This checklist runs at multiple checkpoints — end of each section, end of each writing day, before peer-review phase, before submission.
v3 changes from v2: Dropped "hedging language used", "80-120 references", and format-only metric checks. Replaced with substance checks (citation integrity, conclusion direction, verdict presence, structural discipline).
These are non-negotiable. Any failure must be fixed before continuing.
xxx, [TBD], x):xxx)[N] reconciliation — spot-check 10 random citations per sectionSee CITATION_INTEGRITY.md for the full 5-rule protocol.
## 1., ### 1.1)####) absent from body — deeper grouping via bold lead-in **Topic.**$$...$$) appear only in Boxes, not in body paragraphs[ ] Body uses category descriptors with table cross-reference
# Quick check
for name in HeartFlow Cleerly Caristo "Keya Medical" "Shukun Technology"; do
grep -n "$name" manuscript_draft.md | grep -v "| $name |"
done
# Expected: 0 hits per name
[Figure placeholder] strings before submission# Numbered headings
grep -cE "^#{2,4} [0-9]" manuscript_draft.md
# Expected: 0
# Heading depth violation
grep -c "^#### " manuscript_draft.md
# Expected: 0
# Placeholder DOIs
grep -c "xxx\|x):xxx\|\[TBD\]" manuscript_draft.md
# Expected: 0
# LLM tell phrases
for tell in "has shown promising" "may suggest" "interestingly," "in recent years," "it is worth noting"; do
echo "=== $tell ==="
grep -nF "$tell" manuscript_draft.md
done
# Expected: 0 per tell
# Vendor names in body
for vendor in HeartFlow Cleerly Caristo; do
count=$(grep -c "$vendor" manuscript_draft.md)
in_table=$(grep "| $vendor " manuscript_draft.md | wc -l)
echo "$vendor: total $count, in table $in_table, in body $((count - in_table))"
done
# Expected: in body == 0 for each
# Inline equations
grep -n '\$\$' manuscript_draft.md
# All hits should be inside Box context (check 2 lines before)
# Verdict-sentence presence
grep -nE "currently the most|has yet to demonstrate|best understood as|next [0-9]+ years will" manuscript_draft.md
# Expected: ≥ 3 hits
# Citation count (no quantity target — but useful for sanity)
grep -cE "^[0-9]+\." manuscript_draft.md
# Use as input for body↔bib reconciliation
These were structural illusions of quality. They've been replaced with substantive checks above.
When a checklist item fails during writing:
| Severity | Examples | Action |
|---|---|---|
| CRITICAL | Placeholder DOI, wrong-author list on real paper, citation direction flipped | STOP and fix immediately. These are reviewer-facing trust-killers. |
| HIGH | Body↔bib drift, vendor name in body, verdict absent in axis section | Fix before completing the current section. |
| MEDIUM | Heading numbered, equation inline | Fix at section end. |
| LOW | Multi-citation bracket > 4 refs, table > 20 rows | Note and address during peer-review phase. |