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manuscript-final-housekeeping

Manuscript final housekeeping polish

Metadata

Statusdone
Assignedagent-2563
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Created2026-06-19T11:01:43.300331572+00:00
Started2026-06-19T11:03:00.220897933+00:00
Completed2026-06-19T11:10:46.829697611+00:00
Tagsmanuscript, submission, final-polish, eval-scheduled
Eval score0.94
└ blocking impact0.96
└ completeness0.94
└ constraint fidelity0.10
└ coordination overhead0.93
└ correctness0.95
└ downstream usability0.94
└ efficiency0.90
└ intent fidelity0.52
└ style adherence0.95

Description

Final focused manuscript housekeeping pass. Apply only the requested factual/mechanical edits. Do not reopen the conceptual framing, do not soften the paper, and do not add new analyses or defensive text.

Context from author review: The current framing is strong and should stay. The abstract and Introduction now correctly acknowledge established subtelomeric exchange, define the advance as a systematic population-scale map, and position acrocentric/Robertsonian work as precedents generalized here. The title should stay. The conclusion language asserting recurrent ectopic exchange while reserving uncertainty for causal direction and molecular submechanism should stay. The non-PHR flank control is correctly prominent and should stay.

Required edits:

  1. Restore abstract references. Nature currently asks for a fully referenced summary paragraph. Retain the present abstract wording, but restore citation markers after the first two sentences: citations equivalent to [1-6] after the first sentence and approximately [18-20] after the second. Use normal LaTeX citation commands appropriate for the existing bibliography/order. Do not re-bold the abstract body.
  2. Compress the new pedigree tract-length main-text paragraph. Replace the detailed lower-merge interval count and percentages in published NCO/CO length ranges with this single sentence, preserving candidate/compatibility caution: "A lower-merge rerun recovered intervals spanning published conversion- and crossover-associated tract scales, although tract length alone does not assign event-level mechanism." Keep the full analysis in Methods and/or existing script/report artifacts if already present; do not delete reproducible analysis outputs.
  3. Keep the current closing formulation: shaped and maintained by recurrent ectopic exchange, with uncertainty limited to sequence-proximity directionality and conversion, crossover-associated repair, or larger exchange subclasses.
  4. Change "PAR1 and PAR2 carry the obligate sex-chromosome crossover" because the obligate male crossover is associated with PAR1. Keep PAR2 context accurate without overexplaining.
  5. Distinguish the disease-permissive 4q35 D4Z4 configuration from the homologous 10q26 array.
  6. Write "a 13-fold lower B/W ratio," not "a 13-fold difference."
  7. Use "uniquely mappable non-PHR flanks" if and only if the Methods/analysis formally supports that description; otherwise use the strongest accurate equivalent without weakening the point.
  8. Remove "panmictic population" and correct or define the comparison estimate it is attached to.
  9. Replace "a non-trivial fraction of the genome" with "a substantial amount of subtelomeric sequence."
  10. Clean bibliography annotations, malformed symbols and page ranges if present in the rendered/reference source. Do not invent bibliographic facts; use existing BibTeX fields and stable formatting.
  11. Remove blank contribution sections and empty Tables heading if present.

Scope constraints:

  • No new analysis.
  • No new evidence-hierarchy paragraph.
  • No conceptual rewrite beyond the listed edits.
  • Do not demote the HPRC v2 population-scale map or the non-PHR flank control.
  • Preserve cautious pedigree language: candidate, compatible with, orthogonal confirmation where already appropriate.
  • Keep title unchanged.

Validation:

  • submission/paper.tex contains abstract citations again and no whole-abstract textbf wrapper.
  • The main text has only the compressed tract-length sentence, while detailed analysis remains outside the main Results narrative or in Methods/artifacts.
  • All listed mechanical phrases are fixed or explicitly absent.
  • No empty Tables heading or blank contribution sections remain in the PDF/source.
  • Build from submission succeeds using the repository compile path; final paper.log has zero undefined-reference hits.
  • Commit changes with WG provenance message, e.g. feat: manuscript-final-housekeeping (agent-NNN), and push if the worker workflow supports it.

Depends on

Required by

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