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Bound xylan mediation, mercury evidence and Z123 functional inference (batch77) - #1643
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Source-based self-adversarial review at exact head 76c0dec; not independent approval.
Repairs #1637-#1639 addressed; non-graph #1642 unresolved.
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Empty Nasal graph remains needs_research: stable assembly and differential challenge outcomes need source-backed nodes after scoped Edison research; no arbitrary record change.
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Retain hydrogen-transfer evidence and both positive outcomes; qualify utilization mediation and replace the context-only enzyme arrow with the source hypothesis.; Preserve increased N. frontalis utilization and distinguish it from polymer depolymerization.; Preserve normalized enzyme gains with enzyme/time/organism boundaries, not uniform panel maxima.
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Retain measured geochemistry; remove the co-occurrence arrow and unsupported transport/niche annotation.; Preserve mer/hgc potential with unbinned methylator, paralog and activity limits; replace aim-fragment evidence with actual result excerpts.; Preserve diversity without temporal stability or demonstrated niche partitioning.; Preserve measured gaseous Hg(0) while separating microbial potential from geogenic and abiotic contributions.; Preserve proposed sulfur/iron/mercury coupling without unsupported syntrophy or transport annotation.
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Qualify proposed genomic/proteomic differentiation without discarding measured polymer and enzyme outcomes; missing endpoint topology stays needs_research.
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Every whole record and original node/arrow reviewed after a fresh both-root baseline. Empty Nasal is explicitly needs_research, not omitted or reported complete. No topology invented to satisfy a sparse-graph heuristic.
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Preserve xylan utilization and extracellular enzyme gains with SUPPORT evidence and correct canonical pairwise directions. Enzyme activities are protein-normalized; increased biomass is not the entire explanation. Abstract maxima span fungi/time/substrates, not uniform PNK2 values.
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Xylan utilization is distinct from polymer depolymerization. Preserve both existing causal links with partial/hypothesized mediation. Replace shared-context wording by the actual source proposal involving sugar uptake and xylose repression; do not claim a selective hydrogen-removal or repression-rescue perturbation.
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Ngawha mer/hgc findings are positive sequence evidence. hgcA sequences could not be binned, no definitive methylator taxon is assigned, HMM MerA hits require paralog filtering and Tiger Bath nondetection is depth-bounded. Replace an abstract aim fragment with actual result excerpts, not false activity certainty.
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Ngawha atmospheric Hg(0) really was measured: retain the environmental outcome. Do not attribute the measurement solely to microorganisms because deep geological inputs and abiotic reactions were not isolated. Main manuscript Results and Methods and Table2 were checked; this is not a microbial flux assay.
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Retain unexpectedly diverse sampled microbiomes without temporal-stability or niche-partitioning claims. Remove the last environment-to-diversity context arrow while preserving the earlier four-edge removal. Keep the sulfur/iron/cinnabar conceptual model without syntrophy or transport ontology overclaims.
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Z123 uses genomics plus proteomics, not merely gene prediction. Preserve reported polymer losses and recombinant enzyme assays. Putative GC-MS compounds are not traced assimilation/mineralization; half-dose comparators do not establish full-dose synergy or assign enzyme necessity to a live strain. Missing endpoint nodes remain research work.
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Nasal source read distinguishes experiment5 from swab experiments1-4, one control plus two reactors per challenge strain, nondetected residents from nine-member inoculum, and proposed tyrosine mechanism from isolated causal rescue. Prior969-972 fixes retained. Fresh full-text access failed; previous cache provenance is explicit.
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Only22 words of selected author-manuscript Results were appended to one cache, with URL, version and PDF SHA. Original abstract and919 other caches remain unchanged; no publication PDF or full manuscript body is committed. Three result snippets total22 words, verified by test.
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Nine nodes and three original arrows are accounted for; nine nodes/two arrows remain. Three histories,457 unchanged records and non-graph raw blocks preserved. Canonical taxonomy and auditor rules unchanged. Forty-four baseline warnings and connectivity census must be preserved exactly, not interpreted as resolved member activity.
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Two separate one-record Edison LITERATURE dry runs completed, with no provider submissions or credits. Scoped asynchronous questions are unanswered; preselection is not approval and earlier denied scopes are unchanged. Research1640/1641 and metadata1642 stay OPEN after repairs1637-1639 merge.
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Schema, strict, terms, full-record references, snippets, histories, both-root inventory/network/rank, regression/lint and deterministic rendering outputs are captured. Exact descriptions are parsed across456 pages, not browser screenshots. Exact-commit review publication and postcommit docs-current remain separate gates. Self-review is not independent approval or corpus completion.
686 passed in 188.36s (0:03:08); nine new focused tests. Schema, strict, terms, full-record references and snippets passed for all four records; all three histories passed. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All12 graph quotations independently match primary abstract or author-PDF extraction; the latter removes marginal line numbers. One cache adds22 quoted words with provenance;919 others are unchanged. String matching is not entailment. Nasal full-text provenance is a prior cache; LDPE remains abstract-bounded. No recertification of all920 caches.
All9 original nodes and3 arrows reviewed;9nodes2arrows remain. Three records repaired; Nasal unchanged but explicitly needs_research. Xylan utilization and enzyme gains, measured Ngawha atmospheric mercury, sequence potential, and actual Z123 polymer/enzyme outcomes are preserved with assay and attribution limits. Missing Nasal/Z123 topology stays in #1640/#1641; metadata #1642 stays OPEN.
All457 unchanged records,919 unchanged caches and raw non-graph blocks verified. One cache adds22 quoted words of Ngawha Results with primary manuscript provenance; no complete paper/PDF uploaded. Canonical taxa and auditor rules unchanged. Zero structural defects;44 baseline warnings and 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 cb8af36dec01f6d582338c33e1fd2d683db3a138379e3a144dcedbd24dc5df13. Every-node/every-arrow decisions,39 actual check outputs/digests and source-based self-adversarial review committed under reports/causal_graph_review, batch77. Final focused rerun:18 passed. Corpus:248 reviewed,184 pending,28 needs_research. Two one-record Edison dry runs; zero paid submissions/credits, scoped questions unanswered. 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 666a476682a69ff9874e787489a37abb4cbc61fa. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 76c0dec3077239bbe236ba6a01e76df3923b6f65, 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 8779cf00cf966c0767135148d7f83c09cfba2b7b8ca617ee560fefe24439054d). 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 05ca410280207d48a52ee9a6c685253d5502e192
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 0b02adacf41d3acab056dc99dbf71a385a462ee8.
The batch-owned binary patch is byte-identical
(SHA-256 8779cf00cf966c0767135148d7f83c09cfba2b7b8ca617ee560fefe24439054d); 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 abd593075b7147a63fb637627db1e43c5ba4d9c5. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 05ca410280207d48a52ee9a6c685253d5502e192, 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 8779cf00cf966c0767135148d7f83c09cfba2b7b8ca617ee560fefe24439054d). 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 53a4229f2e939f36ad41aedc4728a497dd4131fb.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 8779cf00cf966c0767135148d7f83c09cfba2b7b8ca617ee560fefe24439054d.
Tree 7dd3da5a800b039df44e7b850eddb751a9efd7da matches the independently computed clean merge.
Compared with historical tree 153dcd91bf55acb00afbd550e3feee63f6ab45b6, 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 #1637.
Closes #1638.
Closes #1639.
Research #1640/#1641 and non-graph #1642 stay OPEN after graph-repair merge.
Adversarial Review
Verification And Output Records
686 passed in 188.36s (0:03:08); nine new focused tests. Schema, strict, terms, full-record references and snippets passed for all four records; all three histories passed. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All12 graph quotations independently match primary abstract or author-PDF extraction; the latter removes marginal line numbers. One cache adds22 quoted words with provenance;919 others are unchanged. String matching is not entailment. Nasal full-text provenance is a prior cache; LDPE remains abstract-bounded. No recertification of all920 caches.
All9 original nodes and3 arrows reviewed;9nodes2arrows remain. Three records repaired; Nasal unchanged but explicitly needs_research. Xylan utilization and enzyme gains, measured Ngawha atmospheric mercury, sequence potential, and actual Z123 polymer/enzyme outcomes are preserved with assay and attribution limits. Missing Nasal/Z123 topology stays in #1640/#1641; metadata #1642 stays OPEN.
All457 unchanged records,919 unchanged caches and raw non-graph blocks verified. One cache adds22 quoted words of Ngawha Results with primary manuscript provenance; no complete paper/PDF uploaded. Canonical taxa and auditor rules unchanged. Zero structural defects;44 baseline warnings and 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 cb8af36dec01f6d582338c33e1fd2d683db3a138379e3a144dcedbd24dc5df13. Every-node/every-arrow decisions,39 actual check outputs/digests and source-based self-adversarial review committed under reports/causal_graph_review, batch77. Final focused rerun:18 passed. Corpus:248 reviewed,184 pending,28 needs_research. Two one-record Edison dry runs; zero paid submissions/credits, scoped questions unanswered. Not independent approval or corpus completion.
Source Limits
Dependency
Draft depends on #1636. 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.