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Bound wine, Mankai and fungal-leaching mechanisms (batch123) - #1962
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Source-based self-adversarial review at exact head 19010db; not independent approval.
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Preserve positive composition perturbations while distinguishing kinetics from completion and molecular mechanism.; Retain competition as a qualified phenotypic inference without absolute viability or every-pair causality.; Bound the broader non-Saccharomyces metabolic effect to the tested panel and retain detectable S. cerevisiae effects.
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Retain the positive contact-treatment growth phenotype without necessary-gene attribution.; Mark proposed Torulaspora-mediated suppression as partial and hypothetical, not a demonstrated toxin mechanism.; Preserve the 5 h amino-acid difference and 9 h null without inferring transfer, secretion or uptake direction.
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Keep observed compartment differences separate from selectively demonstrated host filtering and niche partitioning.; Retain annotated producer-salvager potential with computational provenance, not observed cross-feeding or strain-matched validation.
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Qualify the proposed polymer handoff; bulk carbohydrate decline also includes medium-sucrose consumption.; Preserve bulk metabolite changes without niche partitioning, uniform acid increases or recipient-specific synthesis.; Keep measured day-12 calcium/silicon leaching and residue changes distinct from isolated physical causality and CO2 sequestration.
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All11nodes and2arrows retained,three coherent renames,no new topology. All four canonical diffs and the narrow cache append read after guarded writes. No dangling targets or anchors; unrelated fields and prior history artifacts preserved.
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Five-species drop-outs/substitutions retain positive treatment effects and completion. Competition remains qualified,not an identified molecular cause or complete pairwise matrix. ARISA is not absolute viable abundance. Non-Saccharomyces breadth is panel-specific and S.cerevisiae effects remain detectable. Available Table1/Methods metadata is separate1958,not a renewed inaccessible-source claim.
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Three-species contact-dependent growth retained,with hypothesized medium-mediated suppression PARTIAL. Early amino-acid difference and9h null retained with supplied-medium amino acids distinguished. No toxin identity,necessary gene or secretion/uptake direction inferred. Prior1111-1113 remain intact; recirculation metadata1959 separate.
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Wolffia compartment differentiation retained without microbial niche partitioning or selectively tested host filtering. Predicted guild retains seven participants and gene-complementarity provenance,not FBA or measured transfer. Operational fractions,MAG gaps and non-strain-matched comparators constrain localization and adaptation. Prior839/840 and direct-flux gap preserved; non-graph roles1960 separate.
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Wollastonite bulk metabolites and positive day12Ca/Si leaching retained. Both existing arrows qualified; polymer transfer not traced,medium sucrose contributes to carbohydrate loss,individual acids need not all rise. Residue morphology does not isolate hyphal force; no measured net carbon sequestration inferred. Non-graph roles1961 separate.
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Thirteen focused tests and twelve targeted in-memory control/mutation/restored-control probes pass. Earlier broader probe receipt retained in scratch; targeted rerun improves isolation of completion,Saccharomyces-effect,acid-pattern and leaching-value mutations. These guard specified assertions,not arbitrary semantic equivalence or every possible textual regression.
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All22graph and4discussion quotes match fresh primary artifacts and caches. One17-word CC BY4 excerpt appended;922othercaches unchanged. Complete local primary main bodies plus publisher Results/Discussion/Methods/Table1 inspected; no figure-pixel,external supplement,raw-data or code audit. Literal matches are not entailment proof.
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Four focused schema/strict/terms/references/snippets/rank/history gates pass.1174selected tests,lint,mypy and deterministic rendering pass.57existing network warnings remain and zero structural defects. Exact descriptions on456pages,1359nodes,522arrows verified,not screenshot QA or full Linux CI certification.
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456otherrecords,unrelated raw fields and all prior history/decision files unchanged. Participant lists/scopes unchanged;299participant-list users and census414community-level,136mixed,278community-only,1568taxa,1281sole-credit preserved. Scope credit is not participant-coverage certification. No schema,connectivity or threshold changes.
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1954-1957 addressed pending protected-main merge;1958-1961 remain non-graph follow-ups. Source-based self-review is not independent approval. No Edison invocation or spend; Ruegeria1883 unchanged authentication blocker not retried. Protected-root1836,actual exact-head CI,merge and branch deletion remain separate requirements.
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Corpus400reviewed,6pending,54needs_research across460records. Overall goal incomplete. Postcommit docs-current and publication must be checked separately,not preasserted.
1174 passed in 372.38s (0:06:12); thirteen focused tests and twelve targeted in-memory control/mutation/restored-control probes. All four records pass schema, strict, terms, full-record references, snippets, rank and history. 41 gates retain commands, output tails and digests. All456otherrecords,922othercaches and unrelated raw fields unchanged; one17-word CC BY4 publisher excerpt appended with provenance.
All11nodes and both existing arrows remain, three renames, no new topology. Wine perturbation outcomes remain positive with mechanisms qualified. Mankai gene-content predictions and compartment profiles remain distinct from demonstrated transfer or host filtering. Fungal bulk metabolites and Ca/Si leaching remain positive with both causal links qualified.
All four whole records and fresh abstracts reviewed. Three open primary main bodies and the five-species publisher Results/Discussion/Methods/Table1 inspected; web retrieval succeeded despite a separate direct-HTTP403 receipt. No original figure-pixel, external supplement, raw-data or analysis-code audit. All26graph/discussion quotations match fresh primary artifacts and caches. Literal matches are not entailment proof.
Corpus400reviewed,6pending,54needs_research. Network57unchanged warnings,zero structural defects. Participant lists and scopes unchanged:299list users,414community-level,136mixed,278community-only,1568taxa,1281solely credited. No schema,threshold or connectivity changes. Exact descriptions on456pages,1359nodes,522arrows and deterministic rendering verified,not screenshots. Postcommit docs-current passed clean; log SHA256 f4191f04845a52f7c8586e11e32526fb774ac71c69c19176947d8a0e257c1d4a. Selected local passes are not full Linux CI certification.
Decision ledger,provenance,validation,four append-only histories and self-adversarial review committed. Metadata #1958-#1961 remains open. No Edison invocation or spend; prior Ruegeria #1883 configured authentication blocker unchanged. This COMMENT is self-review,not independent approval. Root #1836 requires actual protected checks. No artificial CI,protection bypass,merge or premature branch deletion.
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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Exact-head self-adversarial restack review at 0fec90c8d14dc9448d33e058deaacbf6022d732b.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 8dc57c11451b4a36e7d919246744e3d2cfde8d3d4f3941c5ed2fff439753e977.
Tree f775daf607473d56aeb497561688943998e7358e matches the independently computed clean merge.
Compared with historical tree e3628b1faedb3c6fc42392a051586a6a12536d27, 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 #1954.
Closes #1955.
Closes #1956.
Closes #1957.
Non-graph metadata #1958-#1961 remain open; this batch does not resolve prior research extensions.
The genuine palette correction #1913 is inherited from the verified parent; required current-head CI remains a separate gate.
Adversarial Review
Verification And Output Records
1174 passed in 372.38s (0:06:12); thirteen focused tests and twelve targeted in-memory control/mutation/restored-control probes. All four records pass schema, strict, terms, full-record references, snippets, rank and history. 41 gates retain commands, output tails and digests. All456otherrecords,922othercaches and unrelated raw fields unchanged; one17-word CC BY4 publisher excerpt appended with provenance.
All11nodes and both existing arrows remain, three renames, no new topology. Wine perturbation outcomes remain positive with mechanisms qualified. Mankai gene-content predictions and compartment profiles remain distinct from demonstrated transfer or host filtering. Fungal bulk metabolites and Ca/Si leaching remain positive with both causal links qualified.
All four whole records and fresh abstracts reviewed. Three open primary main bodies and the five-species publisher Results/Discussion/Methods/Table1 inspected; web retrieval succeeded despite a separate direct-HTTP403 receipt. No original figure-pixel, external supplement, raw-data or analysis-code audit. All26graph/discussion quotations match fresh primary artifacts and caches. Literal matches are not entailment proof.
Corpus400reviewed,6pending,54needs_research. Network57unchanged warnings,zero structural defects. Participant lists and scopes unchanged:299list users,414community-level,136mixed,278community-only,1568taxa,1281solely credited. No schema,threshold or connectivity changes. Exact descriptions on456pages,1359nodes,522arrows and deterministic rendering verified,not screenshots. Postcommit docs-current passed clean; log SHA256 f4191f04845a52f7c8586e11e32526fb774ac71c69c19176947d8a0e257c1d4a. Selected local passes are not full Linux CI certification.
Decision ledger,provenance,validation,four append-only histories and self-adversarial review committed. Metadata #1958-#1961 remains open. No Edison invocation or spend; prior Ruegeria #1883 configured authentication blocker unchanged. This COMMENT is self-review,not independent approval. Root #1836 requires actual protected checks. No artificial CI,protection bypass,merge or premature branch deletion.
Dependency
Draft depends on #1953. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.