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% File: ./01_manuscript/contents/latex_styles/columns.tex
% ======================================================================
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% File: ./01_manuscript/contents/latex_styles/packages.tex
% ======================================================================
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%% -*- coding: utf-8 -*-
%% Timestamp: "2025-09-27 16:01:16 (ywatanabe)"
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%% EOF
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% File: ./01_manuscript/contents/latex_styles/linker.tex
% ======================================================================
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% ======================================================================
% File: ./01_manuscript/contents/latex_styles/formatting.tex
% ======================================================================
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%%%% EOF
\link[supple-]{./02_supplementary/supplementary}
%% ----------------------------------------
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%% ----------------------------------------
% ======================================================================
% File: ./01_manuscript/contents/journal_name.tex
% ======================================================================
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%% ----------------------------------------
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%% ----------------------------------------
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%% Timestamp: "2025-11-10 01:30:00 (ywatanabe)"
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%% =============================================================================
%% Diff Document Metadata (Auto-generated)
%% =============================================================================
%% Comparison: v513391d → v721a65c+
%% Generated: 2026-02-18 21:02:11
%% User: Yusuke Watanabe <[email protected]>
%% Document: manuscript
%% Git commit: 721a65c
%% Git branch: develop
%% =============================================================================
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%% =============================================================================
%% Diff Document Metadata (Auto-generated)
%% =============================================================================
%% Comparison: v513391d → v721a65c+
%% Generated: 2026-02-18 21:02:11
%% User: Yusuke Watanabe <[email protected]>
%% Document: manuscript
%% Git commit: 721a65c
%% Git branch: develop
%% =============================================================================
\begin{document}
%% ----------------------------------------
%% Frontmatter
%% ----------------------------------------
\begin{frontmatter}
% ======================================================================
% File: ./01_manuscript/contents/highlights.tex
% ======================================================================
%% -*- coding: utf-8 -*-
%% \begin{highlights}
%% \pdfbookmark[1]{Highlights}{highlights}
%% \item Highlight \#1
%% \item Highlight \#2
%% \item Highlight \#3
%% \end{highlights}
%%%% EOF
% ======================================================================
% File: ./01_manuscript/contents/title.tex
% ======================================================================
%% -*- coding: utf-8 -*-
\title{
Your Manuscript Title Here
}
%%%% EOF
% ======================================================================
% File: ./01_manuscript/contents/authors.tex
% ======================================================================
%% -*- coding: utf-8 -*-
\author[1]{First Author\corref{cor1}}
\author[2]{Second Author}
\author[3]{Third Author}
\address[1]{First Institution, Department, City, Country}
\address[2]{Second Institution, Department, City, Country}
\address[3]{Third Institution, Department, City, Country}
\cortext[cor1]{Corresponding author. Email: [email protected]}
%%%% EOF
% ======================================================================
% File: ./01_manuscript/contents/graphical_abstract.tex
% ======================================================================
%%Graphical abstract
%\pdfbookmark[1]{Graphical Abstract}{graphicalabstract}
%\begin{graphicalabstract}
%\includegraphics{grabs}
%\end{graphicalabstract}
% ======================================================================
% File: ./01_manuscript/contents/abstract.tex
% ======================================================================
%% -*- coding: utf-8 -*-
\begin{abstract}
\pdfbookmark[1]{Abstract}{abstract}
Replace this text with your manuscript abstract. Typically 150--250 words summarizing objectives, methods, key findings, and conclusions.
\vspace{1em}
\end{abstract}
%%%% EOF
% ======================================================================
% File: ./01_manuscript/contents/keywords.tex
% ======================================================================
% \pdfbookmark[1]{Keywords}{keywords}
\begin{keyword}
keyword one \sep keyword two \sep keyword three \sep keyword four \sep keyword five
\end{keyword}
\end{frontmatter}
%% ----------------------------------------
%% Word Counter
%% ----------------------------------------
% ======================================================================
% File: ./01_manuscript/contents/wordcount.tex
% ======================================================================
%% -*- coding: utf-8 -*-
%% File: 01_manuscript/contents/wordcount.tex
\noindent\small
\readwordcount{./01_manuscript/contents/wordcounts/figure_count.txt} figures,
\readwordcount{./01_manuscript/contents/wordcounts/table_count.txt} tables,
\readwordcount{./01_manuscript/contents/wordcounts/abstract_count.txt} words for abstract, and
\readwordcount{./01_manuscript/contents/wordcounts/imrd_count.txt} words for main text
(\readwordcount{./01_manuscript/contents/wordcounts/introduction_count.txt} for introduction,
\readwordcount{./01_manuscript/contents/wordcounts/methods_count.txt} for methods,
\readwordcount{./01_manuscript/contents/wordcounts/results_count.txt} for results,
\readwordcount{./01_manuscript/contents/wordcounts/discussion_count.txt} for discussion)
\normalsize
%%%% EOF
%% ----------------------------------------
%% INTRODUCTION
%% ----------------------------------------
% ======================================================================
% File: ./01_manuscript/contents/introduction.tex
% ======================================================================
%% -*- coding: utf-8 -*-
\section{Introduction}
Replace this with your introduction. Establish context, review relevant work \cite{example_reference_2020}, identify gaps, and state your objectives.
%%%% EOF
%% ----------------------------------------
%% METHODS
%% ----------------------------------------
% ======================================================================
% File: ./01_manuscript/contents/methods.tex
% ======================================================================
%% -*- coding: utf-8 -*-
\section{Methods}
Replace this with your methods. Describe study design, data collection, and analysis procedures \cite{example_method_2019}. Provide enough detail for reproducibility.
%%%% EOF
%% ----------------------------------------
%% RESULTS
%% ----------------------------------------
% ======================================================================
% File: ./01_manuscript/contents/results.tex
% ======================================================================
%% -*- coding: utf-8 -*-
\section{Results}
Replace this with your results. Present findings with references to figures (Figure~\ref{fig:01_example_figure}) and tables (Table~\ref{tab:01_example_table}).
%%%% EOF
%% ----------------------------------------
%% DISCUSSION
%% ----------------------------------------
% ======================================================================
% File: ./01_manuscript/contents/discussion.tex
% ======================================================================
%% -*- coding: utf-8 -*-
\section{Discussion}
Replace this with your discussion. Interpret findings, compare with previous work, discuss limitations, and state conclusions.
%%%% EOF
%% ----------------------------------------
%% REFERENCE STYLES
%% ----------------------------------------
\pdfbookmark[1]{References}{references}
% Note: Path without ./ prefix allows bibtex to use BIBINPUTS search path
\bibliography{01_manuscript/contents/bibliography}
% ======================================================================
% File: ./01_manuscript/contents/latex_styles/bibliography.tex
% ======================================================================
%% -*- coding: utf-8 -*-
%% File: 00_shared/latex_styles/bibliography.tex
%% ============================================================================
%% BIBLIOGRAPHY STYLE CONFIGURATION
%% ============================================================================
%% ----------------------------------------------------------------------------
%% OPTION 1: NUMBERED CITATIONS (Order of Appearance) - CURRENTLY ACTIVE
%% ----------------------------------------------------------------------------
%% Description: Citations numbered [1], [2], [3]... in the order they first
%% appear in the manuscript
%% Sorting: By first citation order (NOT alphabetical)
%% Example: \cite{Tort2010,Canolty2010} → [1, 2] (if these are first citations)
%% Commands: \cite{key} → [1]
%% \cite{key1,key2} → [1, 2]
%% Best for: Most scientific journals, clear citation tracking
%% Compatible with: natbib package
\bibliographystyle{unsrtnat}
%% ----------------------------------------------------------------------------
%% OPTION 2: NUMBERED CITATIONS (Alphabetical by Author)
%% ----------------------------------------------------------------------------
%% Description: Citations numbered [1], [2], [3]... sorted alphabetically by
%% first author's last name
%% Sorting: Alphabetical by author (Canolty before Tort)
%% Example: \cite{Tort2010,Canolty2010} → [2, 1] (C before T alphabetically)
%% Commands: \cite{key} → [1]
%% Best for: When you want bibliography sorted alphabetically
%% Compatible with: elsarticle class
% \bibliographystyle{elsarticle-num}
%% Alternative alphabetical styles:
% \bibliographystyle{plain} % Basic alphabetical, no natbib features
% \bibliographystyle{ieeetr} % IEEE style, order of appearance
% \bibliographystyle{siam} % SIAM style, alphabetical
%% ----------------------------------------------------------------------------
%% OPTION 3: AUTHOR-YEAR CITATIONS
%% ----------------------------------------------------------------------------
%% Description: Citations show author name and year (Smith, 2020) or (Smith 2020)
%% Format: (Author, Year) or Author (Year) depending on command
%% Example: \cite{Tort2010} → (Tort et al., 2010)
%% \citet{Tort2010} → Tort et al. (2010) [textual]
%% \cite{Tort2010} → (Tort et al., 2010) [parenthetical]
%% Commands:
%% - \citet{key} → Author (Year) [for text: "As shown by Author (2020)..."]
%% - \cite{key} → (Author, Year) [for parentheses: "...as shown (Author, 2020)"]
%% - \cite{key} → Same as \cite{key}
%% Best for: Review papers, humanities, some social sciences
%% Requires: natbib package (already loaded)
% \bibliographystyle{plainnat} % Author-year, alphabetical
% \bibliographystyle{abbrvnat} % Author-year, abbreviated names
% \bibliographystyle{apalike} % APA-like author-year style
%% ----------------------------------------------------------------------------
%% OPTION 4: JOURNAL-SPECIFIC STYLES
%% ----------------------------------------------------------------------------
%% Elsevier journals:
% \bibliographystyle{elsarticle-num} % Numbered, alphabetical
% \bibliographystyle{elsarticle-num-names} % Numbered, alphabetical, full names
% \bibliographystyle{elsarticle-harv} % Author-year (Harvard style)
%% Nature family:
% \bibliographystyle{naturemag} % Nature magazine style
%% IEEE:
% \bibliographystyle{IEEEtran} % IEEE Transactions style
%% APA:
% \bibliographystyle{apalike} % APA-like style
%% ----------------------------------------------------------------------------
%% OPTION 5: ADDITIONAL CITATION STYLES
%% ----------------------------------------------------------------------------
%% Note: Many of these styles require biblatex instead of natbib.
%% To use biblatex, you need to modify the preamble and use biber instead of bibtex.
%% Basic conversion: Replace natbib package with biblatex, and use \printbibliography
%% instead of \bibliographystyle + \bibliography commands.
%% ----------------------------------------
%% CHEMISTRY
%% ----------------------------------------
%% American Chemical Society (ACS):
%% Installation: Download achemso.bst or use biblatex with style=chem-acs
%% Format: Numbered, order of appearance, (1) Author, A. B. Title. Journal Year, Volume, Pages.
%% BibTeX method:
% \bibliographystyle{achemso} % ACS style (requires achemso package)
%% Biblatex method (recommended):
% \usepackage[style=chem-acs]{biblatex}
%% ----------------------------------------
%% MEDICAL & HEALTH SCIENCES
%% ----------------------------------------
%% American Medical Association (AMA) 11th edition:
%% Format: Numbered, order of appearance, superscript numbers
%% Installation: Requires biblatex with biblatex-ama style
%% Method:
% \usepackage[style=ama]{biblatex} % AMA 11th ed (requires biblatex-ama package)
%% Vancouver style (ICMJE):
%% Format: Numbered [1], order of appearance, commonly used in medical journals
%% Note: unsrtnat (currently active) is very similar to Vancouver
% \bibliographystyle{vancouver} % Vancouver/ICMJE style (if .bst available)
% \bibliographystyle{unsrtnat} % Similar to Vancouver (currently active)
%% ----------------------------------------
%% SOCIAL SCIENCES
%% ----------------------------------------
%% American Psychological Association (APA) 7th edition:
%% Format: Author-year, (Author, Year), alphabetical by author
%% BibTeX method (APA-like, not full APA 7th):
% \bibliographystyle{apalike} % APA-like style (simplified)
% \bibliographystyle{apacite} % APA 6th/7th (requires apacite package)
%% Biblatex method (recommended for full APA 7th compliance):
% \usepackage[style=apa]{biblatex} % Full APA 7th edition (requires biblatex-apa)
%% American Sociological Association (ASA) 6th/7th edition:
%% Format: Author-year, (Author Year), alphabetical, similar to Chicago author-date
%% Method:
% \bibliographystyle{asaetr} % ASA-like style (if .bst available)
%% Biblatex method:
% \usepackage[style=authoryear]{biblatex} % Generic author-year (customizable to ASA)
%% American Political Science Association (APSA):
%% Format: Author-year, similar to Chicago author-date
%% Method:
% \usepackage[style=authoryear-comp]{biblatex} % Compressed author-year for APSA
%% ----------------------------------------
%% HUMANITIES
%% ----------------------------------------
%% Chicago Manual of Style 18th edition (author-date):
%% Format: Author-year, (Author Year), commonly used in social sciences and humanities
% \bibliographystyle{chicago} % Chicago author-date (if .bst available)
%% Biblatex method (recommended):
% \usepackage[style=chicago-authordate]{biblatex} % Chicago 18th ed author-date
%% Chicago Manual of Style 18th edition (notes and bibliography):
%% Format: Footnote/endnote citations with full bibliography
%% Method:
% \usepackage[style=chicago-notes]{biblatex} % Chicago 18th ed notes style
%% Chicago Manual of Style 18th edition (shortened notes and bibliography):
%% Format: Shortened footnote citations after first full citation
%% Method:
% \usepackage[style=chicago-notes]{biblatex} % Use with ibidtracker option
%% Modern Language Association (MLA) 9th edition:
%% Format: Author-page, (Author Page), works cited list
%% Method:
% \usepackage[style=mla]{biblatex} % MLA 9th edition (requires biblatex-mla)
%% Modern Humanities Research Association (MHRA) 4th edition:
%% Format: Footnote citations with bibliography
%% Method:
% \usepackage[style=mhra]{biblatex} % MHRA 4th edition (requires biblatex-mhra)
%% ----------------------------------------
%% HARVARD STYLES
%% ----------------------------------------
%% Cite Them Right 12th edition - Harvard:
%% Format: Author-year, (Author, Year), widely used in UK universities
% \bibliographystyle{agsm} % Harvard style (Australian)
% \bibliographystyle{dcu} % Harvard style (Dublin City University)
%% Biblatex method:
% \usepackage[style=authoryear]{biblatex} % Generic Harvard-style (author-year)
%% Elsevier - Harvard (with titles):
%% Format: Author-year with article titles included
% \bibliographystyle{elsarticle-harv} % Elsevier Harvard style (already listed above)
%% ----------------------------------------
%% ENGINEERING & COMPUTER SCIENCE
%% ----------------------------------------
%% IEEE (Institute of Electrical and Electronics Engineers):
%% Format: Numbered [1], order of appearance, widely used in engineering
% \bibliographystyle{IEEEtran} % IEEE Transactions style (already listed above)
%% ----------------------------------------
%% NATURAL SCIENCES
%% ----------------------------------------
%% Nature:
%% Format: Numbered, superscript, order of appearance
% \bibliographystyle{naturemag} % Nature magazine style (already listed above)
% \bibliographystyle{naturemag-doi} % Nature with DOIs
%% ----------------------------------------------------------------------------
%% BIBLATEX SETUP INSTRUCTIONS
%% ----------------------------------------------------------------------------
%% To switch from natbib to biblatex:
%%
%% 1. In packages.tex, replace:
%% \usepackage[numbers]{natbib}
%% with:
%% \usepackage[style=STYLENAME,backend=biber]{biblatex}
%% \addbibresource{path/to/bibliography.bib}
%%
%% 2. In this file (bibliography.tex), replace:
%% \bibliographystyle{...}
%% with:
%% % No \bibliographystyle needed with biblatex
%%
%% 3. In your main .tex file, replace:
%% \bibliography{path/to/bibliography}
%% with:
%% \printbibliography
%%
%% 4. Change compilation command:
%% pdflatex → biber → pdflatex → pdflatex
%% (instead of pdflatex → bibtex → pdflatex → pdflatex)
%%
%% Example biblatex styles:
%% style=numeric-comp → Compressed numeric [1-3,5]
%% style=authoryear → (Author, Year)
%% style=authoryear-comp → (Author1, 2020; Author2, 2021)
%% style=apa → APA 7th edition
%% style=chicago-authordate → Chicago author-date
%% style=ieee → IEEE style
%% style=nature → Nature style
%% style=mla → MLA 9th edition
%% ----------------------------------------------------------------------------
%% CITATION COMMAND REFERENCE (with natbib)
%% ----------------------------------------------------------------------------
%% Basic commands:
%% \cite{key} → [1] or (Author, Year) depending on style
%% \cite{key1,key2} → [1, 2] or (Author1, Year1; Author2, Year2)
%%
%% Advanced natbib commands (only work with natbib-compatible styles):
%% \citet{key} → Author (Year) [textual citation]
%% \cite{key} → (Author, Year) [parenthetical citation]
%% \citet*{key} → Full author list (Year)
%% \cite*{key} → (Full author list, Year)
%% \citealt{key} → Author Year [no parentheses]
%% \citealp{key} → Author, Year [no parentheses]
%% \citeauthor{key} → Author [name only]
%% \citeyear{key} → Year [year only]
%% \citeyearpar{key} → (Year) [year in parentheses]
%%
%% Pre/post notes:
%% \cite[see][p.~10]{key} → (see Author, Year, p. 10)
%% \cite[p.~10]{key} → (Author, Year, p. 10)
%%
%% Multiple citations:
%% \cite{key1,key2,key3} → (Author1, Year1; Author2, Year2; Author3, Year3)
%%
%% Suppressing parts:
%% \cite[e.g.,][]{key} → (e.g., Author, Year)
%% \cite[][see p.~10]{key}→ (Author, Year, see p. 10)
%%
%% ----------------------------------------------------------------------------
%% TROUBLESHOOTING
%% ----------------------------------------------------------------------------
%% Problem: Citations appear as [?] or undefined
%% Solution: Run compilation 3-4 times to resolve all references
%%
%% Problem: Citation numbers out of order [3, 1] instead of [1, 3]
%% Solution: Use unsrtnat (order of appearance) instead of elsarticle-num
%%
%% Problem: "Undefined control sequence \citet"
%% Solution: \citet only works with natbib-compatible styles (unsrtnat, plainnat)
%% Use \cite{} with non-natbib styles
%%
%% Problem: Bibliography not appearing
%% Solution: Ensure \bibliography{path/to/bibfile} command exists in main file
%% Run: pdflatex → bibtex → pdflatex → pdflatex
%%%% EOF
%% ----------------------------------------
%% DATA AVAILABILITY
%% ----------------------------------------
% ======================================================================
% File: ./01_manuscript/contents/data_availability.tex
% ======================================================================
%% -*- coding: utf-8 -*-
\pdfbookmark[1]{Data Availability Statement}{data_availability}
\section*{Data Availability Statement}
The data and code that support the findings of this study are available from the corresponding author upon reasonable request.
\label{data and code availability}
%%%% EOF
%% ----------------------------------------
%% ADDITIONAL INFORMATION
%% ----------------------------------------
% ======================================================================
% File: ./01_manuscript/contents/additional_info.tex
% ======================================================================
%% -*- coding: utf-8 -*-
\pdfbookmark[1]{Additional Information}{additional_information}
\pdfbookmark[2]{Ethics Declarations}{ethics_declarations}
\section*{Ethics Declarations}
Replace with your ethics statement.
\label{ethics declarations}
\pdfbookmark[2]{Contributors}{author_contributions}
\section*{Author Contributions}
Replace with author contributions.
\label{author contributions}
\pdfbookmark[2]{Acknowledgments}{acknowledgments}
\section*{Acknowledgments}
Replace with acknowledgments.
\label{acknowledgments}
\pdfbookmark[2]{Declaration of Interests}{declaration_of_interest}
\section*{Declaration of Interests}
The authors declare that they have no competing interests.
\label{declaration of interests}
\pdfbookmark[2]{Declaration of Generative AI in Scientific Writing}{declaration_of_generative_ai}
\section*{Declaration of Generative AI in Scientific Writing}
Disclose any use of generative AI tools here.
\label{declaration of generative ai in scientific writing}
%%%% EOF
%% ----------------------------------------
%% TABLES
%% ----------------------------------------
\clearpage
\section*{Tables}
\label{tables}
\pdfbookmark[1]{Tables}{tables}
\vspace{1cm}
% ======================================================================
% File: ./01_manuscript/contents/tables/compiled/FINAL.tex
% ======================================================================
% Auto-generated file containing all table inputs
% Generated by gather_table_tex_files()
% Table from: 01_example_table.tex
% ======================================================================
% File: ./01_manuscript/contents/tables/compiled/01_example_table.tex
% ======================================================================
\DIFdelbegin %DIFDELCMD < \pdfbookmark[2]{Table 1_example_table}{table_01_example_table}
%DIFDELCMD < %%%
\DIFdelend \DIFaddbegin \pdfbookmark[2]{Table 01 --- Replace with your table title}{table_01_example_table}
\DIFaddend \begin{table}[htbp]
\centering
\footnotesize
\begin{tabular}{|l|l|l|}
\hline
Category&Value&Description\\
\hline
Example A&1.00&Replace with your data\\
\hline
Example B&2.00&Replace with your data\\
\hline
Example C&3.00&Replace with your data\\
\hline
\end{tabular}
%% Edit this file: 01_manuscript/contents/tables/caption_and_media/01_example_table.tex
\caption{\textbf{Replace with your table title.}\\
\smallskip
Replace with your table legend text. Edit this caption at \texttt{01\_manuscript/contents/tables/caption\_and\_media/01\_example\_table.tex}.
}
\label{tab:01_example_table}
\end{table}
%% ----------------------------------------
%% FIGURES
%% ----------------------------------------
\clearpage
\section*{Figures}
\label{figures}
\pdfbookmark[1]{Figures}{figures}
\vspace{1cm}
% ======================================================================
% File: ./01_manuscript/contents/figures/compiled/FINAL.tex
% ======================================================================
% Generated by compile_figure_tex_files()
% This file includes all figure files in order
% Figure 01
\begin{figure*}[htbp]
\DIFdelbeginFL %DIFDELCMD < \pdfbookmark[2]{Figure 01}{.01}
%DIFDELCMD < %%%
\DIFdelendFL \DIFaddbeginFL \pdfbookmark[2]{Figure 01 --- Replace with your figure title}{.01}
\DIFaddendFL \centering
\includegraphics[width=0.9\textwidth]{./01_manuscript/contents/figures/caption_and_media/jpg_for_compilation/01_example_figure.jpg}
\caption{\textbf{Replace with your figure title.}\\
\smallskip
Replace with your figure legend text. Edit this caption at \texttt{01\_manuscript/contents/figures/caption\_and\_media/01\_example\_figure.tex}.
}
\label{fig:01_example_figure}
\end{figure*}
% Figure 02
\begin{figure*}[htbp]
\DIFdelbeginFL %DIFDELCMD < \pdfbookmark[2]{Figure 02}{.02}
%DIFDELCMD < %%%
\DIFdelendFL \DIFaddbeginFL \pdfbookmark[2]{Figure 02 --- Replace with your figure title}{.02}
\DIFaddendFL \centering
\includegraphics[width=0.9\textwidth]{./01_manuscript/contents/figures/caption_and_media/jpg_for_compilation/02_another_example.jpg}
\caption{\textbf{Replace with your figure title.}\\
\smallskip
Replace with your figure legend text. Edit this caption at \texttt{01\_manuscript/contents/figures/caption\_and\_media/02\_another\_example.tex}.
}
\label{fig:02_another_example}
\end{figure*}
%% ----------------------------------------
%% END of DOCUMENT
%% ----------------------------------------
\end{document}
%%%% EOF
/