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Separate study-specific Staphylococcus-Candida observations and remove cross-study causal joins #1829

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@realmarcin

Finding

CommunityMech:000326 combines six studies of the same species pair, not a single resolved strain/condition experiment. Remove the two arrows that turn observations from one PMID into mechanisms of another. Preserve the six reported observations, but aggregate suppression or one-way fungal inhibition is not demonstrated reciprocal competition, and context-dependent biomass is not universal mutualism. Keep the copper study authors mutualism interpretation explicitly HYPOTHESIZED/PARTIAL, separate proteomic inference from aggregate biomass, and do not treat RNA-seq ontology enrichment as demonstrated colonization, altered genotype or infection severity. This is a metadata/evidence repair only: no new pathogen growth, biofilm, survival, resistance, virulence or colonization enhancement procedures, genetic designs, strain-selection advice or new mechanisms. The six primary abstracts were read; available PMCID leads do not imply full-body review.

Lifecycle

Address in the dependent batch106 PR; close only after protected-main merge. Self-adversarial review is not independent approval. No paid provider submission or new topology is part of this repair.

Activity

  1. realmarcin commented on Oct 8, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1835 at 2d931ac; self-review: #1835 (review). 959 passed in 793.39s (0:13:13); postcommit docs-current passed.41gate outputs/digests, decisions, provenance and four append-only histories committed.18nodes/5qualified directions retained;1workflow node and5unsupported/restatement arrows removed; all36reviewed quotations match fresh primary text and unchanged caches. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Non-graph1833 stays open. Not independent approval; close only after protected-main merge.

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