diff --git a/.gitignore b/.gitignore
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+# Windows "downloaded from the internet" marker files.
+# These carry no content (just zone/referrer metadata) and only appear
+# because files were unzipped on Windows before being copied into WSL.
+*:Zone.Identifier
+
+# LaTeX build artifacts
+*.aux
+*.bbl
+*.bcf
+*.blg
+*.fdb_latexmk
+*.fls
+*.log
+*.out
+*.run.xml
+*.synctex.gz
+*.toc
+*.loe
+*.lof
+*.lot
+*.nav
+*.snm
+*.vrb
+*.xdv
+
+# OS junk
+.DS_Store
+Thumbs.db
diff --git a/CLAUDE.md b/CLAUDE.md
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+# MDPI "AI in Medicine" manuscript
+
+## What this project is
+Writing a journal article for MDPI's **AI in Medicine** journal (short name
+`aimed`, ISSN 3042-6707), on predicting no-reflow / slow-flow complications
+after PCI from IVUS images.
+
+## Source material — reference only, not a source of facts
+Timeline, oldest first:
+1. [Reference/卒業論文_金子_最終.pdf](Reference/卒業論文_金子_最終.pdf) — the
+   original graduation thesis (Japanese).
+2. [Reference/main.tex](Reference/main.tex) / [main_ja.tex](Reference/main_ja.tex)
+   (+ their rendered [main.pdf](Reference/main.pdf) / [main_ja.pdf](Reference/main_ja.pdf))
+   — a later MIDL 2026 short paper built on the thesis.
+
+**The dataset and experiments have since changed.** These documents are
+useful for prose style, structure, and terminology — they are NOT a source
+of current facts. Never cite numbers, case counts, AUC/results, dataset
+descriptions, ethics approval numbers, etc. from these files as if they
+still hold for the new manuscript. Any such detail needed in the new paper
+must come from current data/results the user provides, not by copying it
+from these references.
+
+## The manuscript itself
+- [template.tex](template.tex) is the official MDPI template and will become
+  the actual manuscript — edit it in place rather than starting a new file.
+- **Not yet configured for this journal**: the `\documentclass` line
+  currently reads `[journal,article,submit,moreauthors]`; before submission
+  this must become `[aimed,article,submit,moreauthors]` (or the correct
+  article type instead of `article`, if this isn't a standard Article).
+- [Definitions/](Definitions/) holds the official MDPI class/style/bst
+  files (`mdpi.cls`, `mdpi.bst`, `journalnames.tex`, logos). Don't edit
+  these — they're MDPI-supplied.
+- `template.tex` references `\bibliography{references}`. [references.bib](references.bib)
+  exists but is only a stub (cite keys `babapoor2022`, `wu2011`,
+  `nishi2021` carried over from the MIDL paper as a starting point) — real
+  bibliographic data still needs to be filled in and verified, and new
+  citations added as the manuscript grows.
+- Math/theorem-like environments should use MDPI's names: Theorem, Lemma,
+  Corollary, Proposition, Characterization, Property, Problem, Example,
+  ExamplesandDefinitions, Hypothesis, Remark, Definition, Notation,
+  Assumption (see comments in template.tex).
+
+## Working environment
+This repo is edited from more than one machine (Windows/WSL and macOS have
+both been used), so don't assume either one — check `uname`/the shell
+you're actually in before relying on platform-specific behavior below.
+
+- **Windows/WSL**: the repo lives on the WSL (Ubuntu) filesystem. When it's
+  accessed from a Windows-side shell (Git Bash/MSYS, PowerShell) via
+  `\\wsl.localhost\...`, WSL's `*:Zone.Identifier` marker files (harmless
+  Windows download metadata, no content value) show up with a mangled
+  colon character, which makes `git status` report spurious
+  deleted/untracked pairs for the same files. These are now covered by
+  `.gitignore` — don't try to "fix" them again. Prefer running `git` (and
+  anything touching filenames with unusual characters) from inside actual
+  WSL, e.g. `wsl.exe -- bash -lc "cd /home/nlab/MDPI && <command>"` from
+  PowerShell, rather than Windows Git Bash. Git Bash accessing the repo
+  over the UNC path may also need a one-time
+  `git config --global --add safe.directory '%(prefix)///wsl.localhost/Ubuntu/home/nlab/MDPI'`
+  (dubious-ownership check) — already set on the Windows machine this was
+  written from.
+- **macOS**: none of the above applies; the repo should behave like a
+  normal local git checkout.
+- **LaTeX toolchain**: as of this writing, no LaTeX toolchain (`pdflatex`,
+  `latexmk`, `bibtex`) was found on the Windows PATH or inside WSL on the
+  machine this file was written from — `template.tex` couldn't be compiled
+  to verify output. Check for one (`which pdflatex`) before relying on
+  Claude Code to compile/check the PDF; if missing, install TeX Live
+  (`sudo apt install texlive-full` on WSL/Linux, `brew install --cask
+  mactex` or the smaller `basictex` on macOS) or compile via Overleaf
+  instead.
+
+## Writing conventions
+- Manuscript language is English (MDPI submission requirement), even
+  though some source material (`main_ja.tex`, the thesis PDF) is Japanese.
+- Follow the MIDL paper's terminology (e.g. "attenuated plaque",
+  "polar coordinate transformation", "CNN-LSTM") for consistency unless a
+  term needs to change for the current data/results or a journal audience.
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+% references.bib — bibliography for the MDPI "AI in Medicine" manuscript.
+%
+% Seeded with the citation keys already used in Reference/main.tex and
+% Reference/main_ja.tex (the MIDL 2026 short paper this journal article
+% expands). Every entry below is a STUB: only the cite key is trustworthy,
+% the bibliographic fields are placeholders and MUST be verified against
+% the real source before compiling/citing. Do not submit with @TODO entries.
+
+@TODO{babapoor2022,
+  note = {TODO: verify — cited in Reference/main.tex for no-reflow/slow flow incidence (~10-20% of PCI cases)}
+}
+
+@TODO{wu2011,
+  note = {TODO: verify — cited in Reference/main.tex for the manual attenuated-plaque scoring system compared against in Results}
+}
+
+@TODO{nishi2021,
+  note = {TODO: verify — cited in Reference/main.tex for the plaque segmentation model used for the ROI-mask comparison method}
+}
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