957 lines
28 KiB
TeX
957 lines
28 KiB
TeX
\newcommand\classname{FrontiersinHarvard} %this file is based in bioninfo.cls
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\newcommand\lastmodifieddate{2016/11/10}
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\newcommand\versionnumber{2.6}
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% For printing crop marks
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\newif\if@cropmarkson \@cropmarksontrue
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\NeedsTeXFormat{LaTeX2e}[2013/26/03]
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\ProvidesClass{\classname}[\lastmodifieddate\space\versionnumber]
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\setlength{\paperheight}{11truein}
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\setlength{\paperwidth}{8.5truein}
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\newif\if@final
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\DeclareOption{draft}{\PassOptionsToPackage{draft}{graphicx}}
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\DeclareOption{paper}{\PassOptionsToPackage{paper}{graphicx}}
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\DeclareOption{a4paper}{\PassOptionsToPackage{a4}{crop}}
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\DeclareOption{centre}{\PassOptionsToPackage{center}{crop}}
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\DeclareOption{crop}{\PassOptionsToPackage{cam}{crop}\global\@cropmarksontrue}
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\DeclareOption{nocrop}{\PassOptionsToPackage{off}{crop}\global\@cropmarksonfalse}
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\DeclareOption{info}{\PassOptionsToPackage{info}{crop}}
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\DeclareOption{noinfo}{\PassOptionsToPackage{noinfo}{crop}}
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\DeclareOption{final}{\global\@finaltrue}
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\DeclareOption{utf8}{\PassOptionsToPackage{utf8}{inputenc}}
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\ExecuteOptions{a4paper,nocrop,centre,info,paper}
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\ProcessOptions
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% Load all necessary packages
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\RequirePackage{inputenc,crop,graphicx,amsmath,array,color,amssymb,flushend,stfloats,amsthm,chngpage,times,datetime,epstopdf}
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\usepackage{parskip}[=v1]
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\def\helvetica{\fontfamily{phv}\selectfont}
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\def\helveticaitalic{\fontfamily{phv}\itshape\selectfont}
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\def\helveticabold{\fontfamily{phv}\bfseries\selectfont}
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\def\helveticabolditalic{\fontfamily{phv}\bfseries\itshape\selectfont}
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\usepackage[usenames,dvipsnames]{xcolor}
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\usepackage[labelsep=quad,indention=10pt]{caption}
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\usepackage[labelfont=bf,list=true]{subcaption}
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\newcommand\@ptsize{0}
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% Set twoside printing
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\@twosidetrue
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% Marginal notes are on the outside edge
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\@mparswitchfalse
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\reversemarginpar
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\renewcommand\normalsize{%
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\@setfontsize\normalsize{12}{12}%
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\abovedisplayskip 10\p@ \@plus2\p@ \@minus5\p@
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\abovedisplayshortskip \z@ \@plus3\p@
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\belowdisplayshortskip 6\p@ \@plus3\p@ \@minus3\p@
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\belowdisplayskip \abovedisplayskip
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\let\@listi\@listI}
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\normalsize
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\let\@bls\baselineskip
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\newcommand\small{%
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\@setfontsize\small{11}{12}%
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\abovedisplayskip 11\p@ minus 3\p@
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\belowdisplayskip \abovedisplayskip
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\abovedisplayshortskip \z@ plus 2\p@
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\belowdisplayshortskip 4\p@ plus 2\p@ minus2\p@
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\def\@listi{\topsep 4.5\p@ plus 2\p@ minus 1\p@
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\itemsep \parsep
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\topsep 4\p@ plus 2\p@ minus 2\p@}}
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\newcommand\footnotesize{%
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\@setfontsize\footnotesize{8}{10}%
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\abovedisplayskip 6\p@ minus 3\p@
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\belowdisplayskip\abovedisplayskip
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\abovedisplayshortskip \z@ plus 3\p@
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\belowdisplayshortskip 6\p@ plus 3\p@ minus 3\p@
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\def\@listi{\topsep 3\p@ plus 1\p@ minus 1\p@
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\parsep 2\p@ plus 1\p@ minus 1\p@\itemsep \parsep}}
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\def\scriptsize{\@setfontsize\scriptsize{11pt}{11pt}}
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\def\tiny{\@setfontsize\tiny{10pt}{11pt}}
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\def\large{\@setfontsize\large{13pt}{14pt}}
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\def\Large{\@setfontsize\Large{14pt}{16}}
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\def\LARGE{\@setfontsize\LARGE{15pt}{17pt}}
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\def\huge{\@setfontsize\huge{22pt}{22pt}}
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\def\Huge{\@setfontsize\Huge{30pt}{30pt}}
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\DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm}
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\DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
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\DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
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\DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
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\DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
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\DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl}
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\DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc}
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% Line spacing
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\setlength\lineskip{1\p@}
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\setlength\normallineskip{1\p@}
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\renewcommand\baselinestretch{}
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% Set inter-para skips
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\setlength\smallskipamount{3\p@ \@plus 1\p@ \@minus 1\p@}
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\setlength\medskipamount{6\p@ \@plus 2\p@}
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\setlength\bigskipamount{12\p@ \@plus 4\p@ \@minus 4\p@}
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% Paragraph dimensions and inter-para spacing
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\setlength\parindent{3mm}
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\setlength{\parskip}{\medskipamount}
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% Page break penalties
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\@lowpenalty 51
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\@medpenalty 151
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\@highpenalty 301
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% Disallow widows and orphans
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\clubpenalty 10000
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\widowpenalty 10000
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% Disable page breaks before equations, allow pagebreaks after
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% equations and discourage widow lines before equations.
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\displaywidowpenalty 100
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\predisplaypenalty 10000
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\postdisplaypenalty 2500
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% Allow breaking the page in the middle of a paragraph
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\interlinepenalty 0
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% Disallow breaking the page after a hyphenated line
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\brokenpenalty 10000
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% Hyphenation; don't split words into less than three characters
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\lefthyphenmin=3
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\righthyphenmin=3
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%
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% Set page layout dimensions
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%
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\setlength\headheight{16\p@} % height of running head
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\setlength\topmargin{1.3pc} % head margin
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\addtolength\topmargin{-1in} % subtract out the 1 inch driver margin
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\setlength\topskip{10\p@} % height of first line of text
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\setlength\headsep{19\p@} % space below running head --
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\setlength\footskip{34\p@} % space above footer line
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\setlength\maxdepth{1\topskip} % pages can be short or deep by half a line?
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\setlength\textwidth{42pc} % text measure excluding margins
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\setlength\textheight{56\baselineskip} % 54 lines on a full page,
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\addtolength\textheight{\topskip} % including the first
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% line on the page
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% Set the margins
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\setlength\marginparsep{3\p@}
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\setlength\marginparpush{3\p@}
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\setlength\marginparwidth{35\p@}
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\setlength\oddsidemargin{4.5pc}
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\addtolength\oddsidemargin{-1in} % subtract out the 1 inch driver margin
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\setlength\@tempdima{\paperwidth}
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\addtolength\@tempdima{-\textwidth}
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\addtolength\@tempdima{-4.5pc}
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\setlength\evensidemargin{\@tempdima}
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\addtolength\evensidemargin{-1in}
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\setlength\columnsep{1.5pc} % space between columns for double-column text
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\setlength\columnseprule{0\p@} % width of rule between two columns
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% Footnotes
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\setlength\footnotesep{9\p@} % space between footnotes
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% space between text and footnote
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\setlength{\skip\footins}{12\p@ \@plus 6\p@ \@minus 1\p@}
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% Float placement parameters
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% The total number of floats that can be allowed on a page.
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\setcounter{totalnumber}{10}
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% The maximum number of floats at the top and bottom of a page.
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\setcounter{topnumber}{5}
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\setcounter{bottomnumber}{5}
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% The maximum part of the top or bottom of a text page that can be
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% occupied by floats. This is set so that at least four lines of text
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% fit on the page.
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\renewcommand\topfraction{.9}
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\renewcommand\bottomfraction{.9}
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% The minimum amount of a text page that must be occupied by text.
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% This should accomodate four lines of text.
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\renewcommand\textfraction{.06}
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% The minimum amount of a float page that must be occupied by floats.
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\renewcommand\floatpagefraction{.94}
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% The same parameters repeated for double column output
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\renewcommand\dbltopfraction{.9}
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\renewcommand\dblfloatpagefraction{.9}
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% Space between floats
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\setlength\floatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
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% Space between floats and text
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\setlength\textfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
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% Space above and below an inline figure
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\setlength\intextsep {18\p@ \@plus 2\p@ \@minus 2\p@}
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% For double column floats
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\setlength\dblfloatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
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\setlength\dbltextfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
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% Space left at top, bottom and inbetween floats on a float page.
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\setlength\@fptop{0\p@} % no space above float page figures
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\setlength\@fpsep{12\p@ \@plus 1fil}
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\setlength\@fpbot{0\p@}
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% The same for double column
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\setlength\@dblfptop{0\p@}
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\setlength\@dblfpsep{12\p@ \@plus 1fil}
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\setlength\@dblfpbot{0\p@}
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% Override settings in mathtime back to TeX defaults
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\DeclareMathSizes{5} {5} {5} {5}
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\DeclareMathSizes{6} {6} {5} {5}
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\DeclareMathSizes{7} {7} {5} {5}
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\DeclareMathSizes{8} {8} {6} {5}
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\DeclareMathSizes{9} {9} {6.5} {5}
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\DeclareMathSizes{10} {10} {7.5} {5}
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\DeclareMathSizes{12} {12} {9} {7}
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% Page styles
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\def\ps@headings
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{%
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\def\@oddfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
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\hbox to \textwidth{\helveticabold\small {Frontiers}\hfill \thepage}%
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}}%
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\def\@evenfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
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\hbox to \textwidth{\helveticabold\small {Frontiers}\hfill \thepage}%
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}}%
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\def\@evenhead{\vbox{\hbox to \textwidth{\fontsize{11}{10}\selectfont
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\helveticabold{\fontshape{it}\selectfont
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\strut\firstAuthorLast}\hfill\strut\rightmark}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
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\def\@oddhead{\vbox{\hbox to \textwidth{\fontsize{11}{10}\selectfont
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\helveticabold{\fontshape{it}\selectfont
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\strut\firstAuthorLast}\hfill\strut\rightmark}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
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\def\titlemark##1{\markboth{##1}{##1}}%
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\def\authormark##1{\gdef\leftmark{##1}}%
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}
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\def\ps@opening
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{%
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\def\@oddfoot{\vbox to 13\p@{\hbox{\rule{\textwidth}{1\p@}}\vss
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\hbox to \textwidth{\helvetica
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\fontsize{7}{9}\fontshape{n}\selectfont \space %
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\hfill\small\helveticabold\thepage}%
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}}%
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\def\@evenfoot{\vbox to 13\p@{\rule{\textwidth}{1\p@}\vss
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\hbox to \textwidth{\helvetica\thepage\hfill
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\fontsize{7}{9}\fontshape{n}\selectfont \space }%
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}}%
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\let\@evenhead\relax
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\let\@oddhead\relax}
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% Page range
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\newif\iflastpagegiven \lastpagegivenfalse
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\newcommand\firstpage[1]{%
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\gdef\@firstpage{#1}%
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\ifnum\@firstpage>\c@page
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\setcounter{page}{#1}%
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\ClassWarning{BIO}{Increasing pagenumber to \@firstpage}%
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\else \ifnum\@firstpage<\c@page
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\ClassWarning{BIO}{Firstpage lower than pagenumber}\fi\fi
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\xdef\@firstpage{\the\c@page}%
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}
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\def\@firstpage{1}
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\def\pagenumbering#1{%
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\global\c@page \@ne
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\gdef\thepage{\csname @#1\endcsname \c@page}%
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\gdef\thefirstpage{%
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\csname @#1\endcsname \@firstpage}%
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\gdef\thelastpage{%
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\csname @#1\endcsname \@lastpage}%
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}
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\newcommand\lastpage[1]{\xdef\@lastpage{#1}%
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\global\lastpagegiventrue}
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\def\@lastpage{0}
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\def\setlastpage{\iflastpagegiven\else
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\edef\@tempa{@lastpage@}%
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\expandafter
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\ifx \csname \@tempa \endcsname \relax
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\gdef\@lastpage{0}%
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\else
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\xdef\@lastpage{\@nameuse{@lastpage@}}%
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\fi
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\fi }
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\def\writelastpage{%
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\iflastpagegiven \else
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\immediate\write\@auxout%
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{\string\global\string\@namedef{@lastpage@}{\the\c@page}}%
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\fi
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}
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\def\thepagerange{%
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\ifnum\@lastpage =0 {\ \bf ???} \else
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\ifnum\@lastpage = \@firstpage \ \thefirstpage\else
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\thefirstpage--\thelastpage \fi\fi}
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\AtBeginDocument{\setlastpage
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\pagenumbering{arabic}%
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}
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\AtEndDocument{%
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\writelastpage
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\if@final
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\clearemptydoublepage
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\else
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\clearpage
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\fi}
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%
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% Sectional units
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%
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% Counters
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\newcounter{section}
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\newcounter{subsection}[section]
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\newcounter{subsubsection}[subsection]
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\newcounter{paragraph}[subsubsection]
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\newcounter{subparagraph}[paragraph]
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\newcounter{figure}
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\newcounter{subfigure}
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\newcounter{table}
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% Form of the numbers
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\newcommand\thepage{\arabic{page}}
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\renewcommand\thesection{\arabic{section}}
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\renewcommand\thesubsection{{\thesection.\arabic{subsection}}}
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\renewcommand\thesubsubsection{{\thesubsection.\arabic{subsubsection}}}
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\renewcommand\theparagraph{\thesubsubsection.\arabic{paragraph}}
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\renewcommand\thesubparagraph{\theparagraph.\arabic{subparagraph}}
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\renewcommand\theequation{\arabic{equation}}
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% Form of the words
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\newcommand\contentsname{Contents}
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\newcommand\listfigurename{List of Figures}
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\newcommand\listtablename{List of Tables}
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\newcommand\partname{Part}
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\newcommand\appendixname{Appendix}
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\newcommand\abstractname{Abstract}
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\newcommand\refname{References}
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\newcommand\bibname{References}
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\newcommand\indexname{Index}
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\newcommand\figurename{Figure}
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\newcommand\tablename{Table}
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% Clearemptydoublepage should really clear the running heads too
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\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}}
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% Frontmatter, mainmatter and backmatter
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\newif\if@mainmatter \@mainmattertrue
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\newcommand\frontmatter{%
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\clearpage
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\@mainmatterfalse
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\pagenumbering{roman}}
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\newcommand\mainmatter{%
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\clearpage
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\@mainmattertrue
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\pagenumbering{arabic}}
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\newcommand\backmatter{%
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\clearpage
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\@mainmatterfalse}
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\newdateformat{mydate}{\THEDAY \ \monthname[\THEMONTH] \THEYEAR}
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\newdateformat{mydate2}{\monthname[\THEMONTH] \THEYEAR}
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%********
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% TITLE *
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%********
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\newlength{\dropfromtop}
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\setlength{\dropfromtop}{\z@}
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% Application Notes
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\newif\if@appnotes
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\newcommand{\application}{%
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% \setlength{\dropfromtop}{-2.25pc}%
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\global\@appnotestrue}
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% Short Title is for the Title of the Article
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% Title is for the Title of the Journal
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\long\def\title{\@ifnextchar[{\short@title}{\@@title}}
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\def\short@title[#1]{\titlemark{#1}\@@@title}
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\def\@@title#1{\authormark{#1}\@@@title{#1}}
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\long\def\@@@title#1{\gdef\@title{#1}}
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\long\def\author{\@ifnextchar[{\short@uthor}{\@uthor}}
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\def\short@uthor[#1]{\authormark{#1}\@@author}
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\def\@uthor#1{\authormark{#1}\@@author{#1}}
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\long\def\@@author#1{\gdef\@author{#1}}
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\def\vol#1{\global\def\@vol{#1}}
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\def\issue#1{\global\def\@issue{#1}}
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\def\address#1{\global\def\@issue{#1}}
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\def\history#1{\global\def\@history{#1}}
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\def\correspondance#1{\global\def\@correspondance{#1}}
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\def\extraAuth#1{\global\def\@extraAuth{#1}}
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\def\address#1{\global\def\@address{#1}}
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\def\date#1{\gdef\@date{#1}}
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%***********
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% Colors *
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%***********
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% Other colors
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\definecolor{black}{cmyk}{0, 0, 0, 1}
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\definecolor{gray}{cmyk}{0, 0, 0, 0.25}
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\definecolor{darkgray}{cmyk}{0, 0, 0, 0.5}
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\newlength{\extraspace}
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\setlength{\extraspace}{\z@}
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\newcommand\maketitle{\par
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\begingroup
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\renewcommand\thefootnote{\@fnsymbol\c@footnote}%
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\def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
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\long\def\@makefntext##1{\parindent 3mm\noindent
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% \@textsuperscript{\normalfont\@thefnmark}\raggedright##1}%
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\@textsuperscript{\normalfont\@thefnmark}##1}%
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\if@twocolumn
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\ifnum \col@number=\@ne
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\@maketitle
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\else
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\twocolumn[\@maketitle]%
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\fi
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\else
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\newpage
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\global\@topnum\z@ % Prevents figures from going at top of page.
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\@maketitle
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\fi
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\thispagestyle{opening}\@thanks
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\endgroup
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\setcounter{footnote}{0}%
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\global\let\thanks\relax
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\global\let\maketitle\relax
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\global\let\@maketitle\relax
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\global\let\@address\@empty
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\global\let\@history\@empty
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\global\let\@extraAuth\@empty
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\global\let\@topic\@empty
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\global\let\@thanks\@empty
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\global\let\@author\@empty
|
|
\global\let\@date\@empty
|
|
\global\let\@title\@empty
|
|
\global\let\@pubyear\@empty
|
|
\global\let\address\relax
|
|
\global\let\topic\relax
|
|
\global\let\extraAuth\relax
|
|
\global\let\title\relax
|
|
\global\let\author\relax
|
|
\global\let\date\relax
|
|
\global\let\pubyear\relax
|
|
\global\let\@copyrightline\@empty
|
|
\global\let\and\relax
|
|
\@afterindentfalse\@afterheading
|
|
}
|
|
|
|
\newlength{\aboveskipchk}%for checking oddpage or evenpage top skip
|
|
\setlength{\aboveskipchk}{\z@}%
|
|
|
|
\def\@maketitle{%
|
|
\let\footnote\thanks
|
|
\clearemptydoublepage
|
|
\checkoddpage\ifcpoddpage\setlength{\aboveskipchk}{-7pc}\else\setlength{\aboveskipchk}{-3pc}\fi%for checking oddpage or evenpage top skip%%
|
|
\vspace*{\aboveskipchk}%
|
|
\vspace{\dropfromtop}%
|
|
\hbox to \textwidth{%
|
|
|
|
\parbox[t]{15pc}{%
|
|
\helvetica
|
|
\hfil
|
|
\flushleft \includegraphics[width=12pc,angle=0]{./logo1.eps}
|
|
|
|
|
|
}}
|
|
|
|
\rule{\textwidth}{1\p@}\par%
|
|
\helvetica
|
|
\hbox to \textwidth{%
|
|
\parbox[t]{36.5pc}{%
|
|
\vspace*{1sp}
|
|
{\helveticabold\fontsize{20}{21}\color{black}\selectfont\raggedright \@title \par}%
|
|
\vspace{4.5\p@}
|
|
{\helveticabold\fontsize{12}{15}\selectfont\raggedright \@author \par}%
|
|
\vspace{4\p@}
|
|
{\helvetica\fontsize{12}{12}\selectfont\raggedright\slshape\@address \Address \\ \par}%
|
|
\vspace{6\p@}
|
|
{\helvetica\fontsize{12}{10}\selectfont\raggedright {Correspondence*:\\ }\@correspondance \corrAuthor \\ \corrEmail \par}
|
|
\vspace{4\p@}
|
|
{\helvetica\fontsize{12}{12}\selectfont\raggedright\@extraAuth \par}%
|
|
\vspace{8\p@}
|
|
}%
|
|
}
|
|
\vspace{14.5\p@}%
|
|
}
|
|
|
|
%***********
|
|
% Abstract *
|
|
%***********
|
|
\newcommand{\absection}[1]{%
|
|
\par\noindent{\bfseries #1}\space\ignorespaces}
|
|
|
|
\newenvironment{abstract}{%
|
|
\begingroup
|
|
\let\section\absection
|
|
\fontfamily{\sfdefault}\fontsize{12}{12}\sffamily\selectfont
|
|
{\fontseries{b}\selectfont ABSTRACT}\par}
|
|
{\endgroup\smallskip\@afterheading\@afterindentfalse\vskip 12pt plus -2pt minus 2pt}
|
|
|
|
% Section macros
|
|
|
|
% Lowest level heading that takes a number by default
|
|
\setcounter{secnumdepth}{5}
|
|
|
|
\renewcommand{\@seccntformat}[1]{\csname the#1\endcsname\quad}
|
|
|
|
\def\section{%
|
|
\@startsection{section}{1}{\z@}
|
|
{-10\p@ plus -3\p@}{3\p@}
|
|
{\reset@font\raggedright\helveticabold\fontsize{13}{13}\color{black}\selectfont\MakeUppercase}}
|
|
|
|
\def\subsection{%
|
|
\@startsection{subsection}{2}{\z@}
|
|
{4\p@ plus 2\p@}{2\p@}
|
|
{\reset@font\raggedright\mathversion{bold}\helveticabold\fontsize{11.5}{12}}}
|
|
|
|
\def\subsubsection{%
|
|
\@startsection{subsubsection}{3}{\z@}
|
|
{2\p@ plus 2\p@}{1\p@}
|
|
{\reset@font\raggedright\mathversion{bold}\helvetica\fontsize{11.5}{12}}}
|
|
|
|
\def\paragraph{%
|
|
\@startsection{paragraph}{4}{\z@}
|
|
{2\p@ plus 1\p@}{1\p@}
|
|
{\reset@font\itshape\helveticabold\fontsize{11.5}{12}}}
|
|
|
|
\def\subparagraph{%
|
|
\@startsection{subparagraph}{5}{\z@}
|
|
{2\p@ plus 1\p@}{1\p@}
|
|
{\reset@font\itshape\helvetica\fontsize{11.5}{12}}}
|
|
|
|
\def\textcolon{\text{\rm :}}
|
|
|
|
% ********************
|
|
% Figures and tables *
|
|
% ********************
|
|
|
|
% Table and array parameters
|
|
\setlength\arraycolsep{.5em}
|
|
\setlength\tabcolsep{.5em}
|
|
\setlength\arrayrulewidth{.5pt}
|
|
\setlength\doublerulesep{2.5pt}
|
|
\setlength\extrarowheight{\z@}
|
|
\renewcommand\arraystretch{1}
|
|
|
|
%\newlength{\abovecaptionskip}
|
|
%\newlength{\belowcaptionskip}
|
|
%\setlength{\abovecaptionskip}{13pt}
|
|
%\setlength{\belowcaptionskip}{10.5pt}
|
|
|
|
\long\def\@makecaption#1#2{\vspace{\abovecaptionskip}%
|
|
\begingroup
|
|
\normalsize
|
|
\textbf{#1.}\enskip{#2}\par
|
|
\endgroup}
|
|
|
|
|
|
% Table rules
|
|
\def\toprule{\noalign{\ifnum0=`}\fi\hrule \@height 0.5pt \hrule \@height 6pt \@width 0pt \futurelet
|
|
\@tempa\@xhline}
|
|
\def\midrule{\noalign{\ifnum0=`}\fi \hrule \@height 6.75pt \@width 0pt \hrule \@height 0.5pt
|
|
\hrule \@height 6pt \@width 0pt \futurelet \@tempa\@xhline}
|
|
\def\botrule{\noalign{\ifnum0=`}\fi \hrule \@height 5.75pt \@width 0pt \hrule \@height 0.5pt \futurelet
|
|
\@tempa\@xhline}
|
|
\def\hrulefill{\leavevmode\leaders\hrule height .5pt\hfill\kern\z@}
|
|
|
|
\def\thefigure{\@arabic\c@figure}
|
|
\def\fps@figure{tbp}
|
|
\def\ftype@figure{1}
|
|
\def\ext@figure{lof}
|
|
\def\fnum@figure{\figurename~\thefigure}
|
|
\def\figure{\@float{figure}}
|
|
\let\endfigure\end@float
|
|
\@namedef{figure*}{\@dblfloat{figure}}
|
|
\@namedef{endfigure*}{\end@dblfloat}
|
|
\def\thetable{\@arabic\c@table}
|
|
\def\fps@table{tbp}
|
|
\def\ftype@table{2}
|
|
\def\ext@table{lot}
|
|
\def\fnum@table{Table~\thetable}
|
|
\def\table{\let\source\tablesource\@float{table}}
|
|
\def\endtable{\end@float}
|
|
\@namedef{table*}{\@dblfloat{table}}
|
|
\@namedef{endtable*}{\end@dblfloat}
|
|
|
|
\newif\if@rotate \@rotatefalse
|
|
\newif\if@rotatecenter \@rotatecenterfalse
|
|
\def\rotatecenter{\global\@rotatecentertrue}
|
|
\def\rotateendcenter{\global\@rotatecenterfalse}
|
|
\def\rotate{\global\@rotatetrue}
|
|
\def\endrotate{\global\@rotatefalse}
|
|
\newdimen\rotdimen
|
|
\def\rotstart#1{\special{ps: gsave currentpoint currentpoint translate
|
|
#1 neg exch neg exch translate}}
|
|
\def\rotfinish{\special{ps: currentpoint grestore moveto}}
|
|
\def\rotl#1{\rotdimen=\ht#1\advance\rotdimen by \dp#1
|
|
\hbox to \rotdimen{\vbox to\wd#1{\vskip \wd#1
|
|
\rotstart{270 rotate}\box #1\vss}\hss}\rotfinish}
|
|
\def\rotr#1{\rotdimen=\ht #1\advance\rotdimen by \dp#1
|
|
\hbox to \rotdimen{\vbox to \wd#1{\vskip \wd#1
|
|
\rotstart{90 rotate}\box #1\vss}\hss}\rotfinish}
|
|
|
|
\newif\ifsub@@figure \sub@@figuretrue
|
|
\def\thesubfigure{\@arabic\c@figure\alph{subfigure}}
|
|
\def\fps@subfigure{tbp}
|
|
\def\ftype@subfigure{1}
|
|
\def\ext@subfigure{lof}
|
|
\def\fnum@subfigure{Figure \thesubfigure}
|
|
\def\subfigure{\ifsub@@figure\global\sub@@figurefalse\stepcounter{figure}\fi%
|
|
\@float{subfigure}}
|
|
\let\endsubfigure\end@float
|
|
\@namedef{subfigure*}{\ifsub@@figure\global\sub@@figurefalse%
|
|
\stepcounter{figure}\fi \@dblfloat{subfigure}}
|
|
\@namedef{endsubfigure*}{\end@dblfloat}
|
|
|
|
\def\endfigure{\global\sub@@figuretrue\end@float}
|
|
\@namedef{endfigure*}{\global\sub@@figuretrue\end@dblfloat}
|
|
|
|
\newdimen\tempdime
|
|
\newbox\temptbox
|
|
|
|
% From ifmtarg.sty
|
|
% Copyright Peter Wilson and Donald Arseneau, 2000
|
|
\begingroup
|
|
\catcode`\Q=3
|
|
\long\gdef\@ifmtarg#1{\@xifmtarg#1QQ\@secondoftwo\@firstoftwo\@nil}
|
|
\long\gdef\@xifmtarg#1#2Q#3#4#5\@nil{#4}
|
|
\long\gdef\@ifnotmtarg#1{\@xifmtarg#1QQ\@firstofone\@gobble\@nil}
|
|
\endgroup
|
|
|
|
\def\tablesize{\@setfontsize\tablesize{10\p@}{10\p@}}
|
|
|
|
\newenvironment{processtable}[3]{\setbox\temptbox=\hbox{{\tablesize #2}}%
|
|
\tempdime\wd\temptbox\@processtable{#1}{#2}{#3}{\tempdime}}
|
|
{\relax}
|
|
|
|
\newcommand{\@processtable}[4]{%
|
|
\if@rotate
|
|
\setbox4=\vbox to \hsize{\vss\hbox to \textheight{%
|
|
\begin{minipage}{#4}%
|
|
\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
|
|
\vskip7\p@\noindent
|
|
\parbox{#4}{\fontsize{10}{10}\selectfont #3\par}%
|
|
\end{minipage}}\vss}%
|
|
\rotr{4}
|
|
\else
|
|
\hbox to \hsize{\hss\begin{minipage}[t]{#4}%
|
|
\vskip2.9pt
|
|
\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
|
|
\vskip6\p@\noindent
|
|
\parbox{#4}{\fontsize{8}{9}\selectfont #3\par}%
|
|
\end{minipage}\hss}\fi}%
|
|
|
|
\newcolumntype{P}[1]{>{\raggedright\let\\\@arraycr\hangindent1em}p{#1}}
|
|
|
|
% ******************************
|
|
% List numbering and lettering *
|
|
% ******************************
|
|
\def\labelenumi{{\rm\arabic{enumi}.}}
|
|
\def\theenumi{\arabic{enumi}}
|
|
\def\labelenumii{{\rm\alph{enumii}.}}
|
|
\def\theenumii{\alph{enumii}}
|
|
\def\p@enumii{\theenumi}
|
|
\def\labelenumiii{{\rm(\arabic{enumiii})}}
|
|
\def\theenumiii{\roman{enumiii}}
|
|
\def\p@enumiii{\theenumi(\theenumii)}
|
|
\def\labelenumiv{{\rm(\arabic{enumiv})}}
|
|
\def\theenumiv{\Alph{enumiv}}
|
|
\def\p@enumiv{\p@enumiii\theenumiii}
|
|
\def\labelitemi{{\small$\bullet$}}
|
|
\def\labelitemii{{\small$\bullet$}}
|
|
\def\labelitemiii{{\small$\bullet$}}
|
|
\def\labelitemiv{{\small$\bullet$}}
|
|
|
|
\def\@listI{\leftmargin\leftmargini \topsep\medskipamount}
|
|
\let\@listi\@listI
|
|
\@listi
|
|
\def\@listii{\topsep\z@\leftmargin\leftmarginii}
|
|
\def\@listiii{\leftmargin\leftmarginiii \topsep\z@}
|
|
\def\@listiv{\leftmargin\leftmarginiv \topsep\z@}
|
|
\def\@listv{\leftmargin\leftmarginv \topsep\z@}
|
|
\def\@listvi{\leftmargin\leftmarginvi \topsep\z@}
|
|
|
|
\setlength{\leftmargini}{3mm}
|
|
\setlength{\leftmarginii}{\z@}
|
|
\setlength{\leftmarginiii}{\z@}
|
|
\setlength{\leftmarginiv}{\z@}
|
|
|
|
% Changes to the list parameters for enumerate
|
|
\def\enumargs{%
|
|
\partopsep \z@
|
|
\itemsep 3\p@
|
|
\parsep \z@
|
|
\labelsep 0.5em
|
|
\listparindent \parindent
|
|
\itemindent \z@
|
|
\topsep 2\p@
|
|
}
|
|
|
|
\def\enumerate{%
|
|
\@ifnextchar[{\@numerate}{\@numerate[0]}}
|
|
|
|
\def\@numerate[#1]{%
|
|
\ifnum \@enumdepth >3 \@toodeep\else
|
|
\advance\@enumdepth \@ne
|
|
\edef\@enumctr{enum\romannumeral\the\@enumdepth}
|
|
\list{\csname label\@enumctr\endcsname}{%
|
|
\enumargs
|
|
\setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@enumdepth\endcsname}
|
|
\usecounter{\@enumctr}
|
|
\settowidth\labelwidth{#1}
|
|
\addtolength{\leftmargin}{\labelwidth}
|
|
\addtolength{\leftmargin}{\labelsep}
|
|
\def\makelabel##1{\hss \llap{##1}}}%
|
|
\fi
|
|
}
|
|
\let\endenumerate\endlist
|
|
|
|
% Changes to the list parameters for itemize
|
|
\def\itemargs{%
|
|
\partopsep \z@
|
|
\itemsep 3\p@
|
|
\parsep \z@
|
|
\labelsep 0.5em
|
|
\rightmargin \z@
|
|
\listparindent \parindent
|
|
\itemindent \z@
|
|
\topsep 2\p@
|
|
}
|
|
|
|
\def\itemize{%
|
|
\@ifnextchar[{\@itemize}{\@itemize[$\bullet$]}}
|
|
|
|
\def\@itemize[#1]{%
|
|
\ifnum \@itemdepth >3 \@toodeep\else
|
|
\advance\@itemdepth \@ne
|
|
\edef\@itemctr{item\romannumeral\the\@itemdepth}
|
|
\list{\csname label\@itemctr\endcsname}{%
|
|
\itemargs
|
|
\setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@itemdepth\endcsname}
|
|
\settowidth\labelwidth{#1}
|
|
\addtolength{\leftmargin}{\labelwidth}
|
|
\addtolength{\leftmargin}{\labelsep}
|
|
\def\makelabel##1{\hss \llap{##1}}}%
|
|
\fi
|
|
}
|
|
\let\enditemize\endlist
|
|
|
|
\newenvironment{unlist}{%
|
|
\begin{list}{}%
|
|
{\setlength{\labelwidth}{\z@}%
|
|
\setlength{\labelsep}{\z@}%
|
|
\setlength{\topsep}{\medskipamount}%
|
|
\setlength{\itemsep}{3\p@}%
|
|
\setlength{\leftmargin}{2em}%
|
|
\setlength{\itemindent}{-2em}}}
|
|
{\end{list}}
|
|
|
|
|
|
% ***********************
|
|
% Quotes and Quotations *
|
|
% ***********************
|
|
\def\quotation{\par\begin{list}{}{
|
|
\setlength{\topsep}{\medskipamount}
|
|
\setlength{\leftmargin}{2em}%
|
|
\setlength{\rightmargin}{\z@}%
|
|
\setlength\labelwidth{0pt}%
|
|
\setlength\labelsep{0pt}%
|
|
\listparindent\parindent}%
|
|
\item[]}
|
|
\def\endquotation{\end{list}}
|
|
\let\quote\quotation
|
|
\let\endquote\endquotation
|
|
|
|
\skip\@mpfootins = \skip\footins
|
|
\fboxsep=6\p@
|
|
\fboxrule=1\p@
|
|
|
|
% *******************
|
|
% Table of contents *
|
|
% *******************
|
|
\newcommand\@pnumwidth{4em}
|
|
\newcommand\@tocrmarg{2.55em plus 1fil}
|
|
\newcommand\@dotsep{1000}
|
|
\setcounter{tocdepth}{4}
|
|
|
|
\def\numberline#1{\hbox to \@tempdima{{#1}}}
|
|
|
|
\def\@authortocline#1#2#3#4#5{%
|
|
\vskip 1.5\p@
|
|
\ifnum #1>\c@tocdepth \else
|
|
{\leftskip #2\relax \rightskip \@tocrmarg \parfillskip -\rightskip
|
|
\parindent #2\relax\@afterindenttrue
|
|
\interlinepenalty\@M
|
|
\leavevmode
|
|
\@tempdima #3\relax
|
|
\advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
|
|
{\itshape #4}\nobreak
|
|
\leaders\hbox{$\m@th
|
|
\mkern \@dotsep mu\hbox{.}\mkern \@dotsep
|
|
mu$}\hfill
|
|
\nobreak
|
|
\hb@xt@\@pnumwidth{\hfil}%
|
|
\par}%
|
|
\fi}
|
|
|
|
\newcommand*\l@author{\@authortocline{2}{0pt}{30pt}}
|
|
\newcommand*\l@section{\@dottedtocline{3}{11pt}{20pt}}
|
|
\newcommand*\l@subsection{\@dottedtocline{4}{31pt}{29pt}}
|
|
\newcommand*\l@subsubsection[2]{}
|
|
|
|
|
|
|
|
% ***********
|
|
% Footnotes *
|
|
% ***********
|
|
|
|
\def\footnoterule{\noindent\rule{\columnwidth}{0.5pt}}
|
|
\def\@makefnmark{\@textsuperscript{\normalfont\@thefnmark}}%
|
|
\newcommand\@makefntext[1]{\noindent{\@makefnmark}\enskip#1}
|
|
|
|
% ***********
|
|
% References *
|
|
% ***********
|
|
|
|
\providecommand{\newblock}{}
|
|
\newenvironment{thebibliography}{%
|
|
\section{\bibname}%
|
|
\begingroup
|
|
\small
|
|
\begin{list}{}{%
|
|
\setlength{\topsep}{\z@}%
|
|
\setlength{\labelsep}{\z@}%
|
|
\settowidth{\labelwidth}{\z@}%
|
|
\setlength{\leftmargin}{4mm}%
|
|
\setlength{\itemindent}{-4mm}}\small}
|
|
{\end{list}\endgroup}
|
|
|
|
\RequirePackage{natbib}
|
|
|
|
|
|
% **********
|
|
% Appendix *
|
|
% **********
|
|
\newif\ifappend
|
|
\def\appendix{\par
|
|
\setcounter{section}{0}
|
|
\setcounter{subsection}{0}
|
|
\appendtrue
|
|
}
|
|
|
|
%Math parameters
|
|
|
|
\setlength{\jot}{5\p@}
|
|
\mathchardef\@m=1500 % adapted value
|
|
|
|
\def\frenchspacing{\sfcode`\.\@m \sfcode`\?\@m \sfcode`\!\@m
|
|
\sfcode`\:\@m \sfcode`\;\@m \sfcode`\,\@m}
|
|
|
|
% Theorems
|
|
\def\th@plain{%
|
|
%% \let\thm@indent\noindent % no indent
|
|
\thm@headfont{\quad\scshape}% heading font is bold
|
|
\thm@notefont{\upshape\mdseries}% same as heading font
|
|
\thm@headpunct{.}% no period after heading
|
|
\thm@headsep 5\p@ plus\p@ minus\p@\relax
|
|
\itshape % body font
|
|
}
|
|
|
|
\vbadness=9999
|
|
\tolerance=9999
|
|
\doublehyphendemerits=10000
|
|
\doublehyphendemerits 640000 % corresponds to badness 800
|
|
\finalhyphendemerits 1000000 % corresponds to badness 1000
|
|
|
|
\flushbottom
|
|
\frenchspacing
|
|
\ps@headings
|
|
\twocolumn
|
|
|
|
% Screen PDF compatability
|
|
\newcommand{\medline}[1]{%
|
|
\unskip\unskip\ignorespaces}
|
|
|
|
|
|
%%%%for smaller size text
|
|
\newenvironment{methods}{%
|
|
\begingroup
|
|
\def\section{%
|
|
\@startsection{section}{1}{\z@}
|
|
{-24\p@ plus -3\p@}{4\p@}
|
|
{\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
|
|
\def\subsection{%
|
|
\@startsection{subsection}{2}{\z@}
|
|
{-5\p@ plus -2\p@}{4\p@}
|
|
{\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
|
|
\def\subsubsection{%
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\@startsection{subsubsection}{3}{\z@}
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{-6\p@ plus -1\p@}{-1em}
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{\reset@font\normalfont\normalsize\itshape}}
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\footnotesize
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\par}
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{\par\endgroup\bigskip\@afterheading\@afterindentfalse}
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\graphicspath{{g:/artwork/oup/bioinfo/}}
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\language=2
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\hyphenation{Figure Table Figures Tables}
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\newcommand{\href}[2]{#2}
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\renewenvironment{proof}[1][\proofname]{\par
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\normalfont \topsep6\p@\@plus6\p@\relax
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\labelsep 0.5em
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\trivlist
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\item[\hskip\labelsep\hskip1em\textsc{#1}.]\ignorespaces
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}{\endtrivlist\@endpefalse}
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%%Different Bonds
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\def\sbond{\ensuremath{\raise.25ex\hbox{${-}\!\!\!\!{-}$}}\kern -.9pt}
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\def\dbond{\ensuremath{\raise.25ex\hbox{=$\!$=}}}
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\def\tbond{\ensuremath{\raise.20ex\hbox{${\equiv}\!\!\!{\equiv}$}}}
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\newcommand{\query}[2][0pt]{}%
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\renewcommand{\dag}{{\mathversion{normal}$^{\dagger}$}}
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\endinput
|