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Preserve plant outcomes and mixture assay contrasts (batch121) - #1946
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Source-based self-adversarial review at exact head ec8ee08; not independent approval.
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Retain complementary biofilm and defense phenotypes without asserting reciprocal microbial benefit.; Keep treatment-induced host oxylipin activation distinct from bacterial production or transfer.; Preserve biosynthesis-inhibition and overexpression evidence at pathway rather than individual-compound scope.
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Keep measured whole-C1 fungal inhibition without a bilateral-competition interpretation.; Retain positive greenhouse protection and root weight without claiming superiority or identified mediation.
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Retain whole-C6 plate inhibition without bilateral competition or automatic greenhouse benefit.; Bound auxin production to the calibrated colorimetric assay without assigning reciprocal benefit or plant delivery.; Preserve measured Arabidopsis root shortening without turning a correlation into a hormone-mediated growth benefit.; Keep positive member supernatants and the negative whole-C6 supernatant outcome together.; Keep positive member volatile assays distinct from the non-significant whole-C6 mixture result.
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Preserve the positive SMC disease and grain outcomes without an unsupported bilateral-competition mechanism.; Keep relative community-profile observations distinct from colonization facilitation and inferred ecological functions.
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All 14 original nodes and two arrows accounted for: 12 nodes and both directions retained, two inoculum-preparation nodes removed, six renames, no new topology. Targets and discussion anchors resolve. Prior C1/C6 workflow-arrow deletions are not undone.
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Tomato complementary biofilm/host-defense functions are not reciprocal microbial fitness. Keep positive protection comparable to the 38-member precursor and intensified host oxylipin responses. Biofilm mediation remains PARTIAL. Biosynthesis inhibition abolishes protection and SlLOX5/SlDES1 overexpression increases resistance; do not erase these stronger causal experiments or promote separate necessity of each divinyl ether.
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C1 retains 37.00% plate inhibition and positive greenhouse root-rot/root-weight effects. Equal-ratio assembly is preparation, not colonization facilitation. No demonstrated superiority over the best single strain; persistence was explicitly unassessed. Whole-mixture cell-free and volatile results are not inferred from individual members.
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C6 retains 34.48% direct plate inhibition and 11.76 ug/mL IAA-calibrated Salkowski output. Colorimetry is not resolved compound identity or plant delivery. Arabidopsis primary-root shortening is not growth promotion or significant wheat protection. The source negative-r-squared notation is not copied as a valid statistic.
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C6 individual members have positive cell-free and volatile results, but assembled-mixture supernatants are null and C6 is absent from the significant volatile-mixture list. Both positive members and null mixture observations stay together. No universal inefficacy claim and no new assay-to-assay causal arrows.
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Crown-rot SMC retains positive disease reduction from 86.45% to 25.93% and challenged TKW +10.39%. Relative DNA profiles and correlation networks are not viability, colonization, nutrient flux, reciprocal cooperation or ecological necessity. Added allantoin/dihydrodaidzein positive host assays and negative direct fungal assays remain explicit, not erased or promoted to intact-SMC necessity.
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Twenty-four graph and 10 discussion quotes match fresh primary and caches. Three unique studies: complete wheat C1/C6 and crown-rot main bodies, methods, results, discussion, tables and captions read; tomato abstract-bounded. No original figure pixels, external supplements, raw data or code audit. Crown-rot license CC BY-NC-ND 4.0, not unrestricted CC BY. Three short excerpts, 21 words, appended with verified Zhou attribution; old cache prefix preserved. Cache/source wording and treatment-assignment discrepancies remain #1945.
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Four guarded writes and append-only histories preserve 456 other records, 922 unchanged caches, unrelated raw YAML blocks and previous histories/decisions. Canonical taxa, participant lists and scopes unchanged. Shared evidence aliases detached. Non-graph member/role, metal/abundance and provenance/timing findings remain #1943-#1945.
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Fifteen focused tests and 12 control/mutation/restored-control probes pass. Mutations reject tomato mutualism, unique-biofilm promotion, erased biosynthesis/overexpression positives, restored C1 assembly, best-single superiority, C6 auxin mutualism, root-growth promotion, erased supernatant/volatile nulls, erased crown-rot grain benefit and profile-to-colonization promotion. No canonical writes in probes.
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All four records pass schema, strict, terms, full-record references, snippets, rank and history. 1146 selected tests including palette pass; not full Linux CI certification. Network: 57 unchanged warnings, zero structural defects. Exact descriptions on 456 pages, 1359 nodes and 522 arrows and deterministic rendering verified, not screenshot QA.
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Participant lists and scopes unchanged: 299 list users, 414 community-level, 136 mixed, 278 community-only, 1568 taxa, 1281 solely credited. Scope credit is not certification of actual participant coverage. Connectivity logic and thresholds unchanged.
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Issues #1939-#1942 addressed pending protected-main merge; #1943-#1945 remain open. No Edison extension or credits. Prior Ruegeria #1883 configured-authentication blocker not retried unchanged. Source-based self-review is not independent approval; root #1836 and actual exact-head protected checks still required.
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Corpus: 392 reviewed, 14 pending, 54 needs_research across 460 records. Overall goal, protected merge and branch deletion remain incomplete. Postcommit docs-current and exact-head publication are separate gates, not preasserted here.
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The initial 1146-test run passed, then lint identified two SIM300 assertion-operand-order violations. Only operand order was corrected. Original gate/probe outputs are preserved; focused tests, all1146selected tests, all12mutation probes and lint were rerun successfully against the corrected file. No assertion or canonical-data weakening.
1146 passed in 406.93s (0:06:46); fifteen focused tests and twelve real in-memory mutation probes. All four edited records pass schema, strict, terms, full-record references, snippets, rank and history. 41 gate outputs retain commands, output tails and digests. All 456 other records, 922 caches and unrelated raw fields remain unchanged; one cache has a prefix-preserving short-excerpt append.
All 14 original nodes/two arrows reviewed. Twelve nodes and both directions remain; two inoculum-preparation nodes removed; six renames; no new topology. Tomato retains pathway-level biosynthesis-inhibition and overexpression positives without reciprocal bacterial mutualism or individual-compound necessity. C1 retains plate and greenhouse benefits without superiority over the best single strain. C6 retains direct plate inhibition, Salkowski output and Arabidopsis root shortening, while preserving positive individual members versus negative mixture cell-free/volatile results. Crown-rot treatment benefits remain distinct from relative DNA profiles and inferred mechanisms.
Three unique primary studies checked. Complete wheat C1/C6 and crown-rot main bodies, methods, results, discussion, tables and captions read; tomato repairs are abstract-bounded. No original figure pixels, external supplements, raw data or analysis-code audit. All 34 graph/discussion quotes match fresh sources and caches; this is not entailment certification. Three short crown-rot excerpts, 21 words, appended with verified attribution and CC BY-NC-ND4.0 license. No full-body import; old cache wording preserved for source/provenance follow-up #1945.
Corpus: 392 reviewed, 14 pending, 54 needs_research; 57 unchanged network warnings, zero structural defects. Participant lists and scopes unchanged: 299 list users, 414 community-level, 136 mixed, 278 community-only, 1568 taxa, 1281 solely credited. No connectivity logic or threshold edits. Descriptions on 456 pages, 1359 nodes and 522 arrows exactly match the source, with deterministic rendering, not screenshot certification. Postcommit docs-current passed clean; log SHA256 fdbfdb63f0b73d5ab5578bbc0f3c3908a2149fa4bf846f55e0c456cfad87e52a. Selected local passes are not full Linux CI certification; corpus snippet audit remains informational.
Decision ledger, provenance, validation, four append-only histories and self-adversarial review are committed. Non-graph member/role, metal/abundance and source-provenance/timing #1943-#1945 remain open. No Edison invocation or new topology; prior Ruegeria #1883 still needs configured authentication. This COMMENT is self-review, not independent approval. Root blocker #1836 requires actual protected checks. No artificial CI, protection bypass, merge or premature branch deletion.
Network integrity findingsWarnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build. The full report is attached to the workflow run as an artifact. |
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Exact-head self-adversarial restack review at d018b9aa996dbae8f321b171487045668e2847fc.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 5c728c88d9f4a55d7bede5106e9e77fc1d412edb53aea7d717c6b5b924aba707.
Tree da03b5bf98437260a578eac03d4bbd1ce11b94d3 matches the independently computed clean merge.
Compared with historical tree a0eac0886a3e4e3df6f557ccbe02037155931356, only scripts/.vendored_canon_ref
changes, incorporating main PR #1834's pin 849f336e025510316a5f235eb0af8547b8bd50cc.
All curated records, source caches, review outputs, histories, regression tests, and rendered
pages remain unchanged. No new primary-source review or local scientific-test rerun is claimed.
This PR is now part of native stack #1973, rooted at #1363 on main. No protected merge
has occurred. Fresh eligible PR/merge-group CI remains mandatory. No rule bypass, fabricated
status, merge into a topic parent, or premature branch deletion.
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Superseded by the protected cumulative merge #1975 at Patch-inclusion receipt. Existing issue-closing links were transferred to #1975; unresolved research and non-graph gaps are not closed by this action. This PR is being closed as superseded, not represented as individually merged. Archival provenance tags retain source commits; cleanup removes branch refs only and preserves worktree files. |
1 participant
Scope
Closes #1939.
Closes #1940.
Closes #1941.
Closes #1942.
Non-graph member/role, metal/abundance and provenance #1943-#1945 remain open; this batch does not resolve prior research extensions.
The genuine palette correction #1913 is inherited from the verified parent; required current-head CI remains a separate gate.
Adversarial Review
Verification And Output Records
1146 passed in 406.93s (0:06:46); fifteen focused tests and twelve real in-memory mutation probes. All four edited records pass schema, strict, terms, full-record references, snippets, rank and history. 41 gate outputs retain commands, output tails and digests. All 456 other records, 922 caches and unrelated raw fields remain unchanged; one cache has a prefix-preserving short-excerpt append.
All 14 original nodes/two arrows reviewed. Twelve nodes and both directions remain; two inoculum-preparation nodes removed; six renames; no new topology. Tomato retains pathway-level biosynthesis-inhibition and overexpression positives without reciprocal bacterial mutualism or individual-compound necessity. C1 retains plate and greenhouse benefits without superiority over the best single strain. C6 retains direct plate inhibition, Salkowski output and Arabidopsis root shortening, while preserving positive individual members versus negative mixture cell-free/volatile results. Crown-rot treatment benefits remain distinct from relative DNA profiles and inferred mechanisms.
Three unique primary studies checked. Complete wheat C1/C6 and crown-rot main bodies, methods, results, discussion, tables and captions read; tomato repairs are abstract-bounded. No original figure pixels, external supplements, raw data or analysis-code audit. All 34 graph/discussion quotes match fresh sources and caches; this is not entailment certification. Three short crown-rot excerpts, 21 words, appended with verified attribution and CC BY-NC-ND4.0 license. No full-body import; old cache wording preserved for source/provenance follow-up #1945.
Corpus: 392 reviewed, 14 pending, 54 needs_research; 57 unchanged network warnings, zero structural defects. Participant lists and scopes unchanged: 299 list users, 414 community-level, 136 mixed, 278 community-only, 1568 taxa, 1281 solely credited. No connectivity logic or threshold edits. Descriptions on 456 pages, 1359 nodes and 522 arrows exactly match the source, with deterministic rendering, not screenshot certification. Postcommit docs-current passed clean; log SHA256 fdbfdb63f0b73d5ab5578bbc0f3c3908a2149fa4bf846f55e0c456cfad87e52a. Selected local passes are not full Linux CI certification; corpus snippet audit remains informational.
Decision ledger, provenance, validation, four append-only histories and self-adversarial review are committed. Non-graph member/role, metal/abundance and source-provenance/timing #1943-#1945 remain open. No Edison invocation or new topology; prior Ruegeria #1883 still needs configured authentication. This COMMENT is self-review, not independent approval. Root blocker #1836 requires actual protected checks. No artificial CI, protection bypass, merge or premature branch deletion.
Dependency
Draft depends on #1938. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.