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Bound core enrichment, conditional rescue and substrate mediation (batch74) - #1625
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Source-based self-adversarial review at exact head 3e84468; not independent approval.
Repairs #1620-#1623 addressed; non-graph #1624 unresolved.
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Retain putative plasmid enrichment; symbiotic mechanism is PARTIAL, not measured mutualism.; Retain genomic functional potential without asserting measured cross-feeding.; Correct operational-core and host/source boundaries; remove two analytical-workflow arrows.
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Retain toxic potential and production-to-mitigation link, not exclusive inhibition.; Retain measured formaldehyde lowering; recipient rescue remains incomplete.; Correct methionine direction and preserve two condition-specific positive growth assays, not autonomous mutualism.; Bound resource competition using PCA, supplement and spent-medium controls; remove engineering-workflow arrow.
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Retain reported colonization facilitation with PARTIAL mediation arrow.; Preserve treatment gains; remove unsupported reciprocal-fitness classification and shared-outcome arrow.; Retain metabolite accumulation, not traced cross-feeding or demonstrated growth mediation.
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Retain causal substrate response; qualify composition-to-degradation mediation.; Preserve O-glycan versus N-glycan and residual-added-glycan distinctions without claiming resolved cross-feeding.; Retain measured metabolite profiles and prior analyte fix; pool changes are not transfer flux.
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Read all four whole records and every original node/arrow after the both-root baseline. Read three complete primary main bodies, captions and embedded tables; no separate supplement, raw-data or figure-pixel audit. Moss scope is primary abstract only after full access403, not evidence of absent controls.
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Preserve108 retained cyanobacterial consortia and25 operational core species. Species occurrence18.5%-68.5% contradicts universal membership. Both host and source effects are significant; authors explicitly lack cyanobacteria-free controls. Repair the name, description and stale evidence explanation, not only the headline.
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Genomic and plasmid enrichment are positive observations. Putative plasmid cobinning,98% noncircularized contigs and bioinformatic removal do not prove biological plasmid dependence, metabolite exchange or reciprocal fitness. Remove analytical-workflow edges without deleting observed nodes.
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Retain formaldehyde generation0.6-0.8mM, C.fimi inhibition threshold0.5mM, and experimentally reduced accumulation with M.extorquens. The formaldehyde-free PCA control still inhibits C.fimi; do not claim detoxification completely restores growth or dominates inhibition.
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Preserve two positive exchange results under their actual conditions. Selected CM4744 supports C.fimi without supplied methionine only with added methanol/succinate; wild type does not. Separately C.fimi supports methylotroph growth. Correct methionine donor direction; no claim of autonomous mutual codependence.
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Iron/supplement rescue and spent-medium inhibition support multiple mechanisms, not an exclusive depleted resource. Remove competition-to-engineered-exchange arrow because investigator selection is not biological induction of overproduction. No new reverse edge or separate node added.
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Moss primary abstract supports reported colonization facilitation, growth/soil gains and altered metabolite pools. Preserve positive results while bounding endpoint comparators and colonization mediation. Shared-treatment outcomes do not establish growth causing metabolite accumulation; joint application is not measured reciprocal fitness.
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Mucin substrate changes directly affect composition, degradation and fermentation profiles. Retain composition-to-degradation as PARTIAL mechanism, not a composition-only intervention. Preserve BSM O-glycan limitation versus N-glycan degradation, residual added glycans and yeast-extract contribution. Do not infer A.muciniphila sialic-acid utilization from enrichment.
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Preserve existing MDSC pairwise-flux discussion and closed957/958/959 repairs. No taxonomy, strain identifier or non-graph change. Metadata1624 separately tracks remaining whole-record scope; no synthetic member-specific arrows invented.
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Adversarial diff review found a remaining host-independent evidence explanation. Corrected before commit, added explicit regression coverage and retained17 superseded outputs, then reran all affected and corpus gates. No stale pre-fix pass is presented as final verification.
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All13 nodes and7 original arrows have decisions;3 remain,4 noncausal links removed. All456 other records,920 caches and raw non-graph blocks verified unchanged. Four append-only record/history events. Structural defects zero;44 baseline warnings unchanged, connectivity census unchanged.
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Actual schema, strict, terms, references, snippets, history, both-root inventory/network/rank, repeat renders, regression and lint results retained with digests. Exact descriptions parsed across456 pages, not browser screenshots. Postcommit docs-current remains a separate publication gate.
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Dedup scanned906 all-state issue titles/bodies and31 ignored/hidden local matches with explicit git/docs/site/cache exclusions; prior957/958/959 fixes inspected. No exhaustive PR-comment audit or global source-absence claim. Repair1620-1623 stays OPEN until protected-main merge;1624 stays OPEN afterward.
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No new causal topology and no paid provider submission. Existing denied/pending scoped authorizations unchanged. Self-adversarial COMMENT is not independent approval and does not certify corpus completion.
662 passed in 202.52s (0:03:22); seven new focused tests. Schema, strict, terms, full-record references, snippets and history checks passed for all four records. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All21 graph quotations match selected caches;17 automatically match fresh primary XML and4 moss quotations were visually checked against the publisher-indexed primary abstract. Cache matching is not entailment. Full moss access403; all920 caches unchanged, not recertified. Prior batch73 gallium non-graph reference exception remains outside this batch.
All13 original nodes retained;7 original arrows become3 after4 workflow/shared-outcome links are removed. No new topology or paid run. Core enrichment, formaldehyde lowering, conditional methionine rescue, moss treatment gains and mucin-substrate responses remain. Non-graph #1624 stays OPEN.
All456 other records,920 caches and raw non-graph blocks verified unchanged. Canonical taxa and auditor rules unchanged. Zero structural defects;44 baseline warnings preserved exactly; connectivity census unchanged. Repeat renders deterministic, exact descriptions parsed across456 pages, not browser screenshots.
Postcommit just check-docs-current passed with clean tree; log SHA256 e7c4b8c6aa5326cf49335afc6eb3e6ecacc078b60b7058c075bad422d3669878. Every-node/every-arrow decisions,40 actual final check outputs/digests plus17 superseded pre-correction outputs, and self-adversarial review committed under reports/causal_graph_review, batch74. Final focused rerun:16 passed. Corpus:239 reviewed,196 pending,25 needs_research. Not independent approval or corpus completion.
Protected-main merge 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 fb7f047629a6ab4cf125c831fe5da77605b0aadc. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 3e844683b766944da3bd8fbec2308ecb7a0982c4, 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 0bd559834348aad4641ed3bdca92916a751821b3a25c1afe895cf0506be72457). 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 27326ff602c0928300ad98a29fdc9b317b28d05e
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 2316064b25548c37fde4eb838fa07ab7148f02f9.
The batch-owned binary patch is byte-identical
(SHA-256 0bd559834348aad4641ed3bdca92916a751821b3a25c1afe895cf0506be72457); 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 f0f6ba5a8a7c66a9683bfdfa29c91971aa44bca0. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 27326ff602c0928300ad98a29fdc9b317b28d05e, 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 0bd559834348aad4641ed3bdca92916a751821b3a25c1afe895cf0506be72457). 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 9da40da1200dbe688493d07053fd4a0ff3540d56.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 0bd559834348aad4641ed3bdca92916a751821b3a25c1afe895cf0506be72457.
Tree 32bda5df5a067204ccd837696c89e5891b10d1cd matches the independently computed clean merge.
Compared with historical tree 7f8e2a3f847dee71b262ec857f9e7a21a91c00c3, 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 #1620.
Closes #1621.
Closes #1622.
Closes #1623.
Non-graph #1624 stays OPEN after graph repair merge.
Adversarial Review
Verification And Output Records
662 passed in 202.52s (0:03:22); seven new focused tests. Schema, strict, terms, full-record references, snippets and history checks passed for all four records. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All21 graph quotations match selected caches;17 automatically match fresh primary XML and4 moss quotations were visually checked against the publisher-indexed primary abstract. Cache matching is not entailment. Full moss access403; all920 caches unchanged, not recertified. Prior batch73 gallium non-graph reference exception remains outside this batch.
All13 original nodes retained;7 original arrows become3 after4 workflow/shared-outcome links are removed. No new topology or paid run. Core enrichment, formaldehyde lowering, conditional methionine rescue, moss treatment gains and mucin-substrate responses remain. Non-graph #1624 stays OPEN.
All456 other records,920 caches and raw non-graph blocks verified unchanged. Canonical taxa and auditor rules unchanged. Zero structural defects;44 baseline warnings preserved exactly; connectivity census unchanged. Repeat renders deterministic, exact descriptions parsed across456 pages, not browser screenshots.
Postcommit just check-docs-current passed with clean tree; log SHA256 e7c4b8c6aa5326cf49335afc6eb3e6ecacc078b60b7058c075bad422d3669878. Every-node/every-arrow decisions,40 actual final check outputs/digests plus17 superseded pre-correction outputs, and self-adversarial review committed under reports/causal_graph_review, batch74. Final focused rerun:16 passed. Corpus:239 reviewed,196 pending,25 needs_research. Not independent approval or corpus completion.
Source Limits
Dependency
Draft depends on #1619. Do not merge into the topic parent. Require eligible exact-head CI and protected main queue after the parent merges. Move dependents before deleting parent branches.