# Manuscript Consistency Report
_Harmonization of the three Project Tolera manuscripts. Science bodies were left untouched; all edits are front-matter, disclosures, and end-matter._

## Standard applied (from consistency_decisions.md)
- **Byline:** `Ruth-Anne Pai, PhD¹,²` — sole author. Claude AI removed from all bylines.
- **Affiliations:** ¹ Citizen Scientist, EoE patient-researcher; Built with Claude: Life Sciences Hackathon (June–July 2026); ² Pai Advisory, LLC.
- **Correspondence:** Ruth-Anne Pai (Pai Advisory, LLC) — advising@ruthannepai.com.
- **Front-matter disclosure banner (verbatim, all 3):** "Preprint — not peer reviewed. This manuscript was generated with substantial AI assistance (Anthropic Claude Science platform) under human direction. All results are computational (in-silico); no experimental validation has been performed. This document is research and informational content only and is not medical advice."
- **End-matter (all 3):** Funding · Competing interests · Author contributions · AI-use disclosure · Acknowledgments (naming Anthropic, Gladstone Institutes, Cerebral Valley), plus each manuscript's existing Data & Code Availability.

## Per-manuscript changes

### pMHC-II (`EoE_manuscript_personalized__harmonized.docx`)
- Removed "and Claude AI (research support)" from byline; removed the Anthropic-platform affiliation line (³).
- Standardized correspondence line and preprint/disclosure banner (kept the subject-area line).
- **Competing interests rewritten:** removed CZ Biohub employment and all IP-claim language per author instruction; retained the Hill/Spergel companion-diagnostic freedom-to-operate note (relevant only here).
- Added Funding block; added standalone AI-use disclosure; standardized Acknowledgments.

### CCL26 / POSTN (`CCL26_POSTN_Final_Manuscript_Main__harmonized.docx`)
- Removed "and Claude AI (research support)" from byline.
- Added missing affiliation line ² Pai Advisory LLC, correspondence line, and disclosure banner (previously had neither contact nor banner).
- Added full end-matter set (Funding, Competing interests, Author contributions, AI-use disclosure, Acknowledgements) — previously only "Data and code availability" existed.

### EAC / Barrett's (`EAC_manuscript_and_supplements__harmonized.docx`)
- **Replaced placeholders:** `[Author list to be finalized]` → sole author; `[Institution]` → the two standard affiliations; `[email]` → corresponding contact.
- Standardized disclosure banner.
- **Competing interests:** `[To be declared.]` → standardized statement (no Hill/Spergel note — not applicable to the cancer work).
- Fixed the author-contributions block: "Final author list … to be completed." → author named and responsible.
- Added Funding block; standardized Acknowledgements.

## Lay-summary misfile fixed
- The CCL26/POSTN Drive folder contained `lay_summary_pMHC_nanoparticle.docx` (wrong content/name for that folder).
- Uploaded a correctly-named `lay_summary_CCL26_POSTN.docx` (correct CCL26/POSTN plain-language content) into that folder, with a harmonized AI-generated/not-peer-reviewed/not-medical-advice footer.
- **Recommendation:** remove the stray `lay_summary_pMHC_nanoparticle.docx` from the CCL26/POSTN folder (leave the pMHC lay summary in the pMHC folder). Left in place pending your confirmation.

## Delivery status (non-destructive — originals untouched)
| File | Drive upload | Artifact |
|---|---|---|
| pMHC harmonized | ✅ uploaded to pMHC folder | ✅ |
| EAC harmonized | ✅ uploaded to EAC folder | ✅ |
| CCL26/POSTN lay summary (corrected) | ✅ uploaded to CCL26 folder | ✅ |
| CCL26/POSTN manuscript harmonized | ⚠️ connector upload failed twice (generic "Internal error encountered"; the ~2 MB file is the largest of the set, so a payload-size limit is the likely but unconfirmed cause) | ✅ saved as artifact — drag into Drive manually |

## Verification
All 12 automated consistency checks pass on all three harmonized files: sole-author byline, both affiliations, contact email, "not peer reviewed", "in-silico", "not medical advice", Funding block, Competing-interests block, hackathon acknowledgment, Gladstone named, and no CZ Biohub reference.