{
  "slug": "super-enhancer-cell-identity",
  "file": "super-enhancer-cell-identity.review.md (shipped review)",
  "authoring_model": "Sol 6.1",
  "adversarial_reviewer": "Claude Opus 5.5 (Anthropic)",
  "date": "2026-10-14",
  "level_before": "Β",
  "level_after": "Β",
  "confidence_before": "Moderate",
  "confidence_after": "Moderate",
  "pmids_checked": 66,
  "pmids_failed": 0,
  "claims_spot_checked": 10,
  "findings": [
    {
      "id": "S1",
      "severity": "Major",
      "location": "decisive-perturbation inventory, paragraph after the tally",
      "original": "Pivotal symptom studies remain informative; missing registration or mediator verification is an audit limitation, not evidence that dopamine has no effects or that antipsychotics lack efficacy.",
      "corrected": "Pivotal native-locus perturbations remain informative; a missing activity-matched comparator or unverified class-specific mediation is an audit limitation, not evidence that enhancer clusters lack regulatory effects or that super-enhancer calling has no descriptive utility.",
      "evidence": "Template bleed from an unrelated dopamine/antipsychotic case; neither term appears anywhere else in the review."
    },
    {
      "id": "S2",
      "severity": "Minor",
      "location": "decisive-perturbation inventory, tally sentence",
      "original": "Tally: 0 positive ... 10 screened discriminating contrast units. (eight items printed above)",
      "corrected": "Same counts, plus a clause stating that the ten discriminating contrasts are a different set from the eight decisive perturbations, naming records [3] and [7] as the difference.",
      "evidence": "Score card evidence_inventory: decisive_perturbation true for 8 records ([4],[5],[6],[8],[9],[10],[36],[61]); discriminating_contrast true for 10 (plus [3],[7]). Both numbers correct; the prose did not say they count different things. Resolves the item the earlier checkpoint pass flagged and left open."
    },
    {
      "id": "S3",
      "severity": "Minor",
      "location": "final score / M-S-D role derivation, revision-checkpoint blockquote, REVIEWER NOTES, four Access/status lines",
      "original": "(step1)..(step5); three Step15 scoring blocks; Prior ranks43/44 and rank49; ErratumIn:",
      "corrected": "(step 1)..(step 5); three Step 1-5 scoring blocks; Prior ranks 43/44 and rank 49; Erratum In:",
      "evidence": "Known renderer defect dropping spaces around numerals."
    },
    {
      "id": "S4",
      "severity": "Minor",
      "location": "scorecard final_score.confidence_rationale",
      "original": "66 primary reports with 12 selected partial-body examinations; density, heterogeneous controls and incomplete access set the confidence, not correctness.",
      "corrected": "Rationale re-derived on evidence density and reproducibility, access depth struck; Moderate stands.",
      "evidence": "Lead policy on confidence bands. Remaining determinants are substantive: additive alpha-globin series, cluster deletions ranging from dispensable to near-essential, strong non-called enhancers, interchangeable facilitators, unresolved phase specificity, few activity-matched comparators."
    },
    {
      "id": "S5",
      "severity": "Editorial",
      "location": "current-source-checkpoint.review.md banner and ADVERSARIAL REVIEW AND APPROVAL heading, both copies",
      "original": "Build intermediate carried a plain adversarial banner and approval section with no indication that it is not a review.",
      "corrected": "Banner and section preamble amended to state the file is a superseded build intermediate, that the pass was performed on the intermediate before that was understood, and that it does not approve the Super-enhancer Model review; the approved review is named.",
      "evidence": "Lead adjudication. The earlier pass was genuine and produced the template-bleed and tally findings carried into S1 and S2; deleting its record would erase a review that happened. Kept and qualified instead. Applied identically to both copies and hash-verified."
    }
  ],
  "rejected_findings": [
    "Best-supported rival label correct: models_evaluated[0] is the rank-1 model with is_nominal false.",
    "Weakest-link aggregation min(B,B,G)=B correct and matches the printed headline.",
    "Momentum 'Mechanistic only' correct; the artifact states no named ongoing class-discriminating experiment is asserted.",
    "No collective-author defect of either known form; no leading-comma instance and no organisation fragment as a surname.",
    "Reference 66 prints the italicised Emu that the PubMed title field drops; the review is more accurate than the metadata.",
    "PubMed titles dropping italicised gene/marker names at references 15 and 24 - declared non-error.",
    "Banner phrase '54 complete abstract/status examinations': the document claims complete abstracts, never complete papers, and the notes record zero complete-paper audits. Not an overclaim.",
    "No spliced 'earlier adversarial approval' sentence present.",
    "Scope-matched sensitivity reported as B for a conjunctive claim: argued both ways, left as published; the headline is set by the preregistered weakest-link rule regardless."
  ],
  "lead_policy_applied": {
    "confidence_bands": "Access depth struck; band re-derived. Moderate stands on reproducibility and control-design reservations.",
    "momentum": "Value is 'Mechanistic only'; the completed-work test does not bite.",
    "collective_authors": "Both variants checked, including organisation-fragment surnames and dropped nobiliary particles. None found.",
    "checkpoint_reconciliation": "Lead-adjudicated: banner and approval retained but qualified on both checkpoint copies; approval scoped to the intermediate only."
  },
  "validator": "PASS - 0 fail, 0 warn, 31 pass",
  "scorecard_changed": true,
  "related_files": {
    "build_intermediate": "current-source-checkpoint.review.md - marked superseded; reviewed separately, see ADVERSARIAL_REVIEW.current-source-checkpoint.md",
    "note": "The shipped review and the build intermediate are NOT byte-identical: they differ in registered-claim wording, selection provenance and sections carried."
  },
  "residual_limitations": [
    "Twelve of 66 records examined at partial-body depth.",
    "Five requested targets unavailable."
  ]
}