Final manuscript check: AI disclosure, word count, citations and DOCX integrity

The last pass should begin outside the manuscript. Save the target journal's author instructions, article-type page, AI policy and submission-portal prompts with the access date. The ICMJE Recommendations say to follow an individual journal's instructions when they differ from ICMJE and currently identify the Recommendations as updated January 2026. That is the right hierarchy: the journal and the live portal govern the submission; a publisher page, society guideline or this checklist supplies context, not permission.

Write a one-page requirement record before editing. Name the journal, manuscript type, deadline and time zone, required template, anonymisation model, reporting checklist, file types, limits and every portal-only question. Save the actual pages or PDFs, not only bookmarks: instructions can change during revision, and the record lets co-authors see which version you applied.

Resolve contradictions now. If the publisher policy says one thing but the journal page or portal asks something narrower, record both and ask the editorial office when the answer changes what you would disclose or upload. Do not silently choose the easier instruction. A dated written reply belongs in the submission record.

Freeze requirements, not assumptions: exact journal, exact article type, exact submission round and exact access date.

Do not answer an AI question from the product name alone. Reconstruct what the tool actually did: grammar correction, translation, prose generation, outlining, code generation, data analysis or figure creation can fall under different rules even when one application performed all of them. Use your work log and chat history; do not rely on a vague memory that the tool was used only for editing.

ICMJE's current authorship guidance says AI tools cannot be authors or co-authors. It places writing assistance in Acknowledgements, use for data collection or analysis and figure generation in Methods, and says authors should disclose use in the cover letter too. Humans remain responsible for accuracy, attribution, source checking and plagiarism. Those rules apply to journals that use ICMJE guidance; other venues can require different wording, locations or prohibitions.

For a cross-publisher comparison, use the separate AI disclosure policy guide, then re-open the target journal's own rules. Keep a row for each use: tool and version, date, purpose, affected section, output retained, data sent, human verification and disclosure location. The declaration should state actions, not advertise the tool or claim that AI merely 'helped.'

Check the manuscript, acknowledgements, Methods, cover letter and portal answers as one system. A statement in one location does not automatically answer a separate portal question. If a use may have violated confidentiality, image or research-integrity rules, disclosure does not retroactively make it permissible; pause and give the editor or integrity office an accurate account before submission.

Classify by purpose, disclose in the required places, and make every version of the account consistent.

There is no universal journal word-count formula. Record what this journal includes and excludes before trying to shorten anything: title page, structured or unstructured abstract, main text, quotations, footnotes, acknowledgements, declarations, table text, figure legends, references and online supplements may be treated differently. Also record separate limits for the title, abstract, highlights and individual sections.

The ICMJE manuscript-preparation guidance gives a useful medical-journal example: the text word count excludes the abstract, acknowledgements, tables, figure legends and references, and authors should also report a separate abstract word count. That is not a universal rule. Copying that definition into a humanities, engineering or even another medical journal can produce the wrong number. The target journal's definition controls.

After each pass, recount using the same recorded method. Do not remove a reporting-checklist item merely because the main-text counter is high, and do not move substantive text into a caption or supplement unless the journal permits it and readers can still interpret the work. If the paper remains over the limit, keep a cut log: removed passage, reason, affected citation or cross-reference, and where essential material was relocated.

Freeze high-risk content during language work: exact data, units, equations, code, search strategies, eligibility rules and required legal or ethics statements. The Methods and Results revision checklist explains how to separate expression from scientific invariants. A lower detector score or cleaner sentence never proves that a factual revision is correct.

Citation work has two layers. First verify evidence: every in-text citation still supports the claim beside it, quotations and page locators are accurate, no source became detached when sentences moved, and every cited item has one reference-list entry and vice versa. Only then standardise punctuation, ordering, names, titles, dates, identifiers and journal abbreviations to the verified journal style. Authors remain responsible for reference accuracy under ICMJE guidance; a reference manager or converter cannot assume that responsibility.

Use the journal's named style and examples, not a generic label such as 'Harvard.' If the required variant is unclear, the Harvard variant guide shows how to locate the authoritative local specification. Convert a small sample containing your hardest source types, inspect it, then process the full list. Never repair a citation problem by sending the surrounding argument to an AI humanizer.

Word fields are live document objects, not ordinary text. Copy-paste, unlinking or accepting changes can leave a visually plausible but stale number. Follow the Word fields and long-document guide, update on a working copy, reopen the file and search for field-error text. Then compare the abstract, main text, tables, figures, captions and supplements for the same sample size, label, unit and result.

Copy this list into the project record and add an owner, completion date and evidence link to each line. A tick should mean that someone opened the relevant source or file and verified it; it should not mean 'probably handled.'

1. Save the governing instructions. Archive the target journal author guide, article-type page, publisher and journal AI policies, portal wording and access dates.
2. Confirm the submission contract. Record manuscript type, every required file and template, reporting checklist, anonymisation rule, deadline, clock time and time zone.
3. Classify every AI use. Map each purpose to the journal rule and required manuscript, cover-letter and portal disclosure; reconcile all versions of the statement.
4. Define the exact word-count scope. Write down what is included and excluded plus separate title, abstract, highlight and section limits; save the counted values.
5. Complete substantive edits and humanizing first. Verify every changed claim, number, qualifier and citation against the authors' source of truth.
6. Condense second. Cut repetition and low-value framing while preserving required reporting items, evidence, uncertainty and limitations; recount with the same scope.
7. Standardise citations last. Reconcile claims to sources, run the forward/reverse reference check, then apply the journal's exact style and inspect difficult source types.
8. Update every document object. Refresh fields, contents, cross-references and numbering; reconcile tables, figures, captions, footnotes, equations and supplements with the text and upload set.
9. Produce and inspect a clean copy. Resolve tracked changes and comments, inspect visible markup, headers and footers, then run metadata inspection on a duplicate rather than the sole source file.
10. Archive the working record. Keep the source document, dated clean submission copy, requirement and policy snapshots, AI-use log, cut log and completed checklist with unambiguous versions.
11. Upload the complete package. Match each required file to the manifest, use intelligible filenames, verify the selected article type and replace stale versions rather than trusting upload order.
12. Open the portal-generated PDF before confirming. Read it page by page for conversion, order, identity, font, symbol, table, figure, link and supplement problems; correct the source or upload and regenerate until it matches the intended submission.

Use a manifest rather than memory: filename, purpose, source version, clean/anonymised status, required format, portal slot, uploaded checksum or timestamp, and reviewer initials. Include title page, main manuscript, figures, tables, supplements, cover letter, declarations, reporting checklist and any response document that this submission round requires. Mark genuinely inapplicable items as `N/A` with a reason so an empty cell cannot be mistaken for completion.

This checklist reduces preventable submission errors; it does not certify journal compliance, research validity, acceptance or any detector result.

Keep the editable source with its history, then make a dated submission copy. In the source, resolve every tracked change and comment deliberately: accept or reject changes one by one where meaning matters, answer unresolved comments, and use Word's All Markup view to inspect deletions, formatting changes and comment threads. Turning off Track Changes or switching to No Markup only changes the view; it does not remove revisions.

On the duplicate, use Word's `File > Info > Check for Issues > Inspect Document`. Microsoft's Document Inspector guidance warns that removed information may not be recoverable and recommends working on a copy. The inspector can identify comments and revisions, document properties and personal information, headers, footers and watermarks, hidden text, custom XML and invisible content. Review each finding before removal.

Document Inspector is not a complete anonymisation method. It cannot judge whether an acknowledgement names the lab, a self-citation reveals the authors, a filename contains an identity, or a screenshot exposes a path. It also does not replace visible All Markup review. Apply only the target journal's blind-review rule: removing every contextual clue can itself damage a methods section or required disclosure.

• Reopen the clean DOCX after inspection and verify it is not corrupted, protected unexpectedly or missing links and fields.
• Search for author names, institutions, initials, email addresses, grant identifiers, tracked-change balloons and `Error!` field messages when blind review applies.
• Compare page count, section order, tables, figures, equations and reference-list ending against the reviewed source.
• Give source and clean copies distinct dated filenames; never overwrite the only version that preserves revision evidence.

After upload, stop checking the local DOCX. Confirm the portal shows the intended article type, title, author order, affiliations, corresponding author, abstract, keywords, funding, conflicts, data statement, AI declaration and file designations. Compare manually entered metadata with the manuscript; a correct document does not repair a wrong portal field.

Many systems assemble a review PDF or proof from uploaded files. Opening that generated PDF before final confirmation is a HumanPen workflow recommendation, not an ICMJE rule. Read from the first title-page element to the last supplement callout. Check file order, missing pages, anonymous versus named version, substituted fonts, mathematical symbols, superscripts, hyperlinks, line breaks, clipped tables, figure resolution, caption placement and reference characters.

Only confirm after a named author has reviewed the generated artifact and the portal summary. Save the final PDF or confirmation preview when the system permits, the submission identifier, timestamp and receipt. If a co-author makes a late change, do not patch just the portal copy: return to the versioned source, rerun the affected checks, replace the files and inspect the regenerated PDF again.

The button below opens HumanPen's journal-submission workflow for revising the DOCX prose. It does not submit to the journal or guarantee policy compliance, acceptance or a detector outcome. Keep the source, compare the returned document, verify citations and invariants, and then resume this checklist at the appropriate step.

Final means reproducible: another co-author can identify the governing rules, the exact clean file, every uploaded component and the PDF that was actually approved.