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Review final pending causal graphs and bound evidence (batch124) #1972

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41 changes: 38 additions & 3 deletions docs/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.html
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Expand Up @@ -570,21 +570,56 @@ <h2>Ecological Interactions</h2>
<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which wastewater source and initial chemistry, MLSS source, bacterial activation procedure, HRAP geometry, working volume, retention time, outdoor light and temperature regime, and inoculation ratio were used for the AM-AB Chlorella-MLSS consortium?
Which reported HRAP conditions can now be curated from the full text, and which outdoor operating conditions remain unspecified?
</h3>
<p class="prewrap">The PubMed abstract names the Chlorella vulgaris/MLSS partners, separate activation before AM-AB assembly, outdoor HRAP cultivation, and the nitrogen, phosphate, ammonia, and BOD endpoints, but it does not report the underlying wastewater chemistry, mixed-liquor source, MLSS activation recipe, inoculation ratio, or HRAP operating conditions.</p>
<p class="prewrap">The full primary Methods and Tables 1-3 are now available and identify wastewater/sludge sources, activation, pond geometry, inoculation and initial chemistry. These are no longer abstract-access gaps. Reconcile the non-graph fields with those sections; do not transfer indoor algal-stock light and temperature settings to outdoor treatment. The graph review leaves that metadata curation separate.</p>

<p class="muted small">Attaches to: <code>taxonomy#Activated MLSS bacterial consortium</code>, <code>growth_media#wastewater outdoor HRAP medium</code>, <code>cultivation_setup</code></p>




</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which consortium-level treatment effects and qualified mechanisms belong in the currently empty graph?
</h3>
<p class="prewrap">The primary study compares the combined culture with activated algae alone. Retain improved late total-nitrogen removal, but early nitrogen removal is slower, phosphate reaches the detection limit in both conditions, and BOD removal is not uniformly better. Biomass correlations do not establish a transfer mechanism. New nodes require a separately authorized Edison causal-graph review; none were added in this repair pass.</p>

<p class="muted small">Attaches to: <code>ecological_interactions</code></p>



<details class="evidence-list">
<summary class="muted small">1 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42429207/" rel="nofollow noreferrer">PMID:42429207</a>


</div>
<p class="snippet small prewrap">phycoremediation using the AM–AB consortium delayed the removal of nitrogen compared to standalone activated C. vulgaris treatment</p>
<p class="muted small prewrap">The algae-only control prevents an unqualified faster-removal or universal-synergy graph.</p>
</div>

</details>


</div>

</section>
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49 changes: 42 additions & 7 deletions docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html
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Expand Up @@ -650,9 +650,9 @@ <h2>Ecological Interactions</h2>

<div class="interaction-card">
<div class="interaction-header">
<h3>Hydrogen Cofactor Reductive-Dechlorination Module</h3>
<h3>Inferred Hydrogen Cofactor Reductive-Dechlorination Module</h3>
</div>
<p class="prewrap interaction-description">Metagenomic analysis connected the four-genus synergistic alliance to a coupled metabolic module containing hydrogen production, cofactor synthesis, and reductive dechlorination functions during TCP transformation.</p>
<p class="prewrap interaction-description">HYPOTHESIZED functional coupling: community and metagenomic analyses associate the four named genera with hydrogen production, cofactor synthesis and reductive dechlorination. This is a consortium-level reconstruction, not measured intergenus hydrogen/cofactor transfer or a demonstrated genus-specific dechlorination pathway.</p>



Expand Down Expand Up @@ -709,7 +709,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41736479/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41736479</a>

- SUPPORT (IN_VITRO)
- PARTIAL (COMPUTATIONAL)
</div>

<div class="snippet">"realized through a coupled metabolic module of &#34;hydrogen production, cofactor synthesis, and reductive dechlorination&#34;"</div>
Expand All @@ -724,7 +724,7 @@ <h4>Evidence</h4>
<div class="interaction-header">
<h3>Co-Metabolic Substrate Enhanced TCP Removal</h3>
</div>
<p class="prewrap interaction-description">Sodium acetate and lactate stimulation increased the consortium&#39;s TCP degradation efficiency and supported complete removal in the domesticated culture.</p>
<p class="prewrap interaction-description">Sodium acetate and lactate amendments enhanced TCP degradation in the domesticated consortium. The abstract reports an overall average degradation rate of 19.06 umol L-1 d-1 and complete removal within 3.5 days; those values are not separately assigned to each amendment or to an individual genus.</p>



Expand Down Expand Up @@ -804,7 +804,7 @@ <h4>Evidence</h4>
<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>

<div class="discussion">
<h3>
Expand All @@ -814,9 +814,44 @@ <h3>
</h3>
<p class="prewrap">The accessible PubMed abstract names the four-genera consortium and overall hydrogen/cofactor/reductive-dechlorination module, but it does not expose species or strain IDs, original inoculum details, full medium composition, substrate concentrations, transfer cadence, or the role of each named genus within the module.</p>

<p class="muted small">Attaches to: <code>taxonomy</code>, <code>engineering_design</code>, <code>growth_media</code>, <code>ecological_interactions#Hydrogen Cofactor Reductive-Dechlorination Module</code></p>
<p class="muted small">Attaches to: <code>taxonomy</code>, <code>engineering_design</code>, <code>growth_media</code>, <code>ecological_interactions#Inferred Hydrogen Cofactor Reductive-Dechlorination Module</code></p>




</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which inferred functions actually mediate the observed amendment response?
</h3>
<p class="prewrap">Positive substrate-amendment effects remain distinct from metagenome-inferred coupling. The retrieved abstract does not resolve intergenus transfer, necessary cofactors or functional perturbations; the publisher full text was not retrieved. Keep the two existing nodes without inventing a module-to-removal arrow. Prior removal of syntrophy assertions and dangling phenotype arrows is preserved.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Inferred Hydrogen Cofactor Reductive-Dechlorination Module</code>, <code>ecological_interactions#Co-Metabolic Substrate Enhanced TCP Removal</code></p>



<details class="evidence-list">
<summary class="muted small">1 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">COMPUTATIONAL</span>
<span class="badge small">PARTIAL</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/41736479/" rel="nofollow noreferrer">PMID:41736479</a>


</div>
<p class="snippet small prewrap">realized through a coupled metabolic module of &#34;hydrogen production, cofactor synthesis, and reductive dechlorination&#34;</p>
<p class="muted small prewrap">The abstract attributes this coupled module to community and metagenomic analyses; it does not independently demonstrate transfer or assign each function to a named genus.</p>
</div>

</details>


</div>
Expand Down Expand Up @@ -1233,7 +1268,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Hydrogen Cofactor Reductive-Dechlorination Module",
label: "Inferred Hydrogen Cofactor Reductive-Dechlorination Module",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
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