{
 "slug": "current-source-checkpoint",
 "actual_subject": "Super-enhancer Model of Cell Identity",
 "round": 2,
 "date": "2026-10-14",
 "authoring_model": "Sol 6.1",
 "adversarial_reviewer": "Claude Opus 5.5 (Anthropic)",
 "canonical_path": "hsef_v53_final_nine_2026-10-12/super-enhancer-cell-identity/current-source-checkpoint.review.md",
 "misfiling": {
  "explanation": "current-source-checkpoint.review.md is a build-tool working filename, not a review subject. This copy reviews the Super-enhancer Model of Cell Identity (remaining-priority position 16, editorial list 2026-10-09) and sits in case folders named for other slugs.",
  "same_review_copies": [
   "hsef_v53_final_nine_2026-10-12/super-enhancer-cell-identity/current-source-checkpoint.review.md",
   "hsef_v53_remaining_priority_16_19_2026-10-12/super-enhancer-cell-identity/current-source-checkpoint.review.md"
  ],
  "inventory_divergent_copies_are_a_different_hypothesis": [
   "hsef_v53_final_nine_2026-10-12/enhancer-promoter-looping/current-source-checkpoint.review.md",
   "hsef_v53_remaining_priority_11_15_2026-10-11/enhancer-promoter-looping/current-source-checkpoint.review.md"
  ],
  "different_hypothesis_subject": "Enhancer-Promoter Looping as Causal (57 primary reports) - group 14's assignment; not touched",
  "recommendation": "Have the builder emit <slug>.checkpoint.review.md; treat current-source-checkpoint as an artifact class, not a review slug."
 },
 "level_before": "Β",
 "level_after": "Β",
 "confidence_before": "Moderate",
 "confidence_after": "Moderate",
 "role_before": "reinforcing / stabilizing factor",
 "role_after": "reinforcing / stabilizing factor",
 "counts": {
  "critical": 0,
  "major": 1,
  "minor": 2,
  "editorial": 0,
  "flagged_not_fixed": 1,
  "distinct_string_corrections": 7,
  "occurrences_replaced": 7
 },
 "pmids_checked": 66,
 "pmids_failed": 0,
 "retraction_flags": 0,
 "claims_spot_checked": 10,
 "collective_author_bug_present": false,
 "validator": {
  "note": "no score card accompanies this file; indicative run paired with the sibling super-enhancer-cell-identity.scorecard.json using the bundled validator v2.3",
  "result": "PASS",
  "fail": 0,
  "warn": 0,
  "pass": 31,
  "output": "validator-current-source-checkpoint.txt"
 },
 "findings": [
  {
   "id": 1,
   "severity": "Major",
   "class": "misstatement/template-bleed",
   "location": "Decisive-perturbation inventory, paragraph after the tally",
   "old": "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.",
   "new": "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": "Boilerplate from a dopamine/schizophrenia case; neither dopamine nor antipsychotics appear anywhere else in this review or bear on its claim."
  },
  {
   "id": 2,
   "severity": "Minor",
   "class": "rendering",
   "location": "Evidence and causal interpretation, rubric-fit line",
   "old": "Rubric fit: Rubric03 applies",
   "new": "Rubric fit: Rubric 03 applies"
  },
  {
   "id": 3,
   "severity": "Minor",
   "class": "rendering",
   "location": "Final score / M-S-D, role-derivation paragraph",
   "old": "(step1) ... (step5)",
   "new": "(step 1) ... (step 5)",
   "occurrences": 5
  }
 ],
 "flagged_not_corrected": [
  {
   "issue": "Causal tally states 10 screened discriminating contrast units but the inventory prints 8 bracketed items ([4],[5],[6],[8],[9],[10],[36],[61]).",
   "also_in": [
    "hsef_v53_final_nine_2026-10-12/super-enhancer-cell-identity/super-enhancer-cell-identity.review.md",
    "hsef_v53_final_nine_2026-10-12/super-enhancer-cell-identity/super-enhancer-cell-identity.scorecard.json (causal_tally_audit.screened_discriminating_contrasts = 10)"
   ],
   "why_not_fixed": "Cannot determine whether two inventory entries were dropped in rendering or the count is wrong; the score card and the finalised review belong to group 17's assignment.",
   "owner": "lead / group 17"
  }
 ],
 "rejected_findings": [
  "Scope-matched sensitivity Β: argued both ways; the registered claim is conjunctive and no single subclaim's scope covers the conjunction, so the weaker conjunct stands. Headline is set by the preregistered weakest-link rule anyway.",
  "Weakest-link arithmetic min(Β,Β,Γ)=Β is correct.",
  "Identical Scope column for SC1-SC3 carries a pre-outcome scope qualifier, not the subclaim scope.",
  "Momentum 'Mechanistic only' carries its artifact.",
  "'Twelve selected body reports' is correct: twelve receipts exist and the final correction log says twelve; an intermediate build script's 'ten' was superseded.",
  "The review's refusal to reuse PMID 40592831's reversed EDL/soleus descriptors is correct handling of a source defect.",
  "Reference titles at #15 (PMID 33107387) and #24 (PMID 36138028) differ from PubMed only by PubMed dropping italicised gene and marker names."
 ],
 "propagate_to": [
  "hsef_v53_remaining_priority_16_19_2026-10-12/super-enhancer-cell-identity/current-source-checkpoint.review.md"
 ],
 "consensus_question": "When high-ChIP super-enhancer clusters are compared with conventional enhancer clusters matched for total activity, constituent number and promoter context, do native combinatorial deletions reveal non-additive interaction specific to the super-enhancer class?",
 "sha256_review_md_after": "90df53ff0bdc680494e8c7d2d82e6bb77c2edadc8825085b437c0aa5e3aad0da",
 "bytes_review_md_after": 99758
}