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Qualify KZ and kombucha claims and record research gaps (batch60) - #1544
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Source-based self-adversarial review at exact head e1b40d0; not independent approval.
Repairs #1539 and #1540 addressed; #1541, #1542 and #1543 remain unresolved.
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Bound KZ catabolic roles to the reported assays and flag unresolved corrigendum verification.
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Qualify KMC pellicle cooperation and remove the unsupported recruitment-to-mutualism arrow.
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Expose the unresolved empty Komagataella-E. coli causal biosynthesis graph.
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Whole three records read; all four original nodes and both arrows assessed, plus the absent Komagataella interaction field. Missing structure is not certified absence of biology.
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KZ retains positive consortium outcomes and complementary biomass-normalized assays. Community-level scope with both exact canonical strain labels removes unverified SZ-3-to-CW-D3T transfer direction without erasing the division-of-labor interpretation. No new node or arrow.
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KZ full Methods and linked correction body remain unread. PubMed identifies PMID41456976; official publisher API returns core metadata only and openaccessArticle=false. Third-party OA labels do not establish access or scientific correction content. Keep needs_research under1541; do not assume the correction is immaterial.
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KMC source Introduction explicitly states pellicle-supported biochemical interplay. Retain that existing arrow as HYPOTHESIZED, grounded by a primary-matched excerpt, while distinguishing observed pellicle/morphotype association from selective mediation of reciprocal benefit.
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Remove the accessory-composition-to-mutualism arrow because potential fermentation capacity is not measured reciprocal benefit among the four core genera. Preserve positive composition changes and probable cabbage-derived lactobacillus persistence; do not convert relative read proportions into absolute growth or niche partitioning.
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KMC four canonical genera are a partial core representation, not every organism in every treatment. No canonical taxonomy edit. Non-graph assertions about separately cultivating members, categorical shaking effects and ingredients remain separately unresolved under1543.
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Komagataella public abstract and publisher Introduction/section previews report compatible co-growth, common induction and biosynthetic relays. Lack of engineered population-balancing crosstalk is not biological neutralism; common induction is not cross-feeding. Exact host/construct assignments and full Methods remain unresolved; do not borrow unmatched monoculture titres as experimental controls.
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Komagataella stays needs_research under1542, with zero nodes/arrows and its originally absent interaction field preserved. The reviewed one-community LITERATURE dry-run query contains7457 characters; zero provider submissions or credits. No report or completed extension is claimed.
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KMC full extracted primary main text and main/supplement captions were read. Original figure pixels, Table1 numerical cells, supplementary PDF and raw sequences were not inspected. KZ/Komagataella complete abstracts plus selected public publisher previews were read, not complete primary bodies. No access-control workaround.
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Full biological diffs, exact participant registry and focused test assertions reviewed.457 other record hashes and920 cache hashes unchanged; raw non-graph blocks preserved. Both-root census explicitly measures KZ scope change, with no auditor-rule edit.36 network warnings preserved and zero structural defects.
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Actual per-record schema/strict/term/reference/snippet/rank/history gates and regression outputs/digests recorded. Repeat renders and456-page exact description parser passed, not browser screenshots. Post-commit docs-current is a separate publication gate.
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839 all-state issue titles/bodies and19 scoped ignored/hidden local matches searched; all three matching issue bodies read, not every comment/PR or local file. Repair1539/1540 addressed but OPEN until protected-main merge; research1541/1542 and metadata1543 remain unresolved. Exact-head self-review is COMMENT, not independent approval.
552 passed in 188.20s (0:03:08); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 42 snippets match selected caches. The retained KMC arrow's short excerpt independently matches fresh publisher main text and the unchanged cache. All920 reference caches unchanged. MATCH does not certify all historical cache provenance or non-graph content;1543 remains unresolved. CLI Total checks counts reported issues, not executed checks; coverage476, Linux DOI lookup1091 and writer artifact1095 remain limitations.
All4 original nodes and2 arrows reviewed: retain4 bounded nodes and1 HYPOTHESIZED arrow; remove1 unsupported arrow. KZ remains needs_research under1541 because the linked correction body and complete mechanism remain unread. Komagataella's0-node/0-arrow graph remains needs_research under1542, not evidence of absent interactions. Zero structural errors; all36 baseline network warnings remain without additions.457 other records and raw non-graph blocks unchanged. Measured census:{"community_level_only": 267, "credited_solely_by_the_rule": 1238, "mixed": 124, "records": 460, "taxa": 1507, "with_community_level": 391}.
Repeat renders deterministic and descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 13f6171cf3d35231ddbb718f3b73357d8600ced9b4649d679d822fc5ff416596.
Every-node/every-arrow decisions,32 actual command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch60. Not independent approval. Corpus194 reviewed /245 pending /21 needs_research; corpus-wide work is not complete.
Protected-main merge remains pending.
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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Self-adversarial integration review at exact head 9d5e25d13089fe473cabe2b2ae6bb9793daef98f. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head e1b40d0123d5fe47d5ce14bab5fda21f4469997a, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 1937584099740edb20c88887c08057d2b6c28d26be8b3d8870d1a9791b3ebf8b). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.
Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.
An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.
Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.
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Self-adversarial review refreshed at exact head e66e638a9faef6dd3d653ad37d733c3f032d51c5
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 1068527a69460e54dcce92e5cfac2ef9bbfd7f69.
The batch-owned binary patch is byte-identical
(SHA-256 1937584099740edb20c88887c08057d2b6c28d26be8b3d8870d1a9791b3ebf8b); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.
The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.
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Self-adversarial governance integration review at exact head ebc423a2688294b07fc25cf934eb0df9075eb92c. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head e66e638a9faef6dd3d653ad37d733c3f032d51c5, exactly two files changed: scripts/.vendored_canon_ref and tests/test_id_label_empty_adapter.py. Each resulting tree differs from its old tree by the exact binary patch from main, and each batch-owned binary patch remains byte-identical (SHA-256 1937584099740edb20c88887c08057d2b6c28d26be8b3d8870d1a9791b3ebf8b). These invariants passed on all 74 published branches. Original heads are retained in local archive refs/archive/communitymech-pre-governance-20261007. No scientific record, source cache, history, decision ledger, schema, runtime code or generated page changed in this integration.
Adversarial inspection: the adapter regression still checks the empty sentinel and case-insensitive caching, now with an isolated fake oaklib module and a one-call selector assertion. No validation threshold or runtime behavior was relaxed. Fresh regressions at both stack ends: 337 passed in 214.19s (0:03:34); 917 passed in 402.58s (0:06:42). Docs-current and pinned vendored-sync passed at batches26/99. The 72 intermediate combinations were checked by tree/patch hashes, not independently retested. Historical source-review limitations and unresolved issues, including loader #1703 and cache #1091, remain applicable. This is not new paper review, independent approval, or a claim that those outstanding issues are fixed.
Digest-bound integration receipt/logs: /private/tmp/communitymech-governance-integration-20261007/receipt.json. Prior output/review records in reports/causal_graph_review/ remain unchanged. The prior lifecycle receipt is archived and will be updated only after all exact-head comments are verified.
Required CI and independent review must pass for the exact head and protected merge-queue candidate. No CI rerun, manual dispatch, fabricated status, admin merge or protection bypass. Dependents remain draft; move them before deleting a merged parent branch.
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Exact-head self-adversarial restack review at 3bb94cdf6c97a6e07fd824fdc230ecc6bf35232a.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 1937584099740edb20c88887c08057d2b6c28d26be8b3d8870d1a9791b3ebf8b.
Tree d518b20599dd14c4dab4ad6e500f955a896c2122 matches the independently computed clean merge.
Compared with historical tree b1ddc52e711d22d3067c131e200c77631a95ae35, 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 #1539.
Closes #1540.
Related #1541 remains OPEN: KZ correction and complete mechanistic verification.
Related #1542 remains OPEN: Komagataella graph extension needs authorized research and exact primary-system verification.
Related #1543 remains OPEN: KMC cultivation and ingredient metadata.
Adversarial Review
Verification And Output Records
552 passed in 188.20s (0:03:08); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 42 snippets match selected caches. The retained KMC arrow's short excerpt independently matches fresh publisher main text and the unchanged cache. All920 reference caches unchanged. MATCH does not certify all historical cache provenance or non-graph content;1543 remains unresolved. CLI Total checks counts reported issues, not executed checks; coverage476, Linux DOI lookup1091 and writer artifact1095 remain limitations.
All4 original nodes and2 arrows reviewed: retain4 bounded nodes and1 HYPOTHESIZED arrow; remove1 unsupported arrow. KZ remains needs_research under1541 because the linked correction body and complete mechanism remain unread. Komagataella's0-node/0-arrow graph remains needs_research under1542, not evidence of absent interactions. Zero structural errors; all36 baseline network warnings remain without additions.457 other records and raw non-graph blocks unchanged. Measured census:{"community_level_only": 267, "credited_solely_by_the_rule": 1238, "mixed": 124, "records": 460, "taxa": 1507, "with_community_level": 391}.
Repeat renders deterministic and descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 13f6171cf3d35231ddbb718f3b73357d8600ced9b4649d679d822fc5ff416596.
Every-node/every-arrow decisions,32 actual command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch60. Not independent approval. Corpus194 reviewed /245 pending /21 needs_research; corpus-wide work is not complete.
Dependency
Draft depends on #1538. Do not merge into the topic parent. Require eligible exact-head CI and protected main queue after parent merges. Move dependent PRs before deleting parent branches. Komagataella's single-community Edison dry-run metadata is included; zero paid submissions or credits. No new graph structure.