528 lines
16 KiB
TeX
Executable File
528 lines
16 KiB
TeX
Executable File
% A template for eLife submissions.
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%
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% Created by Overleaf (writeLaTeX).
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%
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\NeedsTeXFormat{LaTeX2e}
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\ProvidesClass{elife}[2022/06/01, v1.11]
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%% Move all option processing before loading class
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\newif\if@reqslineno
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\DeclareOption{lineno}{\@reqslinenotrue}
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%% Linespacing.
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\newif\if@onehalfspacing
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\newif\if@doublespacing
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\DeclareOption{onehalfspacing}{\@onehalfspacingtrue}
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\DeclareOption{doublespacing}{\@doublespacingtrue}
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\DeclareOption*{\PassOptionsToClass{\CurrentOption}{extarticle}}
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\ExecuteOptions{}
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\ProcessOptions\relax
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\LoadClass{extarticle}
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\RequirePackage[english]{babel}
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\RequirePackage{calc}
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\RequirePackage{etoolbox}
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\RequirePackage{regexpatch}
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\RequirePackage{ifxetex,ifluatex}
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\newif\ifxetexorluatex
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\ifxetex
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\xetexorluatextrue
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\else
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\ifluatex
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\xetexorluatextrue
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\else
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\xetexorluatexfalse
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\fi
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\fi
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\RequirePackage{amsmath}
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\RequirePackage{mdframed}
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\RequirePackage{lineno}
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\if@reqslineno\linenumbers\fi
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% Note v1.0 of elife.cls used Trueno font; this was
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% changed to use Open Sans in v1.1
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\ifxetexorluatex
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\RequirePackage{unicode-math}
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% v1.7: xits-math font name changed to XITSMath in TL2019
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\RequirePackage[default]{opensans}
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\setmonofont[Scale=MatchUppercase]{Latin Modern Mono}
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% XITSMath is really STIX. Really.
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% https://tex.stackexchange.com/questions/227216/stix-versus-xits
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\setmathfont[Extension = .otf,BoldFont = XITSMath-Bold,]{XITSMath-Regular}
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\else
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\RequirePackage[T1]{fontenc}
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\RequirePackage[utf8]{inputenc}
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\RequirePackage{stix}
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\RequirePackage[default]{opensans}
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\renewcommand{\ttdefault}{lmtt}
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\fi
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\RequirePackage{microtype}
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% Trueno/Open Sans requires a bigger "single" linespread.
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\linespread{1.2}
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\if@onehalfspacing\linespread{1.5}\fi
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\if@doublespacing\linespread{2.0}\fi
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\RequirePackage{graphicx,xcolor}
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\definecolor{eLifeDarkBlue}{HTML}{273B81}
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\definecolor{eLifeLightBlue}{HTML}{0A9DD9}
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\definecolor{eLifeMediumGrey}{HTML}{6D6E70}
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\definecolor{eLifeLightGrey}{HTML}{929497}
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\RequirePackage{booktabs}
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\RequirePackage{authblk}
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\RequirePackage[left=6cm,%
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marginparwidth=4cm,%
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marginparsep=0.5cm,%
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right=1.3cm,%
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top=2cm,%
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bottom=2.5cm,%
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headheight=21pt,%
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headsep=2\baselineskip,%
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columnsep=2em,%
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letterpaper]{geometry}%
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\RequirePackage{changepage}
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\RequirePackage{silence}
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\WarningFilter{caption}{The option `hypcap=true' will be ignored}
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\RequirePackage[labelfont={bf},%
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labelsep=period,%
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justification=raggedright,%
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singlelinecheck=false,%
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tableposition=top,font=small]
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{caption}
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% \captionsetup*[table]{skip=\medskipamount}
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\RequirePackage{natbib}
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\renewcommand{\bibfont}{\small}
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% modifed from https://github.com/gbhutani/vancouver_authoryear_bibstyle/
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\IfFileExists{vancouver-elife-doi-fix.bst}
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{\bibliographystyle{vancouver-elife-doi-fix}}
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{\PackageWarning{elife}{vancouver-elife-doi-fix.bst not found; falling back to apalike bibliography style.}\bibliographystyle{apalike}}
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% Make author in citation italic
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\renewcommand{\NAT@nmfmt}[1]{{\bfseries\itshape\color{eLifeMediumGrey} #1}}
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% ...as well as the year
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\xpatchcmd{\NAT@citex}
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{\@citea\NAT@hyper@{\NAT@nmfmt{\NAT@nm}\NAT@date}}
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{\@citea\NAT@hyper@{\NAT@nmfmt{\NAT@nm}\NAT@nmfmt{\NAT@date}}}
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{}{\PackageWarning{eLife}{Failed to patch year format in citation}}
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\xpatchcmd{\NAT@citex}
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{\else\unskip\NAT@spacechar\NAT@hyper@{\NAT@date}}
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{\else\unskip\NAT@spacechar\NAT@hyper@{\NAT@nmfmt{\NAT@date}}}
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{}{\PackageWarning{eLife}{Failed to patch year format in citation}}
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\xpatchcmd{\NAT@citex}
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{\hyper@natlinkbreak{\NAT@aysep\NAT@spacechar}{\@citeb\@extra@b@citeb}\NAT@date}
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{\hyper@natlinkbreak{\NAT@nmfmt{\NAT@aysep\NAT@spacechar}}{\@citeb\@extra@b@citeb}\NAT@nmfmt{\NAT@date}}
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{}{\PackageWarning{eLife}{Failed to patch year format in citation}}
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\xpatchcmd{\NAT@citex}
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{\@citea\NAT@hyper@{\NAT@date}}
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{\@citea\NAT@hyper@{\NAT@nmfmt{\NAT@date}}}
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{}{\PackageWarning{eLife}{Failed to patch year format in citation}}
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\xpatchcmd{\NAT@citex}
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{{\@citeb\@extra@b@citeb}\NAT@date}
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{{\@citeb\@extra@b@citeb}\NAT@nmfmt{\NAT@date}}
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{}{\PackageWarning{eLife}{Failed to patch year format in citation}}
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%% There, we're finally done with patching the year in citations.
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%
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% headers and footers
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%
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\RequirePackage{fancyhdr} % custom headers/footers
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\RequirePackage{lastpage} % Number of pages in the document
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\pagestyle{fancy} % Enables the custom headers/footers
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\addtolength{\headwidth}{\marginparsep}
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\addtolength{\headwidth}{\marginparwidth}
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\fancyhf{}
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% Removing header in v1.9
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% \chead{%
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% \setlength{\fboxsep}{3pt}
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% \colorbox{eLifeMediumGrey}{\begin{minipage}{\headwidth}\centering\color{white} Manuscript submitted to eLife\end{minipage}}%
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% }
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% Footers
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\rfoot{\small\color{eLifeMediumGrey}\thepage\space of\space\pageref{LastPage}}%
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\preto{\footrule}{\color{eLifeMediumGrey}}
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\renewcommand{\headrulewidth}{0pt}% % No header rule
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\renewcommand{\footrulewidth}{0.4pt}% % No footer rule
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%
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% section/subsection/paragraph set-up
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%
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\setcounter{secnumdepth}{0}
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\RequirePackage[explicit]{titlesec}
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\titleformat{\section}
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{\color{eLifeMediumGrey}\Large\bfseries}
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{\thesection}{}{#1}[]
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\titleformat{\subsection}
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{\large\bfseries}
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{\thesubsection}{}{#1}[]
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\titleformat{\subsubsection}
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{\large}
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{\thesubsubsection}{}{#1}[]
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\titleformat{\paragraph}
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{\color{eLifeMediumGrey}\large}
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{\theparagraph}{}{#1}[]
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\titlespacing*{\section}{0pc}{3ex \@plus4pt \@minus3pt}{0pt}
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\titlespacing*{\subsection}{0pc}{2.5ex \@plus3pt \@minus2pt}{0pt}
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\titlespacing*{\subsubsection}{0pc}{2ex \@plus2.5pt \@minus1.5pt}{0pt}
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\titlespacing*{\paragraph}{0pc}{1.5ex \@plus2pt \@minus1pt}{0pt}
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\RequirePackage{enumitem}
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\setlist{noitemsep}
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\RequirePackage{alphalph}
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\newalphalph{\fnsymbolmult}[mult]{\@fnsymbol}{5}
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\newcounter{authorfn}
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\setcounter{authorfn}{1}
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\newcommand{\authfn}[1]{%
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\fnsymbolmult{\numexpr\value{authorfn}+#1}%
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}
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\def\@correspondence{}
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\def\@contribution{}
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\def\@presentaddress{}
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\def\@deceased{}
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\newcommand{\corr}[2]{%
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\ifx\empty\@correspondence\else\appto{\@correspondence}{; }{}{}\fi
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\appto{\@correspondence}{%
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\url{#1}%
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\ifx\empty#2\else\space(#2)\fi
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}{}{}%
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}
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\newcommand{\contrib}[2][]{
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\appto{\@contribution}{%
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\ifx\empty#1\else\textsuperscript{#1}\fi
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#2\\
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}{}{}
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}
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\newcommand{\presentadd}[2][]{
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\ifx\empty\@presentaddress\else\appto{\@presentaddress}{; }{}{}\fi
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\appto{\@presentaddress}{%
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\ifx\empty#1\else\textsuperscript{#1}\fi
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#2%
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}{}{}
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}
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\newcommand{\deceased}[1]{\def\@deceased{\textsuperscript{#1}Deceased}}
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\reversemarginpar
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%
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% custom title page
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%
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\renewcommand{\Authfont}{\bfseries\large\raggedright}
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\renewcommand{\Affilfont}{\mdseries\large\raggedright}
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\renewcommand{\Authands}{, }
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\setlength{\affilsep}{16pt}
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\renewcommand{\AB@affilsepx}{; \protect\Affilfont}
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\newcommand{\themetadata}{%
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\textbf{*For correspondence:\\} \@correspondence\par
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\ifx\empty\@contribution\else
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\bigskip\@contribution\par\fi
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\ifx\empty\@presentaddress\else
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\bigskip\textbf{Present address: }\@presentaddress\par\fi
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\bigskip
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\ifx\empty\@deceased\else\@deceased\par\fi
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}
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\patchcmd{\@author}{\AB@authlist\\[\affilsep]\AB@affillist}{\AB@authlist\\[\affilsep]
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\marginpar{\raggedright\footnotesize\themetadata\par}\AB@affillist}{}{}
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\renewcommand{\maketitle}{%
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\vskip36pt%
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{\color{eLifeDarkBlue}\raggedright\bfseries\fontsize{22}{27}\selectfont \@title\par}%
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\vskip16pt
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{\@author\par}
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\vskip8pt
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}
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\renewenvironment{abstract}{%
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\setlength{\parindent}{0pt}\raggedright
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\textcolor{eLifeMediumGrey}{\rule{\textwidth}{2pt}}
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\vskip16pt
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\textcolor{eLifeLightBlue}{\large\bfseries\abstractname\space}
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}{%
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\vskip8pt
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\textcolor{eLifeMediumGrey}{\rule{\textwidth}{2pt}}
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\vskip16pt
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}
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%% Insert a grey line to separate floats from main text
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\newcommand{\topfigrule}{\vskip8pt\noindent{\rule{\linewidth}{1pt}}}
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\newcommand{\botfigrule}{\noindent{\rule{\linewidth}{1pt}}\vskip8pt}
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\RequirePackage{newfloat}
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\RequirePackage{wrapfig}
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\AtEndEnvironment{wrapfigure}{\vskip8pt\noindent{\rule{\hsize}{1pt}}}
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% \RequirePackage[lflt]{floatflt}
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% \AtEndEnvironment{floatingfigure}{\vskip8pt\noindent\textcolor{eLifeMediumGrey}{\rule{\hsize}{2pt}}}
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\DeclareFloatingEnvironment[placement=btp,name=Box]{featurebox}
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\captionsetup[featurebox]{font={Large,bf,color=eLifeDarkBlue}}
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% v1.11 2022-06 Updated many caption casing and dashes
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\newcounter{featurefigure}
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\newcounter{featuretable}
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\AtBeginEnvironment{featurebox}{%
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\setcounter{featurefigure}{0}%
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\setcounter{featuretable}{0}%
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\newcommand{\featurefig}[1]{%
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\refstepcounter{featurefigure}%
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\vskip\smallskipamount%
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{\small\textbf{\color{eLifeDarkBlue}Box \arabic{featurebox}---figure \arabic{featurefigure}.}\space #1\par}\medskip}
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\newcommand{\featuretable}[1]{%
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\refstepcounter{featuretable}%
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\vskip\smallskipamount%
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{\small\textbf{\color{eLifeDarkBlue}Box \arabic{featurebox}---table \arabic{featuretable}.}\space #1\par}\medskip}
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}
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\apptocmd{\featurebox}{%
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\begin{mdframed}[linewidth=0pt,backgroundcolor=eLifeLightBlue!10,fontcolor=eLifeDarkBlue]
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\if@reqslineno\addtolength{\linenumbersep}{1em}\internallinenumbers\fi%
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}{}{}
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\pretocmd{\endfeaturebox}{\end{mdframed}}{}{}
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\newenvironment{fullwidth}{%
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\begin{adjustwidth}{-4.5cm}{}%
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\hsize=\linewidth%
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}{\end{adjustwidth}}
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\appto{\appendix}{%
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\captionsetup*[figure]{name={Appendix \arabic{appendix}---figure },font={color=eLifeDarkBlue,small},skip=\smallskipamount}%
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\captionsetup*[table]{name={Appendix \arabic{appendix}---table },font={color=eLifeDarkBlue,small}}%
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}
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\newcounter{figsupp}
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\setcounter{figsupp}{0}
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\newcounter{data}
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\setcounter{data}{0}
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%% Added videos 2021/03/07
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\newcounter{srccode}
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\setcounter{srccode}{0}
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%% Added fig supp data and source code 2022/06
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\newcounter{fsdata}
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\setcounter{fsdata}{0}
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\newcounter{fssrccode}
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\setcounter{fssrccode}{0}
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%% Added videos 2018/06/03
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\newcounter{video}
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\setcounter{video}{0}
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\newcounter{videosupp}
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\setcounter{videosupp}{0}
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\def\supplist{}
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\RequirePackage{newfile}
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\newoutputstream{suppinfo}
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\openoutputfile{\jobname.suppinfo}{suppinfo}
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\addtostream{suppinfo}{\protect\setcounter{figure}{0}}
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% Added video source data and code 2022/06
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\DeclareRobustCommand{\video}[1]{%
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\refstepcounter{video}%
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\setcounter{data}{0}%
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\setcounter{srccode}{0}%
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\bigskip%
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\noindent{\small\textbf{Video \arabic{video}.} #1\par}%
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\bigskip
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}
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\DeclareRobustCommand{\videodata}[1]{%
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\refstepcounter{data}%
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\par\noindent{\small\textbf{Video~\thevideo---source data \arabic{data}.} #1}\par
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}
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\DeclareRobustCommand{\videosrccode}[1]{%
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\refstepcounter{srccode}%
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\par\noindent{\small\textbf{Video~\thevideo---source code \arabic{srccode}.} #1}\par
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}
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% Added fig supp source data and code 2022/06
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\DeclareRobustCommand{\figsuppsrccode}[1]{%
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\protect\refstepcounter{fssrccode}%
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\par\small\textbf{\figurename~\thefigure---figure supplement \arabic{figsupp}---source code~\arabic{fssrccode}. } #1\par
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}
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\DeclareRobustCommand{\figsuppdata}[1]{%
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\protect\refstepcounter{fsdata}%
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\par\small\textbf{\figurename~\thefigure---figure supplement \arabic{figsupp}---source data~\arabic{fsdata}. } #1\par
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}
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\AtBeginEnvironment{figure}{%
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\setcounter{figsupp}{0}
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\setcounter{data}{0}
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\setcounter{videosupp}{0}
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\setcounter{srccode}{0}
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\addtostream{suppinfo}{
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\protect\setcounter{figsupp}{0}
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\protect\refstepcounter{figure}
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}
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}
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\AtBeginEnvironment{wrapfigure}{%
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\setcounter{figsupp}{0}
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\setcounter{data}{0}
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\setcounter{videosupp}{0}
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\setcounter{srccode}{0}
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\addtostream{suppinfo}{
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\protect\setcounter{figsupp}{0}
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\protect\refstepcounter{figure}
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}
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}
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%% Updated 2017/06/30 to allow optional argument
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\DeclareRobustCommand{\figsupp}[3][]{%
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\refstepcounter{figsupp}%
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\addtostream{suppinfo}{%
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\protect\refstepcounter{figsupp}
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\protect\setcounter{fsdata}{0}
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\protect\setcounter{fssrccode}{0}
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}%
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{%
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\ifstrequal{#1}{none}{}{%
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\small\textbf{\figurename~\thefigure---figure supplement \arabic{figsupp}.}
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\ifstrempty{#1}{%
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\renewcommand\figsuppdata[1]{}%
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\renewcommand\figsuppsrccode[1]{}%
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#2}{%
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\renewcommand\figsuppdata[1]{}%
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\renewcommand\figsuppsrccode[1]{}%
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#1}}}\raggedright\par
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\addtostream{suppinfo}{%
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\noindent\protect\begin{minipage}{\linewidth}
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\protect #3\noexpand\par
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\textbf{\figurename~\thefigure---figure supplement \arabic{figsupp}.} #2\noexpand\par
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\vskip8pt
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\protect\end{minipage}
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\vskip16pt
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}
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}
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\DeclareRobustCommand{\figdata}[1]{%
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\refstepcounter{data}
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{\small\textbf{\figurename~\thefigure---source data \arabic{data}.} #1}\par
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}
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%% Added 2021/03/07
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\DeclareRobustCommand{\figsrccode}[1]{%
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\refstepcounter{srccode}
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{\small\textbf{\figurename~\thefigure---source code \arabic{srccode}.} #1}\par
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}
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%% Added 2018/06/03
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\DeclareRobustCommand{\videosupp}[1]{%
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\refstepcounter{videosupp}
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{\small\textbf{\figurename~\thefigure---video \arabic{videosupp}.} #1}\par
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}
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% Added table source data and code 2022/06
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\AtBeginEnvironment{table}{%
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\setcounter{data}{0}
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\setcounter{srccode}{0}
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\setcounter{videosupp}{0}
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}
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\AtBeginEnvironment{wraptable}{%
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\setcounter{data}{0}
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\setcounter{srccode}{0}
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\setcounter{videosupp}{0}
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}
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\DeclareRobustCommand{\tabledata}[1]{%
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\refstepcounter{data}
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{\small\textbf{\tablename~\thetable---source data \arabic{data}.} #1}\par
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}
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\DeclareRobustCommand{\tablesrccode}[1]{%
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\refstepcounter{srccode}
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{\small\textbf{\tablename~\thetable---source code \arabic{srccode}.} #1}\par
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}
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\AtEndDocument{%
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\closeoutputstream{suppinfo}
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% \pagestyle{empty}
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\renewcommand{\footrule}{}
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\rfoot{}
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\input{\jobname.suppinfo}
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}
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\newcounter{appendix}
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\setcounter{appendix}{0}
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\newenvironment{appendixbox}{%
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\setcounter{figure}{0}
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\setcounter{table}{0}
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\refstepcounter{appendix}%
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\clearpage%
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\patchcmd{\ttlf@section}{eLifeMediumGrey}{eLifeDarkBlue}{}{}
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\noindent{\bfseries\Large\color{eLifeMediumGrey}Appendix \arabic{appendix}\par}
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\nolinenumbers%
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|
\begin{mdframed}[hidealllines=true,backgroundcolor=eLifeLightBlue!10,fontcolor=eLifeDarkBlue,leftline=true,linecolor=eLifeLightBlue,linewidth=1em]
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|
\if@reqslineno\addtolength{\linenumbersep}{2em}\internallinenumbers\fi
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}{%
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|
\end{mdframed}
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|
}
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|
|
|
\RequirePackage{hyperref}
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|
\hypersetup{colorlinks=true,allcolors=black,citecolor=eLifeMediumGrey,linkcolor=eLifeMediumGrey,urlcolor=eLifeLightBlue,hypertexnames=false}
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|
\urlstyle{sf}
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|
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|
% Other desired commands
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|
\renewcommand{\equationautorefname}{Eq.}
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|
%% Added autoref support for \figsupp, \figdata, \video, \videosupp, (2021-03-04) \figsrccode
|
|
% Added support for figsupp, video source data and code 2022/06
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|
\newcommand{\figsuppautorefname}{figure Supplement}
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|
\newcommand{\dataautorefname}{source data}
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|
\newcommand{\videoautorefname}{Video}
|
|
\newcommand{\videosuppautorefname}{video}
|
|
\newcommand{\srccodeautorefname}{source code}
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|
\newcommand{\FIGSUPP}[2][]{%
|
|
\ifstrequal{#1}{}{}{\autoref{fig:#1}---}\autoref{figsupp:#2}%
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|
}
|
|
\newcommand{\FIGDATA}[2][]{%
|
|
\ifstrequal{#1}{}{}{\autoref{fig:#1}---}\autoref{figdata:#2}%
|
|
}
|
|
\newcommand{\TABLEDATA}[2][]{%
|
|
\ifstrequal{#1}{}{}{\autoref{tab:#1}---}\autoref{tabdata:#2}%
|
|
}
|
|
\newcommand{\VIDEODATA}[2][]{%
|
|
\ifstrequal{#1}{}{}{\autoref{video:#1}---}\autoref{viddata:#2}%
|
|
}
|
|
|
|
\newcommand{\FIGSRCCODE}[2][]{%
|
|
\ifstrequal{#1}{}{}{\autoref{fig:#1}---}\autoref{figsrccode:#2}%
|
|
}
|
|
\newcommand{\TABLESRCCODE}[2][]{%
|
|
\ifstrequal{#1}{}{}{\autoref{tab:#1}---}\autoref{tabsrccode:#2}%
|
|
}
|
|
\newcommand{\VIDEOSRCCODE}[2][]{%
|
|
\ifstrequal{#1}{}{}{\autoref{video:#1}---}\autoref{vidsrccode:#2}%
|
|
}
|
|
|
|
\newcommand{\VIDEOSUPP}[2][]{%
|
|
\ifstrequal{#1}{}{}{\autoref{fig:#1}---}\autoref{videosupp:#2}%
|
|
}
|
|
\newcommand{\FIG}[1]{\autoref{fig:#1}}
|
|
\newcommand{\TABLE}[1]{\autoref{tab:#1}}
|
|
\newcommand{\VIDEO}[1]{\autoref{video:#1}}
|
|
\newcommand{\EQ}[1]{\autoref{eq:#1}}
|
|
\newcommand{\BOX}[1]{\autoref{box:#1}}
|
|
\let\oldautoref\autoref
|
|
\renewcommand{\autoref}[1]{\emph{\textbf{\oldautoref{#1}}}}
|
|
|
|
\endinput
|