{
  "slug": "enhancer-promoter-looping",
  "round": 2,
  "date": "2026-10-14",
  "authoring_model": "Sol 6.1",
  "adversarial_reviewer": "Claude Opus 5.5 (Anthropic)",
  "canonical": "hsef_v53_final_nine_2026-10-12\\enhancer-promoter-looping\\enhancer-promoter-looping.review.md",
  "level_before": "Β",
  "level_after": "Β",
  "confidence_before": "Moderate",
  "confidence_after": "Moderate",
  "confidence_band_rederived": true,
  "approval": "Approved as revised",
  "pmids_checked": 60,
  "pmids_failed": 0,
  "retractions_found": 0,
  "claims_spot_checked": 11,
  "validator": {"tool": "validate_review.py", "version": "2.3", "ok": true, "FAIL": 0, "WARN": 0, "PASS": 31},
  "counts": {"critical": 0, "major": 1, "minor": 2, "editorial": 0},
  "findings": [
    {
      "id": "EP-1",
      "severity": "Major",
      "category": "confidence band justified by reviewer access depth",
      "location": "AT A GLANCE (new Confidence basis paragraph); final_score.confidence_rationale",
      "original": "57 primary reports with 10 selected partial-body examinations; density, heterogeneous controls and incomplete access set the confidence, not correctness.",
      "corrected": "Rationale grounded in evidence density and reproducibility, with reviewer access depth explicitly excluded.",
      "evidence": "Lead policy; hsef-framework.md section Confidence band. Two-step test applied; detection limits, a shared tether reagent platform, synthetic/ectopic landscapes and burst fraction standing in for burst frequency are valid determinants, so Moderate stands."
    },
    {
      "id": "EP-2",
      "severity": "Minor",
      "category": "rendering defect (glued numerals)",
      "location": "Registered claim and scope; REVIEWER NOTES; final-score causal-direction paragraph",
      "original": "rank43 / Rank43 / (step1)-(step5)",
      "corrected": "rank 43 / Rank 43 / (step 1)-(step 5)",
      "evidence": "Known renderer defect 4, 7 sites. The glued tokens are cross-references to the prior popularity rank and to the role-of-mechanism derivation steps."
    },
    {
      "id": "EP-3",
      "severity": "Minor",
      "category": "internal consistency / provenance header counts",
      "location": "Revision checkpoint block",
      "original": "current credit is 57 empirical primary reports and 10 selected partial-body examinations; ... historical 60-report total",
      "corrected": "credited counts stated as 57 reports / 62 claims against the preserved header's 60 / 65, with an explicit instruction for renderers that extract the provenance header alone",
      "evidence": "Score card, citation ledger and checkpoint all report 57 and 62; the preserved header reports 60 and 65 and disclosed only the source discrepancy. The prior header is left verbatim as revision mode requires; the repair is in the revision block, which is not part of the preserved set."
    }
  ],
  "rejected_findings": [
    "Best-supported rival renderer defect - rank 1 is is_nominal false; nominal M1 ranks 5.",
    "Four print vs e-pub year differences of one (39721581, 30527662, 39626660, 39626663) - standing convention.",
    "Three title mismatches from PubMed dropping italicised gene names (Sox2, Shh x2) - standing convention.",
    "Bare PMID token form in prose and Study field - systematic house token.",
    "Preserved header access figure vs checkpoint figure - same cause as EP-3, covered by the amended revision block; header left verbatim.",
    "REVIEWER NOTES vs Consensus section - no contradiction.",
    "Spliced 'earlier adversarial approval' sentence - absent; this is not a consensus_consistency_audit revised copy.",
    "Collective authors - screened in both forms (leading comma; consortium truncated to its last word) plus nobiliary particles. None present.",
    "One-rung falsification downgrade on SC3 - argued and upheld; index-directed, applied once, correlated predictions counted together, retained contacts correctly refused as a second falsification.",
    "Momentum - already 'Mechanistic only'; named artifacts are completed publications."
  ],
  "residual_limitations": "Access depth unchanged (10 partial-body, remainder abstract/status). Du and Narita correction bodies unexamined. Partial-body figures not re-verifiable from abstracts; not contradicted.",
  "line_ending_note": "The edit pass initially normalised these files from CRLF to LF; that was reversed and the final files are CRLF, matching their pre-edit state.",
  "changed_files": [
    {"path": "enhancer-promoter-looping.review.md", "sha256": "fdbda6b5303462c28aab8bc3f9afa73781e8a2091fa0091ac6fed06798156c8a", "bytes": 97658},
    {"path": "enhancer-promoter-looping.scorecard.json", "sha256": "0dd4d79da86d18e1ca6353f1efe9eea49f3692f6dba1b45cdce77d9093493b7a", "bytes": 278691},
    {"path": "validation-report.json", "sha256": "5347ff6e45b57498a74b6f581cb204416dc63e586ba1d41bb05536ba73d9d545", "bytes": 7084},
    {"path": "SHA256.txt", "sha256": "81bb774a8cc70e3c7461024cd0a2c84c25d133ffe6bd529718e3e168df43b319", "bytes": 213},
    {"path": "current-source-checkpoint.review.md", "sha256": "733cd426087483cf3116973271e0efa64b6f36732aa0ebd4cbb346f532b52c81", "bytes": 86697, "note": "supersession header note only; not reviewed, carries no approval"}
  ],
  "propagate_to": [
    "hsef_v53_remaining_priority_11_15_2026-10-11\\enhancer-promoter-looping\\"
  ],
  "propagation_verified": "All 14 files shared between the two folders hash-match after the copy, restoring the identity that held before the edits. sol61-original backups exist in both folders.",
  "divergent_copies_not_touched": [
    "hsef_v53_popularity_ranks_46_50_2026-10-09\\enhancer-promoter-looping\\enhancer-promoter-looping.review.md",
    "hsef_v53_remaining_priority_11_15_2026-10-11\\enhancer-promoter-looping\\prior-edition\\enhancer-promoter-looping.review.md"
  ],
  "builder_defect_for_lead": "current-source-checkpoint.review.md is a generic build-tool working filename; two different hypotheses in this delivery ship a file of that exact name (enhancer-promoter-looping and super-enhancer-cell-identity), which is what caused the inventory to list it as a separate review. The builder should emit a slug-specific name, and the shipped review's link to the 'current source checkpoint' then needs re-pointing.",
  "package_level_strings_for_lead": [],
  "consensus_questions": [
    "At a native mammalian locus, has any experiment rapidly and reversibly released enhancer-promoter contact while leaving enhancer activity, transcription-factor occupancy and polymerase competence intact, and measured the effect on transcriptional bursting?"
  ]
}