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Engineered gut metadata: refresh obsolete cache-access limitation without inventing vessel details #1457

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@realmarcin

Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml, PMID:31409662.

Cultivation notes currently say the cached text does not reach Materials and Methods. The current PMID cache includes the primary main body through qPCR, inference, animal and molecular-analysis Methods. Update that obsolete access claim only after checking which vessel/working-volume facts actually belong to which assay; do not turn separate strain preparations into consortium conditions. Preserve the intended amino-acid omission/add-back distinction and the separate 27-hour trajectory versus 24-hour endpoint experiments (#583). The stale DOI-cache pointer and validator filename casing already belong to #1094 and #1091 and should not be duplicated here. No genetic construction or growth-optimization work is requested.

Review scope: whole records and cached primary main bodies, tables and captions read. No figure images, separate supplements or raw data reviewed. Selected Emiliania published peer-review discussion was also read, not the entire exchange. Deduplication searched 772 all-state issue titles/bodies and ignored/hidden-inclusive local content; #583/#529 and #1091/#1094 bodies reviewed. No exact duplicate within that scope; not every issue comment or PR reviewed. This is source-based self-adversarial review, not independent approval.

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  1. realmarcin commented on Oct 6, 2026

    @realmarcin
    ContributorAuthor

    Graph-only repairs published in #1458. This separate follow-up remains OPEN; non-graph raw blocks preserved, not certified. No culture-protocol, cache, top-level wording or taxonomy-role repair is claimed.

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