Submission Preflight (pnasnexus-submission)

When to trigger

• The manuscript is "done" and you're about to upload via the submission portal (pnasnexus.msubmit.net).
• You want a single gate that confirms every other pnasnexus-* skill's output landed.
• You are completing a transfer from PNAS and need to confirm nothing is missing.
• A revision is going back and you need to confirm nothing regressed.

Master preflight checklist

Fit & venue

• Clears the broad, cross-disciplinary significance bar (pnasnexus-fit); a reader from another division would care.
• PNAS Nexus is the right venue (not better at flagship PNAS or a field journal).
• If transferring from PNAS: decline was about fit/priority, not soundness; prior reviews attached.
• Title is declarative, specific, parseable by a non-specialist.

Open access, APC & license

• Confirmed gold OA; APC figure obtained live from the OUP calculator (category + corresponding-author region) — not from memory (pnasnexus-openaccess).
• Waiver/discount checked (LMIC waiver/discount, Read & Publish, membership, discretionary).
• License chosen: ☐ CC BY 4.0 ☐ CC BY-NC 4.0 — CC BY if a funder mandate applies.
• Funder open-access requirements (license + deposit) satisfied.
• (Reminder) no Direct/Contributed track — standard editor-assigned review.

Article type, structure & length

• Article type chosen: ☐ Research Report ☐ Brief Report ☐ Registered Report (S1/S2) ☐ Perspective ☐ Review.
• Within the page budget for that type (Research Report: 6 pp preferred / 12 max); captions, legends, abstract, and Significance Statement counted.
• Order: Title / authors / Significance / Abstract / Intro / Results / Discussion / Materials and Methods (in main text) / back matter.
• Materials and Methods present in the main text (not solely in SI).
• Classification chosen: research area (Biological-Health-Medical / Physical-Engineering / Social-Political) + subcategory.

Significance Statement & abstract

• Significance Statement 50–120 words (Research Reports / Stage 2 Registered Reports), for a broad audience, distinct from the abstract.
• Abstract ≤ 250 words, single paragraph, no headings, ≥1 quantified result.

Figures & display items

• Within the graphical-element budget (~4 for a 6-pp Research Report; secondary items → SI).
• Sized to journal column widths; fonts legible at print size.
• Data shown (points + n); error bars defined; scale bars present.
• Colorblind-safe; color used where it helps (OA, online); raw unprocessed images retained.

Statistics & reproducibility

• Each claim: effect size + CI + n + test + assumptions.
• Biological vs technical replication clear; sample-size rationale stated.
• Randomization/blinding reported or justified; multiplicity controlled.
• Analysis code + scripts public and archived (DOI).

Data, code, materials, ethics

• Data, code, materials, and protocols deposited in a public repository with accession numbers/DOIs (mandatory upon publication; no "on request" only for primary data).
• Data and Code Availability Statement drafted and compliant; datasets/software cited with the [dataset] tag.
• Materials/reagent sharing plan; ethics approvals (IRB/IACUC/permits) as needed.

References

• Any readable style accepted at submission — but the list is consistent, complete, and fully resolvable; DOIs added.
• Data/software cited as formal references with the [dataset] tag.

Required files & metadata

• Main text (title, Significance Statement, abstract, body, Materials and Methods, references).
• Figures at required resolution + figure legends; tables.
• Supporting Information (extended methods, supporting figs/tables, supplementary text); Datasets if any.
• Cover letter (advance + broad significance; article type; transfer note if applicable).
• Author list, affiliations, ORCIDs, corresponding author (drives APC/waiver eligibility — set deliberately).
• Author contributions, competing interests, funding statements.
• Classification + keywords entered in the submission system.

Final integrity sweep

• No over-claiming beyond the evidence (re-read the Significance Statement, abstract, and last paragraph).
• Significance Statement is genuinely broader/plainer than the abstract — not a duplicate — and within 50–120 words.
• Every figure's n, error bar, and test are defined in its legend.
• All accession numbers/DOIs are live and correct.

Templates

• templates/checklist.md — copyable preflight checklist.
• templates/cover_letter_template.md — PNAS Nexus cover-letter scaffold (significance + article type + transfer note + suggested reviewers).

Output format

【Article type】 Research Report / Brief Report / Registered Report / Perspective / Review
【OA/APC/license】 APC confirmed-live; waiver path; license (CC BY / CC BY-NC); funder-compliant?
【Transfer from PNAS?】 N/A | yes (reviews attached; decline was fit/priority)
【Blocking gaps】 [...]  (must fix before upload)
【Warnings】 [...]       (should fix)
【Files ready】 main / figures+legends / SI / cover letter / metadata
【Verdict】 GO / NO-GO + the top 3 fixes
【Next】 submit | pnasnexus-rebuttal (after decision)

Anti-patterns

• Do not upload before the APC, waiver eligibility, and license are settled (pnasnexus-openaccess).
• Do not upload before data/code are deposited with accession numbers/DOIs.
• Do not submit without the Significance Statement (50–120 words) and the classification.
• Do not let the Significance Statement duplicate the abstract.
• Do not put Materials and Methods only in Supporting Information.
• Do not rely on memory; run the checklist top to bottom.