# Consistency Decisions — Project Tolera Final Package
_Locked with Ruth-Anne, before editing. Single source of truth for front/back matter and cross-deliverable consistency._

## 1. Authorship (all 3 manuscripts)
**Byline:** `Ruth-Anne Pai, PhD` — sole author.
- Claude AI is **removed from the byline** and disclosed instead in a standardized AI-use statement.
- Rationale: bioRxiv / ICMJE / journal policy prohibits listing an AI tool as an author (authorship requires accountability a tool cannot hold). Transparency is preserved via the disclosure block.

## 2. Affiliations & contact (all 3 manuscripts)
```
Ruth-Anne Pai, PhD¹,²
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
```

## 3. Standardized front-matter disclosure banner (all 3, verbatim)
> **Preprint — not peer reviewed.** This manuscript was generated with substantial AI assistance (Anthropic Claude Science platform) under human direction.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.

(pMHC keeps its extra subject-area line: "Subject area: Immunology (secondary: Bioinformatics / Molecular Biology).")

## 4. Standardized end-matter blocks (all 3, in this order)
- **Funding.** This work received no external funding. It was conducted during the Built with Claude: Life Sciences Hackathon (2026).
- **Conflicts of Interest.** The author is a person living with eosinophilic esophagitis and the founder of Pai Advisory, LLC. No other competing interests are declared.
- **Data & Code Availability.** All input data are public (sources cited in-text). Designed constructs, structures, analysis outputs, and reusable skills are openly available at https://ruthannepai.netlify.app and https://github.com/ruthannepai-tech.
- **AI-use disclosure.** This research was performed by the author using Anthropic's Claude Science platform for data mining, computational protein design and structure prediction, analysis, and drafting. The author directed the scientific strategy, made all decisions, and is responsible for the content. Claude Science also served as a self-correcting check that flagged and corrected over-claims during the work.
- **Acknowledgments.** Built with Claude: Life Sciences Hackathon — organized by Anthropic, Gladstone Institutes, and Cerebral Valley.

## 5. EAC / Barrett's stream framing
**Full third stream everywhere** — co-equal third manuscript across site, deck, and submission.
Numbers move from "2 manuscripts" → "3 manuscripts" / "three integrated streams". Secondary framing (usable in prose): EAC is also *proof the Specialist Agent generalizes to a new, unrelated disease*.

## 6. Manuscript delivery
Non-destructive: create `…__harmonized` **copies** in the same Drive subfolders; originals untouched.

## 7. Canonical names / URLs (all deliverables)
- Project name: **Project Tolera**
- Live site (canonical): **https://ruthannepai.netlify.app**  ⚠️ footer of current site also shows `ruthannepai.com` — treated as secondary contact link; confirm which is primary.
- GitHub org: **github.com/ruthannepai-tech**
- Streams (canonical names): (1) **pMHC-II tolerance** (personalized antigen-selection engine), (2) **CCL26 / POSTN** effector-target binders, (3) **EAC / Barrett's** dual-arm program (GUCY2C + DKK1).
- Person-first language everywhere: "person living with EoE" (not "EoE patient/sufferer").

## 8. Disclosures on non-manuscript deliverables
Website + deck + submission each carry a visible, plain-language version of: AI-generated, not peer-reviewed, in-silico / not clinically validated, not medical advice.