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Review final pending causal graphs and bound evidence (batch124) - #1972
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Source-based self-adversarial review at exact head f16d4d8; not independent approval.
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Review empty graph against full-text controls; retain a substantive extension gap without inventing nodes, and update the stale abstract-access discussion.
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Qualify reconstructed coupling and correct computational provenance without genus-specific functions.; Retain positive amendment and removal endpoints without assigning culture-wide rates to each substrate.
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Retain engineered hydrolysis division without polymer-catabolism, exclusive-niche or burden-relief overclaims.; Retain temporal succession while qualifying its mechanism.; Retain the condition-specific lipid-fraction benefit and comparable-titer counterpoint.
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Qualify the strain-specific formate/CO2 model.; Retain nitrogen support without nutritional sufficiency or demonstrated return-flow mediation.; Represent the urease effect at culture level with distinct ammonia/CO2 recipients.; Preserve the Nox intervention and early-growth evidence without colonization or universal-recipient claims.
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Retain experimental amino-acid rescue and distinguish three alternative pairs.; Retain sulfur-rescue controls while qualifying the exact transferred compound.; Retain condition-specific obligate growth and species-resolved counts without long-term stability claims.
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Retain augmentation while separating niche-filling interpretation from measurement.; Re-evidence the stability endpoint and preserve unrelated-donor limits.; Re-evidence community resistance without facilitation typing or strain-specific causality.
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All15nodes and8arrows retained, six coherent renames, no new topology. Six canonical diffs and cache changes read. TCP graph-owned YAML anchors preserved so unrelated media/ingredient blocks remain byte-identical. No dangling targets or discussion anchors.
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Algae-only controls bound a future AM-AB graph: early nitrogen removal is slower, phosphate detection limits occur in both conditions, and BOD performance is not uniformly improved. Full Methods metadata is available, not an ongoing abstract-access gap. Extension1968 and metadata1969 stay open.
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TCP metagenomic reconstruction is COMPUTATIONAL/PARTIAL, without invented tools, genus-specific roles or measured transfer. Positive substrate amendments and culture-wide removal remain. Prior1108/1109 repairs preserved; no new coupling-to-removal arrow.
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Yarrowia exact YBGL3/YBXT-XR pair, shared glucose use and substrate succession are distinct from exclusive niches.34% versus26.3% is a lipid-fraction comparison; best titer is comparable and1:2 performs worse. No polymer GO or demonstrated burden-relief claims. Version1 preprint and metadata1970 limits remain.
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Yogurt nutritional modeling, Nox perturbation and urease strain panels stay distinct. Positive interventions retained with early/final and Streptococcus/Lactobacillus recipients separated. Nitrogen sufficiency and universal return-flow mediation are not asserted. Both community-scoped outcomes name both original participants; metadata1971 remains.
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Zymomonas spent-medium and individual-metabolite rescue remain positive, not mere correlation. Cysteine and glutathione are sufficient alternatives; exact natural sulfur compound and release route remain unresolved. Three pairs remain separate, with species-resolved counts and no long-term stability assertion.
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hCom2 stability and resistance have direct endpoint evidence, not an assembly-only citation or colonization-facilitation labels. Donor dependence and dropout architecture confounding limit mechanism/individual-strain claims. Non-graph debt765 remains and no restricted full body is restored.
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Thirteen focused tests and twelve targeted in-memory control/mutation/restored-control probes pass. Probes reject specified scientific regressions, not every possible equivalent wording. Early test development failures included an incorrect test taxon identifier, corrected to unchanged canonical NCBITaxon1585.
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All30graph and6discussion quotes match fresh primary artifacts and caches. Four short excerpt appendices and one independently matched missingTCPabstract;919originalcaches unchanged. Exact read scopes, failed retrievals and successful alternatives recorded; no original figure-pixel,external-supplement,raw-data or code audit.
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Zymomonas reference validation initially failed because its .md cache takes precedence over .txt. Move our exact appendix to .md and restore our text-cache change; preserve failed/recovered logs. No validator changes, fabricated content or weakened checks. EarlierTCPbaseline failure and24recovered checks also remain recorded. Correct algae copyright holder to Water Environment Federation. Staged whitespace gate found trailing spaces in the newTCPcopy; normalize only that copy and rerun affected checks, preserving the original user file and failed-check log.
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Six sets of schema,strict,terms,references,snippets,rank/history checks pass.1187selected tests,lint,mypy and deterministic render pass.57existing network warnings remain;zero structural defects. Exact456page/1359node/522arrow descriptions verified,not screenshots or full Linux CI certification.
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454otherrecords,unrelated raw fields and all prior histories/decision artifacts unchanged. Census415community-level,137mixed,278community-only,1570taxa,1281sole-credit. Yogurt adds two counted taxa but no sole credit;300participant-list users. Exact measured count bounds updated; connectivity code and share guard unchanged.
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1963-1967 addressed pending protected-main merge;1968 extension,1969-1971 metadata and765 remain open. One algae Edison dryrun, no provider submission or spend; priorRuegeria1883 configured-authentication blocker not retried unchanged. Self-review is not independent approval.
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Corpus405reviewed,zero pending,55needs_research across460records. Zero pending does not mean complete graphs or a completed objective. Protected-root1836,actual exact-headCI,merge andbranchdeletion remain separate; postcommit docs-current/publication not preasserted.
1187 passed in 353.41s (0:05:53); thirteen focused tests and twelve in-memory control/mutation/restored-control probes. All six records pass schema, strict, terms, references, snippets, rank and history. 61 completed gates retain commands, tails and digests; original cache-precedence failure and recovered run are retained separately.454otherrecords,919originalcaches and unrelated raw fields unchanged. Four short attributed cache appendices and one independently verified missingTCPabstract; no full-body imports.
All15nodes and8arrows retained, six coherent renames, no new topology. Positive amendment, lipid-fraction, fermentation, rescue and resistance outcomes remain while mechanisms, exact strain pairs, growth stages and alternative explanations are bounded. Algae-only controls constrain its still-empty graph.
All six whole records and fresh primary identities/abstracts reviewed; the ledger specifies actual full-text reading scopes and abstract-only limits. No original figure-pixel,external-supplement,raw-data or code audit. All36graph/discussion quotations match fresh primary artifacts and caches. Literal matches are not entailment proof.
Corpus405reviewed,zero pending,55needs_research; zero pending is not goal completion. Network57unchanged warnings,zero structural defects. Census415community-level,137mixed,278community-only,1570taxa,1281sole-credit,300participant-list users. Yogurt adds two explicitly scoped participants who remain pairwise connected; no new sole credit. Exact measured count bounds updated; connectivity code and share guard unchanged.
Deterministic rendering and exact456page/1359node/522arrow description parsing verified,not screenshots. Postcommit docs-current passed clean; log SHA256 6b998ae72133a8c6260732e12c879f70c184564ce472feb45fb24a9d61535e1e. Local selected passes are not full Linux CI certification.
Decision ledger,provenance,validation,six append-only histories and self-adversarial review committed. Extension #1968,metadata #1969-#1971 and #765 remain open. One algae Edison dryrun; no provider submission or spend. PriorRuegeria #1883 configured-authentication blocker not retried unchanged. Self-review COMMENT is 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 985c5cb81bb72d4ff1c763db31797c31fd6ed099.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 05f6cedabec2b2eab496e71a58e815a736cdc7c1ada8fbbceff902d444705304.
Tree 39c6d2d9ed229d232373eb9755b7d45ef8b05106 matches the independently computed clean merge.
Compared with historical tree 7d70b254f153b1ce92e0ceeeb89e6d63ca23366d, 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 #1963.
Closes #1964.
Closes #1965.
Closes #1966.
Closes #1967.
Graph extension #1968, non-graph metadata #1969-#1971 and #765 remain open; prior research extensions are not resolved.
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
1187 passed in 353.41s (0:05:53); thirteen focused tests and twelve in-memory control/mutation/restored-control probes. All six records pass schema, strict, terms, references, snippets, rank and history. 61 completed gates retain commands, tails and digests; original cache-precedence failure and recovered run are retained separately.454otherrecords,919originalcaches and unrelated raw fields unchanged. Four short attributed cache appendices and one independently verified missingTCPabstract; no full-body imports.
All15nodes and8arrows retained, six coherent renames, no new topology. Positive amendment, lipid-fraction, fermentation, rescue and resistance outcomes remain while mechanisms, exact strain pairs, growth stages and alternative explanations are bounded. Algae-only controls constrain its still-empty graph.
All six whole records and fresh primary identities/abstracts reviewed; the ledger specifies actual full-text reading scopes and abstract-only limits. No original figure-pixel,external-supplement,raw-data or code audit. All36graph/discussion quotations match fresh primary artifacts and caches. Literal matches are not entailment proof.
Corpus405reviewed,zero pending,55needs_research; zero pending is not goal completion. Network57unchanged warnings,zero structural defects. Census415community-level,137mixed,278community-only,1570taxa,1281sole-credit,300participant-list users. Yogurt adds two explicitly scoped participants who remain pairwise connected; no new sole credit. Exact measured count bounds updated; connectivity code and share guard unchanged.
Deterministic rendering and exact456page/1359node/522arrow description parsing verified,not screenshots. Postcommit docs-current passed clean; log SHA256 6b998ae72133a8c6260732e12c879f70c184564ce472feb45fb24a9d61535e1e. Local selected passes are not full Linux CI certification.
Decision ledger,provenance,validation,six append-only histories and self-adversarial review committed. Extension #1968,metadata #1969-#1971 and #765 remain open. One algae Edison dryrun; no provider submission or spend. PriorRuegeria #1883 configured-authentication blocker not retried unchanged. Self-review COMMENT is not independent approval. Root #1836 requires actual protected checks. No artificial CI,protection bypass,merge or premature branch deletion.
Dependency
Draft depends on #1962. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.