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Bound enrichment and Core-20 causal mechanisms (batch51) - #1500
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Source-based self-adversarial review at exact head c931ad0; not independent approval.
Issues #1497, #1498 and #1499 addressed.
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Bound MAG-resolved syntrophy while retaining positive 0B conversion.
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Separate CAZyme protein profiles and inferred methanogenic routes from demonstrated mediation.
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Separate positive Core-20 transcripts and pathogen reduction from proposed immune mediation.
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Whole661-line ammonia,475-line switchgrass and192-line Core-20 records and all nine nodes/six arrows reviewed. Complete cached primary main bodies, Methods and embedded figure captions read, plus ammonia Table1. No original figure images, supplements, raw data or code audited.
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0B positive single-culture butyrate-to-methane conversion remains SUPPORT/IN_VITRO, separate from PARTIAL MAG-resolved syntrophy. Canonical source/target directions and three SYNTROPHY hypotheses retained. Do not transfer YB replication, carbon balance or yeast-extract results to 0B.
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MAG2 incomplete Wood-Ljungdahl annotation is not filled using its relative. MAG-specific flux, carrier partition and partner necessity remain unresolved. Relative Methanothermobacter succession is not rate improvement; proposed MAG5 acetate assimilation is not acetoclastic methane formation. Existing gap/evidence extended, not duplicated or erased.
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Switchgrass maintains positive bulk solubilization and methane outcomes; one sequential reactor and changed vitamins, medium, mixing and adaptation do not isolate a solids-only mechanism. Protein abundance is not catalytic activity, and hydrogenotrophic protein dominance is not a measured methane-flux share.
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Fraction-associated CAZyme profiles remain positive observations supporting the authors' suggested niches, not demonstrated competitive partitioning or a Chloroflexota-to-Thermotogota pair. Explicit participants are the canonical five-member subset for the community phenotype, two profile groups and the archaeal capacity group. All three nodes remain community-scoped.
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Core-20 preserves positive qPCR immune transcripts and the reported78-fold pathogen-load reduction. Transcript abundance is not AMP protein activity, qPCR load is not viable-cell count, and composition differences do not isolate richness. Rename the terminal outcome and qualify proposed immune mediation without falsely claiming that the original incoming edge lacked interpretation wording.
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Core-20 W8131 non-detection was already bounded and remains so. Four passages with changed diversity and relative abundance do not prove unchanged composition or protective efficacy in every passage. Existing broad Bacteria participant remains a placeholder, not a complete strain/host/pathogen roster or newly minted CURIE.
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Structural completeness considered explicitly: proposed direct MAG1 carrier routes, alternative MAG9 functions, AA6/Fenton accessibility and PTS/nutrient competition remain acknowledged gaps. This batch repairs existing claims, not exhaustive mechanism expansion. No new node, arrow or paid Edison job; no speculative route represented as experimentally established.
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Inspected complete record diffs and focused tests. Nine nodes retained and all six existing arrows explicitly PARTIAL. Three guarded writes and append-only history artifacts; all457 other records and920 caches unchanged. Non-graph raw blocks and canonical taxonomy preserved, not certified. One participant registry entry added; measured connectivity census unchanged.
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Actual schema, strict, terms, references, snippets, rank and history gates passed. Network equals baseline with34 prior findings and zero structural errors. Deterministic renders and exact node/arrow descriptions across456 pages parser-checked, not browser screenshots. Actual post-commit docs-current is a separate publication gate.
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Dedup checked806 all-state issue titles/bodies and25 ignored/hidden local files, not every comment or PR review. Closed401/366 concern taxonomy tooling, not these graph repairs. Issues1497/1498/1499 stay open until protected main merge. Self-adversarial review is not independent approval.
489 passed in 185.39s (0:03:05); five new focused tests. Schema, strict, term, reference, snippet and history gates pass. 67 snippets match unchanged caches. Text matching is not independent provenance or scientific support. CLI Total checks counts reported issues, not executed checks. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations.
All nine nodes and six arrows retained, with every arrow explicitly PARTIAL. Both-root baseline retained; zero structural errors and all34 prior network findings unchanged. All457 other records and920 caches preserved, not certified. Measured connectivity census unchanged. One participant registry entry added; no census-bound or production matching change.
Repeat renders deterministic; exact descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 bee3e65e3b81f3cee6f465fa5187a771149540e966cc93dcef8f082b1324ee5c.
Source decisions, actual validation outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch51. Not independent approval. Corpus179 reviewed /267 pending /14 needs_research, 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 review refreshed at exact head 51a58f926d4a7bcf07dfd19c036e498ef6d290d6
after protected main merge of #1339. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 2d03e85012428338d9f8734e7cea9463c99af02b.
The batch-owned binary patch is byte-identical
(SHA-256 adbccc9a2a624089f8c4e1d9c7db4a8bdb92dc130ed0812671342234743a4e2a); 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 review refreshed at exact head b7842e470532b8ca9ff5a4898536de91161de1e3
after protected main merge of #1346. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 2d03e85012428338d9f8734e7cea9463c99af02b.
The batch-owned binary patch is byte-identical
(SHA-256 adbccc9a2a624089f8c4e1d9c7db4a8bdb92dc130ed0812671342234743a4e2a); 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 review refreshed at exact head 2e28cb77f0d6b0600eef7ac2a81f64d0c9655301
after protected main merge of #1350. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 2d03e85012428338d9f8734e7cea9463c99af02b.
The batch-owned binary patch is byte-identical
(SHA-256 adbccc9a2a624089f8c4e1d9c7db4a8bdb92dc130ed0812671342234743a4e2a); 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 review refreshed at exact head 4b8dba1adfcc491e54f75c09a734d4050d3dae19
after protected main merge of #1355. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 2d03e85012428338d9f8734e7cea9463c99af02b.
The batch-owned binary patch is byte-identical
(SHA-256 adbccc9a2a624089f8c4e1d9c7db4a8bdb92dc130ed0812671342234743a4e2a); 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 integration review at exact head b1d2d7f54fb78a3db22c6b46863d26b9d222bf4b. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 4b8dba1adfcc491e54f75c09a734d4050d3dae19, 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 adbccc9a2a624089f8c4e1d9c7db4a8bdb92dc130ed0812671342234743a4e2a). 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 3ac5c40f60a64eb5eef64d751c01ee232cb79e71
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree c80cfa0203cb16d6f1e8d64c21e9e4856fe971eb.
The batch-owned binary patch is byte-identical
(SHA-256 adbccc9a2a624089f8c4e1d9c7db4a8bdb92dc130ed0812671342234743a4e2a); 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 fbdab3d1e1ba9f9a4ef51a3c5ca4fe0e1dd5ca3b. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 3ac5c40f60a64eb5eef64d751c01ee232cb79e71, 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 adbccc9a2a624089f8c4e1d9c7db4a8bdb92dc130ed0812671342234743a4e2a). 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 a48245e4af4f8ef17f8313c869105a3d20a08159.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 adbccc9a2a624089f8c4e1d9c7db4a8bdb92dc130ed0812671342234743a4e2a.
Tree aee09a390ec045521aaa8bc040aa9f4111c35fe5 matches the independently computed clean merge.
Compared with historical tree 040f6011b3372a7e8242314025fdf87243babf0a, 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. |
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Scope
Closes #1497. Closes #1498. Closes #1499.
Adversarial Review
Verification And Output Records
489 passed in 185.39s (0:03:05); five new focused tests. Schema, strict, term, reference, snippet and history gates pass. 67 snippets match unchanged caches. Text matching is not independent provenance or scientific support. CLI Total checks counts reported issues, not executed checks. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations.
All nine nodes and six arrows retained, with every arrow explicitly PARTIAL. Both-root baseline retained; zero structural errors and all34 prior network findings unchanged. All457 other records and920 caches preserved, not certified. Measured connectivity census unchanged. One participant registry entry added; no census-bound or production matching change.
Repeat renders deterministic; exact descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 bee3e65e3b81f3cee6f465fa5187a771149540e966cc93dcef8f082b1324ee5c.
Source decisions, actual validation outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch51. Not independent approval. Corpus179 reviewed /267 pending /14 needs_research, not complete.
Dependency
Draft depends on #1496. Do not merge into the topic parent. Require eligible exact-head CI and the protected main queue after parent merges. Move dependents before deleting merged branches. No Edison job or provider spend for this existing-structure repair.