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Separate SIHUMIx BP5 hypothesis from measured community output #1769
SIHUMIx_Human_Intestinal_Model_Community.yaml (CommunityMech:000080; PMID33622394 and doi:10.3390/microorganisms7120641): genomic adjacency does not show BP5 causes neighboring enzyme activity. The in silico knockout removes rxn15467, not BP5; the authors explicitly leave BP5 mediation hypothetical. Remove expression-to-model and model-to-observed-SCFA arrows while retaining the three bounded observations. Remove COLONIZATION_FACILITATION from expression and CROSS_FEEDING from bulk SCFA measurements; retain explicitly computational exchange predictions without claiming in-vitro transfer. Account for differing single/community growth conditions, positive but limited synthetic-CR2 assay evidence, and the distinct transit-time experiment. No new topology.
Dedup: fresh all-state issue titles/bodies and ignored/hidden-inclusive local search with .git/docs/site/references_cache excluded; relevant caches separately inspected. Matching issues read, not duplicates of these findings. Comments/PRs not exhaustive. Source-based self-adversarial review, not independent approval. Graph-repair issues close only after protected-main merge.
Addressed in #1771 at c33f689; exact-head self-review: #1771 (review). 880 passed in 285.17s (0:04:45); postcommit docs-current passed.43 final validation outputs/digests plus decisions and provenance are committed. Four records changed;14nodes6existingdirections retained. The surviving SF356 pairwise-target finding was corrected with an additional append-only history and complete validation rerun;23 preliminary outputs retained. Non-graph1770 and existing loader1703/Linux DOI-cache1091 remain unresolved. Not independent approval; close only after protected-main merge.
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realmarcin commentedon Oct 7, 2026
Addressed in #1771 at c33f689; exact-head self-review: #1771 (review). 880 passed in 285.17s (0:04:45); postcommit docs-current passed.43 final validation outputs/digests plus decisions and provenance are committed. Four records changed;14nodes6existingdirections retained. The surviving SF356 pairwise-target finding was corrected with an additional append-only history and complete validation rerun;23 preliminary outputs retained. Non-graph1770 and existing loader1703/Linux DOI-cache1091 remain unresolved. Not independent approval; close only after protected-main merge.