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Qualify thermophilic syntrophy mechanisms and assay contrasts (batch114) - #1892
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Source-based self-adversarial review at exact head 62b18e2; not independent approval.
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Retain acetate-linked syntrophy and the reversible pathway; distinguish extracellular carriers from cofactors and avoid all-substrate obligacy.; Retain hydrogen-removing methanogenesis with exact TM/PB expression and hydrogen-pressure context; do not exclude formate use or import DeltaH/butyrate results.; Retain indirectly supported formate transfer as PARTIAL, with the detailed ATP/proton-coupled mechanism HYPOTHESIZED rather than established.
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Retain supported hydrogen syntrophy and separate study-specific density effects; qualify the existing arrow as partial mediation through the higher-density context.; Recast proximity as an explicit two-participant community observation; retain a PARTIAL transport interpretation without colonization or mandatory-contact typing.; Recast growth-phase aggregation/transcription as a community phenotype, with the exact within-culture 292-versus-24 contrast and no extra exchange claim.
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Every original node and direction has a disposition: six nodes and four directions retained, one node renamed. No added topology; all targets and discussion anchors resolve.
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Overcorrection check: retain demonstrated acetate-linked methanogenesis, hydrogen-removal growth benefits and formate involvement supported by the 2001 partner-comparison literature. Qualification of the detailed energy-conservation model does not erase these results or imply universal obligacy.
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Acetate/formate: enzyme assays with artificial acceptors and proteomic abundance support component activities, not the entire reverse-electron-transport pathway. Proton-gradient coupling and physiological acetate reduction were not demonstrated in 2019. Both methanogenesis arrows distinguish overall coupling from carrier partition and measured flux.
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Methanogenesis: preserve exact 2002 TM/PB hydrogen conditions and the mcr/MRI-versus-mrt/MRII result, not universal activation of all genes. TM can use formate; hydrogenotrophic does not mean hydrogen-only. The separate DeltaH/butyrate system is not silently imported.
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Thermotoga: the dialysis and size-fraction observations support proximity, not proven directional colonization, mandatory contact or a specific adhesion mechanism. The original proximity-to-transfer direction remains PARTIAL.
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Phenotype: 292 versus 24 describes within-culture mid-log-to-early-stationary-phase contrasts, not 292 genes in a coculture-versus-monoculture contrast. Aggregation declines in stationary phase. Hydrogen removal supports physiology without isolating every EPS/transcript mediator; growth phase, density and gas handling remain relevant.
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Source scope: six fresh primary abstracts, 2019 full main-body XML, three complete existing cached primary main bodies and the 2001 publisher abstract read. Fresh older full XML retrieval failed; no bypass. Original figure pixels, supplements, raw data and incomplete cached table cells not audited. All 18 graph/discussion quotes match fresh primary texts and existing caches; no new publication bodies or cache files.
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Two guarded records and append-only histories preserve 458 other records, 923 caches, all non-graph raw blocks and prior history/decision artifacts. One explicit participant-list user added. Measured census is 413 community-level, 137 mixed, 276 community-only, 1565 taxa and 1273 solely credited; the added pair already has pairwise credit. Connectivity logic and share guards unchanged.
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Five real in-memory control/mutation/restored-control probes reject formate SUPPORT inflation, colonization typing, the wrong 292 contrast, unqualified hydrogen mediation and exclusion of TM formate use. Actual mutations and rejecting assertions recorded; canonical hashes unchanged; not additional pytest tests.
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Nine focused tests and 1033 combined regressions pass. Both records pass schema, strict, terms, full-record references, snippets, history and rank. The 56 network warnings are unchanged, with zero structural defects. Deterministic rendering and exact HTML-description coverage: 456 pages, 1366 nodes, 531 arrows, not UI screenshots. Local reference passes do not certify Linux; full-corpus snippets remain informational.
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Graph repairs #1888/#1889 await protected-main merge; non-graph #1890/#1891 remain open. No Edison invocation or new topology. Prior Ruegeria extension #1883 and other needs_research records remain incomplete. Self-review is not independent approval; exact-head publication and postcommit docs-current are separate gates. Root CI blocker #1836 is not bypassed; dependent branches are not deleted.
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Corpus: 366 reviewed, 40 pending, 54 needs_research across 460 records. The overall goal remains incomplete.
1033 passed in 414.10s (0:06:54); nine focused tests and five real in-memory mutation probes. Both edited records pass schema, strict, term, full-record reference, local-snippet and history checks. 27 validation outputs retain commands, output tails and log digests. All 458 other records, 923 caches and non-graph blocks are unchanged.
All six original nodes and four directions remain; one node is renamed. Formate involvement retains experimental support while the detailed energy-conservation mechanism remains proposed. Thermotoga proximity and aggregation are scoped community observations, not directional colonization or another exchange. The 292-versus-24 gene counts retain their within-culture growth-phase meaning.
Six fresh primary abstracts, one fresh full main-body extraction, three existing cached primary main bodies and the 2001 formate partner-comparison publisher abstract were read. Fresh full retrieval of older papers failed; original figure pixels, supplements and raw data were not reviewed. All 18 graph/discussion quotations match fresh primary text and existing caches. No new publication bodies or caches were committed.
Corpus: 366 reviewed, 40 pending, 54 needs_research; 56 unchanged network warnings and zero structural defects. One newly mixed record adds two census denominator taxa, both already connected by the pairwise hydrogen-transfer node. No change to connectivity logic or the share guard. Rendering is deterministic with exact HTML-description coverage, not UI screenshot certification. Postcommit docs-current passed clean; log SHA256 d4c52dd393f823f8a659b1b192e95d8b07b89667abb0a5014ea7d376f15369ca. Local reference passes are macOS, not Linux certification; full-corpus snippet results remain informational.
Decision ledger, provenance, validation, two append-only histories and self-adversarial review are committed. Metadata followups #1890-#1891 remain open. No Edison invocation or new topology in this repair; prior Ruegeria extension #1883 still needs authenticated research. This COMMENT is self-review, not independent approval. Root blocker #1836 remains subject to real protected checks; no artificial CI, protection bypass 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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Self-adversarial review refreshed at exact head ce4adc5 after propagating the real CI correction #1899. Not independent approval.
Original head: 62b18e2. Current parent: 2d8312a. Only tests/test_datamodel.py changes in the tree for batches109-114; batch115's whole tree is unchanged. Scientific records, prior histories/decisions, caches, renderings and all other files are byte-identical to the respective reviewed trees. Each batch-owned patch excluding this test is byte-identical (SHA256 153b28aa2ba3d8d04fdf4ac285e413cd1558e3d63ecae82cd896d3b6e3405264).
The stale smoke test now requires the reviewed source and target names, resolving target, canonical pairwise taxa, qualified sucrose mediation and both SUPPORT/PARTIAL evidence. No graph was reverted or test skipped. The batch115 CI artifact records the original failed strict run, reproduction, 24 related test passes and seven rejecting counterfactual probes.
Fresh tests at this head: ............. [100%]
13 passed in 20.09s
Test log SHA256: 6f232d5193d40fba291f0bb9a2d7d41e73de7df9702587c7454fc3d76cefdfb0. Fresh docs-current passed with a clean worktree; log SHA256 d4c52dd393f823f8a659b1b192e95d8b07b89667abb0a5014ea7d376f15369ca.
The propagation-pending entries in batch115's immutable publication report describe the earlier publication state; this exact-head review records the subsequent propagation. Focused tests are not a new full-suite pass. Real exact-head protected CI remains required; #1836 independently blocks the upstream root PR. #1899 remains open until protected-main integration. No artificial CI, protection bypass, merge or branch deletion was performed.
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Exact-head self-adversarial restack review at f3c478d398eb3790edaa1605c5059c8651dbc556.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 153b28aa2ba3d8d04fdf4ac285e413cd1558e3d63ecae82cd896d3b6e3405264.
Tree e69b1922aa2fb002f8ebcc094f8d87a748cc6d12 matches the independently computed clean merge.
Compared with historical tree f25f82e5471547929d544544cc3558540bba6b82, 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 #1888.
Closes #1889.
Metadata #1890-#1891 remain open; this batch does not resolve prior research extensions.
Adversarial Review
Verification And Output Records
1033 passed in 414.10s (0:06:54); nine focused tests and five real in-memory mutation probes. Both edited records pass schema, strict, term, full-record reference, local-snippet and history checks. 27 validation outputs retain commands, output tails and log digests. All 458 other records, 923 caches and non-graph blocks are unchanged.
All six original nodes and four directions remain; one node is renamed. Formate involvement retains experimental support while the detailed energy-conservation mechanism remains proposed. Thermotoga proximity and aggregation are scoped community observations, not directional colonization or another exchange. The 292-versus-24 gene counts retain their within-culture growth-phase meaning.
Six fresh primary abstracts, one fresh full main-body extraction, three existing cached primary main bodies and the 2001 formate partner-comparison publisher abstract were read. Fresh full retrieval of older papers failed; original figure pixels, supplements and raw data were not reviewed. All 18 graph/discussion quotations match fresh primary text and existing caches. No new publication bodies or caches were committed.
Corpus: 366 reviewed, 40 pending, 54 needs_research; 56 unchanged network warnings and zero structural defects. One newly mixed record adds two census denominator taxa, both already connected by the pairwise hydrogen-transfer node. No change to connectivity logic or the share guard. Rendering is deterministic with exact HTML-description coverage, not UI screenshot certification. Postcommit docs-current passed clean; log SHA256 d4c52dd393f823f8a659b1b192e95d8b07b89667abb0a5014ea7d376f15369ca. Local reference passes are macOS, not Linux certification; full-corpus snippet results remain informational.
Decision ledger, provenance, validation, two append-only histories and self-adversarial review are committed. Metadata followups #1890-#1891 remain open. No Edison invocation or new topology in this repair; prior Ruegeria extension #1883 still needs authenticated research. This COMMENT is self-review, not independent approval. Root blocker #1836 remains subject to real protected checks; no artificial CI, protection bypass or premature branch deletion.
Dependency
Draft depends on #1887. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.