Add Kai et al. 2021 (Circ J) as a candidate reference PDF ...

Renal Dysfunction as a Predictor of Slow-Flow/No-Reflow Phenomenon
after PCI in STEMI (Circ J. 2021;85:1770-1778) — not yet cited in the
manuscript or added to references.bib; kept here for future use
(e.g. Related Work), per review discussed in chat.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Add shared VS Code LaTeX Workshop build settings ...

Points the LaTeX Workshop extension's default recipe at build/, so
compiling from the VS Code UI on any machine follows the same
build/-output convention documented in CLAUDE.md instead of littering
the repo root with generated files.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Refine Introduction wording and add two more verified citations ...

- Add wang2026 (USCNet) and hibi2013 (IVUS history review) to
  references.bib after reading the full PDFs; cite them for KSCNet's
  originating kidney-stone-classification architecture and for the
  claim that IVUS can visualize vessel wall/plaque condition,
  respectively.
- Drop "microvascular spasm" as a contributing factor from the
  no-reflow definition, trim an editorializing clause after the
  attenuated-plaque finding, and rephrase the IVUS-focus sentence as
  the paper's own rationale rather than a general background claim.
- Remove the unsupported vasodilator-treatment-limitations sentence
  and the citation-needed marker on preventive-measures (distal
  protection devices/prophylactic vasodilators), per review: none of
  the added source papers support the former, and the latter is
  standard clinical practice not requiring a citation.
- Generalize the poor-prognosis sentence (previously citing specific,
  unsupported outcomes) to a claim not requiring a citation.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Wire up references.bib and verify citations against source PDFs ...

- Add citations/ folder holding the cited papers' PDFs (babapoor2022,
  wu2011, nishi2021), documented in CLAUDE.md so cite keys can be
  filled in/verified directly from the source paper instead of guessed.
- Fill in references.bib entries for all three keys with real
  bibliographic data, and drop a stray "@TODO" in the header comment
  that was making bibtex misparse the file as a malformed entry.
- Switch main.tex from the template's placeholder internal
  bibliography to \bibliography{references}, so citations actually
  resolve (previously rendered as undefined/"?").
- Correct the Introduction's babapoor2022/wu2011 citation claims after
  reading the full papers: babapoor2022 reports separate no-reflow
  (17.1%) and slow-flow (12.9%) rates in a single-center primary-PCI
  cohort, not a general "10-20% of PCI patients" figure; wu2011's
  finding is specific to AMI patients and a composite no-reflow/
  slow-flow (TIMI <=2) endpoint, and only the amount (not presence) of
  attenuated plaque differed significantly.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Draft Introduction via ja-drafter/review/translate pipeline ...

Writes sections/1_introduction.tex through the documented workflow:
Japanese draft (drafts/ja/1_introduction.md), fact-check + content
review against the Notion source of truth, then English translation.
Centers the section on the proposed KSCNet architecture; open claims
without a source yet are left as inline [citation needed] markers.
Also documents the pipeline itself in CLAUDE.md.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Number section files to match reading order ...

sections/*.tex renamed to 1_introduction.tex .. 6_conclusion.tex so the
directory listing sorts in the same order they're \input from main.tex.
No 0_abstract.tex: the abstract must stay inline in main.tex (mdpi.cls
reuses it as PDF pdfsubject metadata, which \input breaks), and a
drafting-only file would just duplicate it with a risk of drifting out
of sync, so CLAUDE.md now says so explicitly.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

CLAUDE.md: add drafting/translation conventions ...

- Don't fill gaps with unstated inference; ask when something needed
  for the manuscript is unclear or unspecified.
- Translate Japanese source material faithfully, not as a loose
  paraphrase, while still producing natural English.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Add build/ as the LaTeX output directory ...

Compile with pdflatex -output-directory=build so generated files (.pdf,
.aux, .log, the epstopdf-converted logo, etc.) land in build/ instead of
cluttering the repo root. build/ is tracked as an empty folder via
build/.gitkeep so it exists right after a fresh clone; its generated
contents stay gitignored.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Split manuscript body into main.tex + sections/, move template to Template/ ...

main.tex is now the actual manuscript to edit and compile, copied from
the official MDPI template. Body content moves out into
sections/{introduction,related_work,method,experiment,discussion,
conclusion}.tex, \input from main.tex right after each \section heading;
figures/ added for images. Abstract stays inline in main.tex since
mdpi.cls reuses it verbatim as PDF pdfsubject metadata, which requires
full expandability that \input breaks.

The pristine template (template.tex/template.pdf) moves into its own
Template/ folder to stay visually distinct from the actual manuscript;
its \documentclass/\includegraphics calls are updated to ../Definitions/
accordingly. It's kept as read-only reference going forward.

Also removes the template's "How to Use this Template" placeholder
section and the unused optional Patents section, and documents the new
layout in CLAUDE.md.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Correct CLAUDE.md: TeX Live 2026 is installed on WSL, just not on PATH for non-interactive shells ...

Verified by compiling template.tex via an interactive zsh shell.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Set up Claude Code environment for the MDPI manuscript ...

- Add CLAUDE.md documenting project context, source-material timeline
  and caveats, manuscript structure, and Windows/WSL/macOS environment
  notes.
- Add references.bib stub seeded with cite keys from the MIDL paper.
- Untrack *:Zone.Identifier marker files and ignore them going forward,
  along with common LaTeX build artifacts.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Add: reference

Add: template

First commit