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Bound digestion mediation, fraction conversion and probiotic growth (batch75) - #1631
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Source-based self-adversarial review at exact head 3a00e0c; not independent approval.
Repairs #1626-#1628 addressed; research #1629 and non-graph #1630 unresolved.
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Retain panel-level anaerobic fermentation gains with explicit unresolved assignment to recipes A/B/C; no new arrow from co-occurring endpoints.; Retain genus-level quality association already PARTIAL, not species-specific causal mediation. Existing protein/ABTS and panel-scope fixes preserved.
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Preserve methane gains and both-consortium propionate reduction; qualify guild hand-off and its downstream mechanism.; Retain metagenomic transfer interpretation as PARTIAL, not expression, direct flux or obligate syntrophy.; Retain environmental selection interpretation and function/stability trade-off; remove unsupported competition label.
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Retain cellulose conversion and direct contribution to decomposition, not mutualism.; Retain measured hemicellulose conversion; proteomic enzyme mechanism is PARTIAL.; Retain lignin fraction contribution; accessibility-barrier mediation remains HYPOTHESIZED.; Retain joint fraction decomposition, not additive yield or reciprocal fitness.
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Preserve co-culture and partner-supernatant growth gains; qualify molecular cross-feeding and per-member absence of antagonism. Missing vesicle outcome remains needs_research.
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Read all four whole records and every original node/arrow after the both-root baseline. Read full probiotic main body, embedded tables and captions, and primary abstracts for the other three. No separate-supplement, raw-data or original-figure-pixel audit. Abstract-only access is not evidence controls were absent.
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Sparse does not imply defective: mulberry retains its two correctly bounded nodes and no arrows. Earlier1103/1104 recipe-panel and protein/ABTS fixes stay intact. Genus-level association does not justify a species-level causal edge or an extra curation history.
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YSJ22% and J8% methane gains share a non-bioaugmented comparator; both reduce propionate1.6-fold. Correct the former YSJ-specific propionate comparison while preserving both positive outcomes and nearly absent YSJ lag.
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Do not convert metagenomic functional association into transcription, direct electrical transfer, electron flux or obligate syntrophy. Retain the proposed staged-processing and environmental-selection arrows as HYPOTHESIZED, not selectively isolated mediation; introduced and native activities remain unresolved.
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Selection does not establish competitive fitness effects. Preserve elevated acetate, reduced propionate and moderate non-inhibitory ammonia context, together with the source function/stability trade-off: J has the more robust network, YSJ greater methane output.
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Corn cellulose34.91%, hemicellulose45.94%, lignin23.34% are distinct fractions, not additive whole-straw yield. Preserve three component-to-whole causal contributions. Joint conversion does not establish reciprocal fitness among eight strains, so MUTUALISM labels are removed.
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Corn proteomic enzyme association is PARTIAL, with a direct measured-fraction snippet added independently. Do not silently repair the unusual primary wording or call xylanases validated ligninases. Lignin contribution is supported; selective barrier-opening mediation remains HYPOTHESIZED.
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Probiotic cell-free-supernatant addition is a positive intervention, not merely a correlation. Preserve that evidence and elevated viable counts while distinguishing diffusible growth promotion from identified nutrient transfer or necessity. Methods give plate counting without member-resolved enumeration; do not equate total growth with universal absence of antagonism.
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Preserve the probiotic MsrA discussion and closed1065 category fix. The missing membrane-vesicle production/properties outcome is not dismissed because the graph is sparse: mark needs_research and track1629. No growth-to-vesicle-yield arrow, universal antioxidant superiority, MsrA necessity, microbiota mediation or human efficacy invented.
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Full-source scrutiny found L-MV ABTS greater than M-MV, Nile Red proxy rather than direct luteolin uptake, no in-vivo biodistribution and a preventive male-mouse DSS model. Animal Results/Methods dosing chronology requires reconciliation in separate1630, not silent certainty in this graph-only patch.
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One-record Edison LITERATURE dry run completed with10231 query characters and zero calls/credits; no submitted response means no inspected report and no extension. Scoped authorization question remains unanswered, not permission. Earlier denied/pending scopes remain unchanged.
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All10 original nodes and5 arrows have decisions. Three records and histories change,457 records including reviewed mulberry remain byte-identical;920 caches and raw non-graph blocks preserved. No taxonomy or auditor-rule change. Zero structural defects and44 baseline warnings unchanged; connectivity census unchanged.
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Actual schema, strict, terms, references, snippets, histories, both-root inventory/network/rank, regression, lint and deterministic render gates retained with digests. Ruff caught a missing strict=True in a new test zip; fixed and reran full regressions plus lint, retaining three superseded outputs including the failed lint check. Exact descriptions parsed across456 pages, not browser screenshots. Postcommit docs-current is a separate publication gate.
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Dedup scanned911 all-state issue titles/bodies and26 ignored/hidden-inclusive local matches; matching1104/1103/1065/310/183 bodies read. Existing183 membership work reused. No exhaustive historical PR-comment audit or global source-absence claim. Repairs1626-1628 stay OPEN until protected-main merge;1629 and1630 stay OPEN afterward. Self-review is not independent approval or corpus completion.
669 passed in 195.80s (0:03:15); seven new focused tests. Schema, strict, terms, full-record references and snippets passed for all four records; all three new histories passed. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All19 graph quotations independently match fresh primary XML/abstract and selected existing caches. Cache matching is not entailment. Three sources abstract-only; all920 caches unchanged, not recertified. Prior batch73 gallium non-graph reference exception remains outside this batch.
All10 original nodes and5 arrows retained. Three records repaired; mulberry reviewed unchanged. Methane gains, component-to-decomposition contributions and positive supernatant growth remain. No new structure or paid provider run. One-community Edison LITERATURE dry run completed; scoped authorization and report inspection pending. Probiotic record stays needs_research for missing vesicle outcome #1629; non-graph #1630 stays OPEN.
All457 unchanged records,920 caches and raw non-graph blocks verified. 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 62bff40e0cc0a68dafb1967704dcf9bce3fd7380350f1bcf2963636852720b28. Every-node/every-arrow decisions,39 actual check outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch75. Final focused rerun:16 passed. Corpus:242 reviewed,192 pending,26 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 c8f0d6fdf82b90fbffe3022527185a45eec13866. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 3a00e0cc7d5a343addb3f766c5f065340af1eb36, 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 702c46c443b970ad40641b8695a2ce0441c1aef36e8d63cec51a14090f425dde). 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 baa1abe98b1655991f858761f119f435a40d7285
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 63491db7babef085248dd8506eb8a22bd739e8ad.
The batch-owned binary patch is byte-identical
(SHA-256 702c46c443b970ad40641b8695a2ce0441c1aef36e8d63cec51a14090f425dde); 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 38a02bb683486cc1da9b3b8792b8a262485c4208. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head baa1abe98b1655991f858761f119f435a40d7285, 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 702c46c443b970ad40641b8695a2ce0441c1aef36e8d63cec51a14090f425dde). 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 dcac22b85c2a55d0b092cebe43218db3412b735a.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 702c46c443b970ad40641b8695a2ce0441c1aef36e8d63cec51a14090f425dde.
Tree e7e10062d2824bbf08e398ffa8c16d5c828d92ea matches the independently computed clean merge.
Compared with historical tree dbd2310892298840b0f883fb8668a7057ea53f08, 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 #1626.
Closes #1627.
Closes #1628.
Research #1629 and non-graph #1630 stay OPEN after graph-repair merge.
Adversarial Review
Verification And Output Records
669 passed in 195.80s (0:03:15); seven new focused tests. Schema, strict, terms, full-record references and snippets passed for all four records; all three new histories passed. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All19 graph quotations independently match fresh primary XML/abstract and selected existing caches. Cache matching is not entailment. Three sources abstract-only; all920 caches unchanged, not recertified. Prior batch73 gallium non-graph reference exception remains outside this batch.
All10 original nodes and5 arrows retained. Three records repaired; mulberry reviewed unchanged. Methane gains, component-to-decomposition contributions and positive supernatant growth remain. No new structure or paid provider run. One-community Edison LITERATURE dry run completed; scoped authorization and report inspection pending. Probiotic record stays needs_research for missing vesicle outcome #1629; non-graph #1630 stays OPEN.
All457 unchanged records,920 caches and raw non-graph blocks verified. 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 62bff40e0cc0a68dafb1967704dcf9bce3fd7380350f1bcf2963636852720b28. Every-node/every-arrow decisions,39 actual check outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch75. Final focused rerun:16 passed. Corpus:242 reviewed,192 pending,26 needs_research. Not independent approval or corpus completion.
Source Limits
Dependency
Draft depends on #1625. 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.