Bound REE maize and Jiangshui causal graphs (batch55)

docs/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.html

@@ -599,59 +599,22 @@ <h2>Ecological Interactions</h2>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Jiangshui LAB screening and ratio assembly</h3>
+                    <h3>Three-Strain 2:3:1 Jiangshui Fermentation</h3>
                 </div>
-                <p class="prewrap interaction-description">LAB isolates from traditional Jiangshui were screened down to Y-5-3, Y-6-2, and HN, then manually combined in 20 ratios to tune a defined Jiangshui SynCom.</p>
+                <p class="prewrap interaction-description">The tested Y-5-3:Y-6-2:HN 2:3:1 formulation had the highest reported sensory score, 89.38 +/- 4.10, among the assayed three-strain fermentation schemes. This is a positive combined-inoculant fermentation result, not an isolated molecular mechanism or proof that the ratio alone explains its difference from natural fermentation. All three canonical strain names remain distinct despite their unresolved species-level identifiers.</p>
 
 
 
 
+                <p><strong>Participating Taxa:</strong>
 
+                    LAB strain Y-5-3,
 
+                    LAB strain Y-6-2,
 
+                    LAB strain HN
 
-
-
-                <div class="interaction-flow">
-                    <strong>Downstream Effects:</strong>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Optimized 2:3:1 Jiangshui fermentation
-                        <p class="prewrap causal-description">The three selected LAB strains were assembled at empirically varied ratios before the optimized Y-5-3:Y-6-2:HN ratio was selected.</p>
-                    </div>
-
-                </div>
-
-
-
-                <h4>Evidence</h4>
-                <ul class="evidence-list">
-
-                    <li class="evidence-item">
-                        <div>
-
-                            <a href="https://pubmed.ncbi.nlm.nih.gov/42425667/"
-                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42425667</a>
-
-                            - SUPPORT (IN_VITRO)
-                        </div>
-
-                        <div class="snippet">"On this basis, 3 high-performance strains (Y-5-3, Y-6-2, HN) were selected and manually combined in 20 ratios to construct SynComs"</div>
-
-                    </li>
-
-                </ul>
-
-            </div>
-
-            <div class="interaction-card">
-                <div class="interaction-header">
-                    <h3>Optimized 2:3:1 Jiangshui fermentation</h3>
-                </div>
-                <p class="prewrap interaction-description">A Y-5-3:Y-6-2:HN ratio of 2:3:1 was the optimal mixed-strain fermentation scheme among the assayed three-strain LAB SynCom ratios.</p>
-
-
-
+                </p>
 
 
 
@@ -675,7 +638,7 @@ <h3>Optimized 2:3:1 Jiangshui fermentation</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> Jiangshui phenol and flavonoid increase
-                        <p class="prewrap causal-description">The optimized 2:3:1 strain ratio increased measured total phenols and flavonoids compared with natural Jiangshui.</p>
+                        <p class="prewrap causal-description">The tested three-strain 2:3:1 fermentation treatment increased measured total phenol and flavonoid contents relative to natural Jiangshui. This positive formulation-level intervention does not isolate the ratio, a particular strain, release versus synthesis, or a molecular mediator as the cause.</p>
                     </div>
 
                 </div>
@@ -719,11 +682,21 @@ <h4>Evidence</h4>
                 <div class="interaction-header">
                     <h3>Jiangshui phenol and flavonoid increase</h3>
                 </div>
-                <p class="prewrap interaction-description">The optimized three-strain LAB scheme increased total phenols and flavonoids relative to natural Jiangshui while reducing off-odors and improving stability.</p>
+                <p class="prewrap interaction-description">The tested three-strain formulation increased total phenols by 72.20 percent and total flavonoids by 61.13 percent relative to natural Jiangshui, with reported P &lt; 0.01. The abstract also reports reduced off-odors and improved stability without the operational detail available in a full protocol. These are total-content endpoints, not identified compound flux, de-novo flavonoid synthesis or demonstrated benefits exchanged between individual strains.</p>
 
 
 
 
+                <p><strong>Participating Taxa:</strong>
+
+                    LAB strain Y-5-3,
+
+                    LAB strain Y-6-2,
+
+                    LAB strain HN
+
+                </p>
+
 
 
                 <p><strong>Metabolites:</strong>
@@ -777,7 +750,7 @@ <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>
@@ -792,6 +765,21 @@ <h3>
 
 
 
+            </div>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which processes underlie the positive formulation-level fermentation endpoints?
+                </h3>
+                <p class="prewrap">Remove screening/ratio assembly and its arrow as researcher workflow; retain the biological fermentation treatment and positive content response. No isolated ratio effect or de-novo biosynthesis is demonstrated by the accessible abstract. Complete cached abstract and indexed publisher fragments read; direct publisher requests returned403 and no primary full body was inspected. Fragments do not map selected strain codes to species or give the fermentation protocol; preserve the existing taxonomy/growth-conditions knowledge gap and prior histories. In-vitro biosafety screens do not establish clinical safety. No original images, supplements, raw data or code audited and no new graph structure added.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Three-Strain 2:3:1 Jiangshui Fermentation</code>, <code>ecological_interactions#Jiangshui phenol and flavonoid increase</code></p>
+
+
+
+
             </div>
 
         </section>
@@ -1054,11 +1042,15 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             var processes = [];
 
-            var evidenceCount = 1;
+
+            processes.push("fermentation");
+
+
+            var evidenceCount = 2;
 
             nodes.push({
                 id: intId,
-                label: "Jiangshui LAB screening and ratio assembly",
+                label: "Three-Strain 2:3:1 Jiangshui Fermentation",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1069,38 +1061,25 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
-        })();
-
-        (function() {
-            var intId = "interaction:1";
-            var intType = "UNKNOWN";
-            var metabolites = [];
-
-            var processes = [];
-
+            var participantKeys = [
 
-            processes.push("fermentation");
+                "LAB strain Y-5-3",
 
+                "LAB strain Y-6-2",
 
-            var evidenceCount = 2;
+                "LAB strain HN"
 
-            nodes.push({
-                id: intId,
-                label: "Optimized 2:3:1 Jiangshui fermentation",
-                type: "interaction",
-                interactionType: intType,
-                metabolites: metabolites,
-                processes: processes,
-                evidenceCount: evidenceCount
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
             });
 
-
-
-
         })();
 
         (function() {
-            var intId = "interaction:2";
+            var intId = "interaction:1";
             var intType = "UNKNOWN";
             var metabolites = [];
 
@@ -1129,6 +1108,21 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "LAB strain Y-5-3",
+
+                "LAB strain Y-6-2",
+
+                "LAB strain HN"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
 
@@ -1150,7 +1144,7 @@ <h4 style="color: var(--text);">Evidence</h4>
         var svg = d3.select("#network-svg");
         var width = container.clientWidth - 32;
         // Dynamic height based on node count: minimum 500px, add 40px per node
-        var nodeCount = 6;
+        var nodeCount = 5;
         var height = Math.max(500, 400 + nodeCount * 20);
         svg.attr("width", width).attr("height", height);
 

history/records/Ion_Adsorption_REE_Indigenous_Community/2026-10-06T174553Z-codex-f8ce0e.yaml

@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml
+  slug: Ion_Adsorption_REE_Indigenous_Community
+session:
+  id: 2026-10-06T174553Z-codex-f8ce0e
+  timestamp: '2026-10-06T17:45:53Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1517
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Separate positive REE laboratory adsorption from proposed weathering and deposit-scale
+    mediation.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml

history/records/Jala_Maize_PGPB_SynCom/2026-10-06T174554Z-codex-56c270.yaml

@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Jala_Maize_PGPB_SynCom.yaml
+  slug: Jala_Maize_PGPB_SynCom
+session:
+  id: 2026-10-06T174554Z-codex-56c270
+  timestamp: '2026-10-06T17:45:54Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1518
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain maize SynCom assay and plant outcomes without workflow causality or proven
+    trait mediation.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml

history/records/Jiangshui_LAB_Directed_Fermentation_SynCom/2026-10-06T174554Z-codex-394a99.yaml

@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml
+  slug: Jiangshui_LAB_Directed_Fermentation_SynCom
+session:
+  id: 2026-10-06T174554Z-codex-394a99
+  timestamp: '2026-10-06T17:45:54Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1519
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain the Jiangshui formulation effect and remove experimental screening from
+    the biological graph.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml