423 lines
12 KiB
TeX
423 lines
12 KiB
TeX
% Options for packages loaded elsewhere
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% Options for packages loaded elsewhere
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\PassOptionsToPackage{unicode}{hyperref}
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\PassOptionsToPackage{hyphens}{url}
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\PassOptionsToPackage{dvipsnames,svgnames,x11names}{xcolor}
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\PassOptionsToPackage{space}{xeCJK}
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%
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\documentclass[
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english,
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12pt,
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letterpaper,
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]{article}
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\usepackage{xcolor}
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\usepackage[margin=1in]{geometry}
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\usepackage{amsmath,amssymb}
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\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
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\usepackage{iftex}
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\ifPDFTeX
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\usepackage[T1]{fontenc}
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\usepackage[utf8]{inputenc}
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\usepackage{textcomp} % provide euro and other symbols
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\else % if luatex or xetex
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\usepackage{unicode-math} % this also loads fontspec
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\defaultfontfeatures{Scale=MatchLowercase}
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\defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
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\fi
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\usepackage{lmodern}
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\ifPDFTeX\else
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% xetex/luatex font selection
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\setmainfont[]{Source Sans 3}
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\setsansfont[Color=39729E]{Gill Sans}
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\setmonofont[]{JetBrains Mono}
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\setmathfont[]{Cambria Math}
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\ifXeTeX
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\usepackage{xeCJK}
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\setCJKmainfont[]{SimHei}
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\fi
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\ifLuaTeX
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\usepackage[]{luatexja-fontspec}
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\setmainjfont[]{SimHei}
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\fi
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\fi
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% Use upquote if available, for straight quotes in verbatim environments
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\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
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\IfFileExists{microtype.sty}{% use microtype if available
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\usepackage[]{microtype}
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\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
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}{}
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\makeatletter
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\@ifundefined{KOMAClassName}{% if non-KOMA class
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\IfFileExists{parskip.sty}{%
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\usepackage{parskip}
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}{% else
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\setlength{\parindent}{0pt}
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\setlength{\parskip}{6pt plus 2pt minus 1pt}}
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}{% if KOMA class
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\KOMAoptions{parskip=half}}
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\makeatother
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\usepackage{longtable,booktabs,array}
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\usepackage{calc} % for calculating minipage widths
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% Correct order of tables after \paragraph or \subparagraph
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\usepackage{etoolbox}
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\makeatletter
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\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
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\makeatother
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% Allow footnotes in longtable head/foot
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\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
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\makesavenoteenv{longtable}
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\usepackage{graphicx}
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\makeatletter
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\newsavebox\pandoc@box
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\newcommand*\pandocbounded[1]{% scales image to fit in text height/width
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\sbox\pandoc@box{#1}%
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\Gscale@div\@tempa{\textheight}{\dimexpr\ht\pandoc@box+\dp\pandoc@box\relax}%
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\Gscale@div\@tempb{\linewidth}{\wd\pandoc@box}%
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\ifdim\@tempb\p@<\@tempa\p@\let\@tempa\@tempb\fi% select the smaller of both
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\ifdim\@tempa\p@<\p@\scalebox{\@tempa}{\usebox\pandoc@box}%
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\else\usebox{\pandoc@box}%
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\fi%
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}
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% Set default figure placement to htbp
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\def\fps@figure{htbp}
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\makeatother
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\ifLuaTeX
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\usepackage[bidi=basic]{babel}
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\else
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\usepackage[bidi=default]{babel}
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\fi
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\ifPDFTeX
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\else
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\babelfont{rm}[]{Source Sans 3}
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\fi
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% get rid of language-specific shorthands (see #6817):
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\let\LanguageShortHands\languageshorthands
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\def\languageshorthands#1{}
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\ifLuaTeX
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\usepackage[english]{selnolig} % disable illegal ligatures
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\fi
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\setlength{\emergencystretch}{3em} % prevent overfull lines
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\providecommand{\tightlist}{%
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\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
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% -----------------------
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% CUSTOM PREAMBLE STUFF
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% -----------------------
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\usepackage{enumitem}
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\usepackage{fontspec}
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\usepackage{float}
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\usepackage[normalem]{ulem}
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\usepackage{hyperref}
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\usepackage{nameref} %needed by zref-xr
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\usepackage{zref-xr,zref-hyperref,zref-user}
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\usepackage{xr-hyper}
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\usepackage[normalem]{ulem}
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\usepackage{setspace}
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\usepackage{lineno}
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\usepackage{caption}
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\captionsetup{singlelinecheck=off}
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\usepackage[UTF8, scheme=plain]{ctex}
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\usepackage{orcidlink}
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% \setkomafont{author}{\normalsize}
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% for revision
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\usepackage{adjustbox}
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% \usepackage{xcolor}
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\usepackage{mdframed}
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\newmdenv[topline=false,
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leftline=true,
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bottomline=false,
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rightline=false,
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linewidth=3pt,
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%backgroundcolor=lightgray,
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linecolor=gray!30,
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backgroundcolor=gray!5,
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skipabove=\topsep,
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skipbelow=\topsep,
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leftmargin=0pt,
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rightmargin=0pt,
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innertopmargin=0pt,
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innerbottommargin=0pt
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]{refquote}
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\newmdenv[topline=false,
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leftline=true,
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bottomline=false,
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rightline=false,
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linewidth=3pt,
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%backgroundcolor=lightgray,
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backgroundcolor=red!3!white,
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linecolor=red!30!white,
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skipabove=\topsep,
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skipbelow=\topsep,
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leftmargin=0pt,
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rightmargin=0pt,
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innertopmargin=10pt,
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innerbottommargin=10pt
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]{question}
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% setup hyperlink for page and line number
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\def\msname{MS}
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\def\smname{SM}
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\setenumerate{labelsep=*, leftmargin=1.0pc}
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%\zexternaldocument*{ManuscriptNew\veraa}
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\zexternaldocument*{\msname}
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\zexternaldocument*{\smname}
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\newcommand{\hlabel}[1]{\label{#1}\hypertarget{#1}{
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\linelabel{line:#1}}}
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%\externaldocument[si-]{\smname\veraa}[\smname\veraa.pdf]
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\makeatletter
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\newcommand{\clab}[2][]{
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\protected@write\@auxout{\let\clab\@secondoftwo}{
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\string\newlabel{r:#1}{{#2}{}}}%
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\hlabel{#1}#2\hlabel{#1end}}
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\makeatother
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\newcommand{\zhypera}[1]{\href[pdfnewwindow]{\msname.pdf\##1}{\\[1ex]\textbf{Page \zpageref{#1}, Line
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\zref{line:#1}--\zref{line:#1end}:}\\}}
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\newcommand{\cref}[1]{\begin{refquote}\zhypera{#1}{\zref{r:#1}}\\[-0.5ex]\end{refquote}}
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% \newenvironment{ra}[1][\unskip]{\par \noindent \\[-1ex] \textbf{Response/Action:}\par\bf}{\ \\}
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\renewenvironment{quote}{\begin{question}}{\end{question}}
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% \renewenvironment{verbatim}{\begin{ra}}{\end{ra}}
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% -----------------
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% Title block stuff
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% -----------------
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% Title
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\makeatletter
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\renewcommand{\title}[1]{\gdef\@title{\large\textbf{#1}}} % Adjust \Huge or other font commands
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\makeatother
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% ------------------
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% Section headings
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% ------------------
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\usepackage{titlesec}
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\titleformat*{\section}{\Large\sffamily\bfseries\raggedright}
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\titleformat*{\subsection}{\large\sffamily\bfseries\raggedright}
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\titleformat*{\subsubsection}{\normalsize\sffamily\bfseries\raggedright}
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\titleformat*{\paragraph}{\small\sffamily\bfseries\raggedright}
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%\titlespacing{<command>}{<left>}{<before-sep>}{<after-sep>}
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% Starred version removes indentation in following paragraph
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\titlespacing*{\section}{0em}{2em}{0.1em}
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\titlespacing*{\subsection}{0em}{1.25em}{0.1em}
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\titlespacing*{\subsubsection}{0em}{0.75em}{0em}
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% ------------------
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% Headers/Footers
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% ------------------
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% \usepackage{fancyhdr}
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% \pagestyle{fancy}
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% \fancyhf{}
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% \fancyhead[L,C,R]{}
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% \fancyfoot[L,C]{}
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% \fancyfoot[R]{\thepage}
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% \renewcommand{\headrulewidth}{1pt}
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% \fancypagestyle{plain}{%
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% \renewcommand{\headrulewidth}{0pt}%
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% \fancyhf{}%
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% \fancyfoot[R]{\thepage}%
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% }
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% \renewcommand\footnoterule{\rule{\linewidth}{0.1pt}\vspace{5pt}}
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% ------------------
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% Captions
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% ------------------
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\usepackage[labelfont=bf,labelsep=period]{caption}
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\captionsetup[figure]{font=footnotesize,justification=raggedright,singlelinecheck=false,format=hang}
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% ---------------------------
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% END CUSTOM PREAMBLE STUFF
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% ---------------------------
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\doublespacing
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\linenumbers
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\let\oldsection\section
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\renewcommand{\section}{\clearpage\oldsection}
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\let\oldsubsection\subsection
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\renewcommand{\subsection}{\clearpage\oldsubsection}
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\makeatletter
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\@ifpackageloaded{float}{}{\usepackage{float}}
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\floatstyle{plain}
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\@ifundefined{c@chapter}{\newfloat{sfg}{h}{lost}}{\newfloat{sfg}{h}{lost}[chapter]}
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\floatname{sfg}{Supplementary Fig.}
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\newcommand*\listofsfgs{\listof{sfg}{List of Supplementary Figures}}
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\makeatother
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\makeatletter
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\@ifpackageloaded{float}{}{\usepackage{float}}
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\floatstyle{plain}
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\@ifundefined{c@chapter}{\newfloat{stb}{h}{lost}}{\newfloat{stb}{h}{lost}[chapter]}
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\floatname{stb}{Supplementary Table}
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\newcommand*\listofstbs{\listof{stb}{List of Supplementary Tables}}
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\makeatother
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\makeatletter
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\@ifpackageloaded{float}{}{\usepackage{float}}
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\floatstyle{plain}
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\@ifundefined{c@chapter}{\newfloat{seq}{h}{lost}}{\newfloat{seq}{h}{lost}[chapter]}
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\floatname{seq}{Supplementary Eq.}
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\newcommand*\listofseqs{\listof{seq}{List of Supplementary Equations}}
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\makeatother
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\makeatletter
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\@ifpackageloaded{float}{}{\usepackage{float}}
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\floatstyle{plain}
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\@ifundefined{c@chapter}{\newfloat{rfg}{h}{lost}}{\newfloat{rfg}{h}{lost}[chapter]}
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\floatname{rfg}{Fig. R}
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\newcommand*\quartorfgref[1]{Fig. \hyperref[#1]{R\ref{#1}}}
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\@ifpackageloaded{caption}{}{\usepackage{caption}}
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\DeclareCaptionLabelFormat{quartorfgreflabelformat}{#1#2}
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\captionsetup[rfg]{labelformat=quartorfgreflabelformat}
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\newcommand*\listofrfgs{\listof{rfg}{List of Revision Figures}}
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\makeatother
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\makeatletter
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\@ifpackageloaded{float}{}{\usepackage{float}}
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\floatstyle{plain}
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\@ifundefined{c@chapter}{\newfloat{rtb}{h}{lost}}{\newfloat{rtb}{h}{lost}[chapter]}
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\floatname{rtb}{Table R}
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\newcommand*\quartortbref[1]{Table \hyperref[#1]{R\ref{#1}}}
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\@ifpackageloaded{caption}{}{\usepackage{caption}}
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\DeclareCaptionLabelFormat{quartortbreflabelformat}{#1#2}
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\captionsetup[rtb]{labelformat=quartortbreflabelformat}
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\newcommand*\listofrtbs{\listof{rtb}{List of Revision Tables}}
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\makeatother
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\makeatletter
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\@ifpackageloaded{float}{}{\usepackage{float}}
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\floatstyle{plain}
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\@ifundefined{c@chapter}{\newfloat{req}{h}{lost}}{\newfloat{req}{h}{lost}[chapter]}
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\floatname{req}{Eq R}
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\newcommand*\quartoreqref[1]{Eq \hyperref[#1]{R\ref{#1}}}
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\@ifpackageloaded{caption}{}{\usepackage{caption}}
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\DeclareCaptionLabelFormat{quartoreqreflabelformat}{#1#2}
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\captionsetup[req]{labelformat=quartoreqreflabelformat}
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\newcommand*\listofreqs{\listof{req}{List of Revision Equations}}
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\makeatother
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\makeatletter
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\@ifpackageloaded{caption}{}{\usepackage{caption}}
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\AtBeginDocument{%
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\ifdefined\contentsname
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\renewcommand*\contentsname{Table of contents}
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\else
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\newcommand\contentsname{Table of contents}
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\fi
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\ifdefined\listfigurename
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\renewcommand*\listfigurename{List of Figures}
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\else
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\newcommand\listfigurename{List of Figures}
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\fi
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\ifdefined\listtablename
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\renewcommand*\listtablename{List of Tables}
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\else
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\newcommand\listtablename{List of Tables}
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\fi
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\ifdefined\figurename
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\renewcommand*\figurename{Fig.}
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\else
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\newcommand\figurename{Fig.}
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\fi
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\ifdefined\tablename
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\renewcommand*\tablename{Table}
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\else
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\newcommand\tablename{Table}
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\fi
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}
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\@ifpackageloaded{float}{}{\usepackage{float}}
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\floatstyle{ruled}
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\@ifundefined{c@chapter}{\newfloat{codelisting}{h}{lop}}{\newfloat{codelisting}{h}{lop}[chapter]}
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\floatname{codelisting}{Listing}
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\newcommand*\listoflistings{\listof{codelisting}{List of Listings}}
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\captionsetup{labelsep=colon}
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\makeatother
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\makeatletter
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\makeatother
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\makeatletter
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\@ifpackageloaded{caption}{}{\usepackage{caption}}
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\@ifpackageloaded{subcaption}{}{\usepackage{subcaption}}
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\makeatother
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\usepackage{bookmark}
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\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
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\urlstyle{same}
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\hypersetup{
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pdftitle={MANUSCRIPT TITLE},
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pdfauthor={Xxxxx Yyyy; Ming Su; Min Yang},
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pdflang={en},
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colorlinks=true,
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linkcolor={blue},
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filecolor={Maroon},
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citecolor={Blue},
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urlcolor={blue},
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pdfcreator={LaTeX via pandoc}}
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\title{MANUSCRIPT TITLE}
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\usepackage{etoolbox}
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\makeatletter
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\providecommand{\subtitle}[1]{% add subtitle to \maketitle
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\apptocmd{\@title}{\par {\large\sffamily\bfseries #1 \par}}{}{}
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}
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\makeatother
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\subtitle{Supplementary Information}
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\author{\footnotesize Xxxxx Yyyy \and \footnotesize Ming
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Su \and \footnotesize Min Yang}
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\date{}
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\begin{document}
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% for some reason this does not work in header
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\renewcommand{\abstractname}{Abstract.}
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% add the short title to the fancy header
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\maketitle
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%\noindent \rule{\linewidth}{.5pt}
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%\noindent \rule{\linewidth}{.5pt}
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\thispagestyle{empty}
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Figures and/or tables are provided below as the supplementary evidences
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to the main text.
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\newpage{}
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\clearpage
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{
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\hypersetup{linkcolor=black}
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\setcounter{tocdepth}{3}
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\tableofcontents
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}
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\newpage{}
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\begin{sfg}
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\centering{
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\begin{verbatim}
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#> NULL
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\end{verbatim}
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}
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\caption{\label{sfg-demo}Caption of demo figure}
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\end{sfg}%
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\end{document}
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