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update-abstract-rename

Update abstract: rename ABSTRACT.md to ABSTRACT_BoG.md; create ABSTRACT_nature.md in Nature format

Metadata

Statusdone
Assignedagent-883
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Modelclaude:opus
Created2026-05-06T01:43:32.430632376+00:00
Started2026-05-06T02:20:33.447961908+00:00
Completed2026-05-06T02:22:41.709149551+00:00
Tagspaper-prep, abstract, nature-format, eval-scheduled
Tokens502375 in / 8190 out
Eval score0.94
└ blocking impact0.95
└ completeness0.95
└ constraint fidelity0.70
└ coordination overhead0.95
└ correctness0.95
└ downstream usability0.90
└ efficiency0.95
└ intent fidelity0.76
└ style adherence0.95

Description

GOAL: split the canonical abstract into two anchored versions — the BoG-talk-aligned current one (renamed) and a tight Nature-format one for the manuscript.

CONTEXT: We just produced a 15-slide BoG v2 talk plan (slides/v2/SLIDES_v2_PLAN.md) that incorporates the full v2 results: NJ-tree named clades (PAR1/PAR2/acrocentric/10p-18p/{22q,21q,19q,1q,13q,17q}/4q-10q DUX4), Hi-C bulk Mantel ρ=0.66→0.79 with exclusions, single-cell 3D in GM12878+sperm, mouse meiotic Hi-C with zygotene peak ρ=0.715, pedigree direct evidence (538 patches, 92% within community, 133 gene-conversion-like + 16 crossover-like). The current ABSTRACT.md (the talk-aligned version) ran ~360 words. Nature Article format requires ≤200 words (current limit; verify against nature.com/nature/for-authors/formatting-guide if you have web access). The BoG version stays as-is (rename only); the Nature version is a fresh tight rewrite.

INPUTS:

  • paper_prep/synthesis/ABSTRACT.md (current, to be renamed)
  • paper_prep/synthesis/CROSSWALK.md (chapter-to-claim map)
  • paper_prep/synthesis/AUDIT_REPORT.md
  • paper_prep/synthesis/REWRITE_PLAN.md (changes from CROSSWALK §6)
  • slides/v2/SLIDES_v2_PLAN.md + slides/v2/slide_*.md (v2 talk content)
  • end-to-end-report/ (Andrea's 14-chapter substrate; especially ch.07 integrated, ch.11 summary, ch.14 pedigree, ch.05 Hi-C)

PIPELINE:

  1. git mv paper_prep/synthesis/ABSTRACT.md paper_prep/synthesis/ABSTRACT_BoG.md (preserves current as the talk-aligned version; do NOT modify content).
  2. Write paper_prep/synthesis/ABSTRACT_nature.md as a NEW Nature-format abstract:
    • ≤200 words (hard cap)
    • No citations
    • No section headers; structured as a single paragraph or 2 short paragraphs
    • Implicit arc: opening significance/context → method (implicit pangenome graph + 466 HPRC v2 haplotypes + ~12% pairwise sampling/ER connectivity) → empirical findings (extended interchromosomal homology comparable to PAR2 + named cladistic clades + population structure + 3D mechanism + meiotic bouquet via mouse zygotene + pedigree direct evidence of ongoing exchange) → significance/thesis (ongoing recombination + concerted evolution).
    • Title and authors at top, matching BoG version: 'Concerted evolution and unorthodox recombination of human subtelomeres' / 'Andrea Guarracino and Erik Garrison'.
    • Add a frontmatter line indicating venue: 'Target: Nature (companion to HPRC v2 main paper)'.
    • Numbers to include if word budget allows: 466 haplotypes, ~12% pairwise sampling (or 230× ER threshold), 538 pedigree patches at 92% within community, mouse zygotene Mantel ρ=0.715. Drop the least essential if cap is tight.
  3. Single commit: 'docs: split abstract into ABSTRACT_BoG (renamed current) + ABSTRACT_nature (new ≤200-word Nature-format version)'.

ACCEPTANCE:

  • paper_prep/synthesis/ABSTRACT_BoG.md exists (renamed; byte-identical to prior ABSTRACT.md modulo any added frontmatter line)
  • paper_prep/synthesis/ABSTRACT_nature.md exists; word count ≤ 200 (excluding title/authors/frontmatter); no citations; covers all 8 canonical claims (C1-C8) at high level
  • Single commit
  • wg artifact records both files

DO NOT modify CROSSWALK.md, AUDIT_REPORT.md, REWRITE_PLAN.md, slides/v2/, end-to-end-report/, or any figure.

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