/nidash/nidm#NIDM_0000135>
prefix nidm <http://purl.org/nidash/nidm#>
Expand All @@ -86,7 +87,6 @@ prefix nidm_IndependentParameter <http://purl.org/nidash/nidm#NIDM_0000073>
prefix nidm_randomFieldStationarity <http://purl.org/nidash/nidm#NIDM_0000120>
prefix nidm_hasDriftModel <http://purl.org/nidash/nidm#NIDM_0000088>
prefix nidm_voxelUnits <http://purl.org/nidash/nidm#NIDM_0000133>
prefix nidm_ContrastWeights <http://purl.org/nidash/nidm#NIDM_0000014>
prefix nidm_varianceMapWiseDependence <http://purl.org/nidash/nidm#NIDM_0000126>
prefix nidm_userSpecifiedThresholdType <http://purl.org/nidash/nidm#NIDM_0000125>
prefix nidm_SubjectCoordinateSystem <http://purl.org/nidash/nidm#NIDM_0000077>
Expand All @@ -109,7 +109,7 @@ entity(niiri:coordinate_0003_1,[prov:type = 'nidm:NIDM_0000015', prov:label = "C
entity(niiri:coordinate_0003_4,[prov:type = 'nidm:NIDM_0000015', prov:label = "Coordinate 0003_4", nidm:NIDM_0000086 = "[-57.4,31.8,-2.12]" %% xsd:string, nidm:NIDM_0000139 = "[46,45, 22]" %% xsd:string])
entity(niiri:coordinate_0003_3,[prov:type = 'nidm:NIDM_0000015', prov:label = "Coordinate 0003_3", nidm:NIDM_0000086 = "[-63.4,3.78,0.366]" %% xsd:string, nidm:NIDM_0000139 = "[48,37, 21]" %% xsd:string])
entity(niiri:drift_model_id,[prov:type = 'fsl:GaussianRunningLineDriftModel', prov:label = "FSL's Gaussian Running Line Drift Model", fsl:driftCutoffPeriod = "2" %% xsd:integer])
entity(niiri:contrast_id_1,[prov:type = 'nidm:NIDM_0000014', prov:label = "Contrast Weights: Generation", prov:value = "[1, 0, 0, 0]" %% xsd:string, nidm:NIDM_0000123 = 'obo:STATO_0000176', nidm:NIDM_0000085 = "Generation" %% xsd:string])
entity(niiri:contrast_id_1,[prov:type = 'obo:STATO_0000323', prov:label = "Contrast Weights: Generation", prov:value = "[1, 0, 0, 0]" %% xsd:string, nidm:NIDM_0000123 = 'obo:STATO_0000176', nidm:NIDM_0000085 = "Generation" %% xsd:string])
entity(niiri:peak_0003_5,[prov:type = 'nidm:NIDM_0000062', prov:label = "Peak 0003_5", prov:location = 'niiri:coordinate_0003_5', nidm:NIDM_0000116 = "1.22151e-05" %% xsd:float, nidm:NIDM_0000092 = "4.22" %% xsd:float])
entity(niiri:peak_0003_4,[prov:type = 'nidm:NIDM_0000062', prov:label = "Peak 0003_4", prov:location = 'niiri:coordinate_0003_4', nidm:NIDM_0000116 = "9.77365e-06" %% xsd:float, nidm:NIDM_0000092 = "4.27" %% xsd:float])
entity(niiri:coordinate_0001_2,[prov:type = 'nidm:NIDM_0000015', prov:label = "Coordinate 0001_2", nidm:NIDM_0000086 = "[-9.14,30.5,23.7]" %% xsd:string, nidm:NIDM_0000139 = "[33,43, 28]" %% xsd:string])
Expand Down
4 changes: 2 additions & 2 deletions nidm/nidm-results/fsl/example001/fsl_nidm.ttl
View file
Expand Up @@ -21,7 +21,6 @@
@prefix nidm_ContrastEstimation: <http://purl.org/nidash/nidm#NIDM_0000001> .
@prefix nidm_ContrastStandardErrorMap: <http://purl.org/nidash/nidm#NIDM_0000013> .
@prefix nidm_inCoordinateSpace: <http://purl.org/nidash/nidm#NIDM_0000104> .
@prefix nidm_ContrastWeights: <http://purl.org/nidash/nidm#NIDM_0000014> .
@prefix nidm_statisticType: <http://purl.org/nidash/nidm#NIDM_0000123> .
@prefix nidm_contrastName: <http://purl.org/nidash/nidm#NIDM_0000085> .
@prefix nidm_CoordinateSpace: <http://purl.org/nidash/nidm#NIDM_0000016> .
Expand Down Expand Up @@ -90,6 +89,7 @@
@prefix nidm_equivalentZStatistic: <http://purl.org/nidash/nidm#NIDM_0000092> .
@prefix nidm_PeakDefinitionCriteria: <http://purl.org/nidash/nidm#NIDM_0000063> .
@prefix nidm_minDistanceBetweenPeaks: <http://purl.org/nidash/nidm#NIDM_0000109> .
@prefix obo_contrastweightmatrix: <http://purl.obolibrary.org/obo/STATO_0000323> .
@prefix obo_tstatistic: <http://purl.obolibrary.org/obo/STATO_0000176> .
@prefix obo_Toeplitzcovariancestructure: <http://purl.obolibrary.org/obo/STATO_0000357> .
@prefix obo_Zstatistic: <http://purl.obolibrary.org/obo/STATO_0000376> .
Expand All @@ -114,7 +114,7 @@ niiri:contrast_standard_error_map_id_1 a prov:Entity , nidm_ContrastStandardErro
crypto:sha512 "8529f3ff9f10da8f332ced9d579990321475c1498b56d79ede560ba2eccf6d68718757dc7af78eb1e86617a41e6c9f55161f756d184e2b0fb06c3d419dc99856"^^xsd:string ;
prov:wasGeneratedBy niiri:contrast_estimation_id_1 .

niiri:contrast_id_1 a prov:Entity , nidm_ContrastWeights: ;
niiri:contrast_id_1 a prov:Entity , obo_contrastweightmatrix: ;
rdfs:label "Contrast Weights: Generation" ;
prov:value "[1, 0, 0, 0]"^^xsd:string ;
nidm_statisticType: obo_tstatistic: ; # obo:'t-statistic'
Expand Down

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