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thesissty.sty
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thesissty.sty
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%%
%% This file includes all personal style options, macros, etc.
%%
%% \RCS $RCSfile$
%% \RCS $Revision$
%% \RCS $Date$
%%
%% Minor style details
%%
\renewcommand{\@biblabel}[1]{#1.}
\setcounter{secnumdepth}{3}
\setcounter{tocdepth}{4}
%%
%% Acronyms
%%
%% Define an acronym macro that will print the long form of the acronym
%% first time, and the short form on subsequent occasions.
\RequirePackage{xspace}
\def\defacro#1#2#3{%
% \def#1{#2\hspace{0cm} (#3)\def#1{#2\xspace}\xspace}} % AA (An Acronym)
\def#1{#3\hspace{0cm} (#2)\def#1{#2\xspace}\xspace}} % An Acronym (AA)
%% For acronyms that occur in equations
\def\mathac#1{\ensuremath{\mathrm{#1}}}
\defacro\aaph{AAPH}{2,2$^{\prime}$-azobis(2-ami\-dino\-prop\-ane)
dihydrochloride}
\defacro\asa{5-ASA}{5-aminosalicylic acid}
\defacro\bdh{BDH}{British Drug House}
\defacro\bsa{BSA}{bovine serum albumin}
\defacro\bso{BSO}{buthionine sulfoximine}
\defacro\cd{CD}{Crohn's disease}
\defacro\dss{DSS}{\emph{dextran sulfate sodium}}
\defacro\dhb{DHB}{dihydroxybenzoate}
\defacro\dname{\textsc{d}-NAME}{nitro-\textsc{d}-arginine methyl ester}
\defacro\dnp{DNP}{Dinitrophenyl}
\defacro\dnph{DNPH}{dinitrophenylhydrazine}
\defacro\dtnb{DTNB}{5,5$^{\prime}$-dithiobis(2-nitrobenzoic acid)}
\defacro\ec{EC}{electrochemical}
\defacro\esr{ESR}{electron spin resonance spectroscopy}
\defacro\fmlp{fMLP}{\emph{formylmethionyl-leucyl-phenylalanine}}
\defacro\gapdh{GAPDH}{glyceraldehyde-3-phosphate dehydrogenase}
\defacro\gsh{GSH}{glutathione}
\defacro\gssg{GSSG}{glutathione disulfide}
\defacro\hbss{HBSS}{Hank's balanced salt solution}
\defacro\hplc{HPLC}{high performance liquid chromatography}
\defacro\iam{[$^{14}$C]-IAM}{[$^{14}$C]-iodoacetamide}
\defacro\ibd{IBD}{Inflammatory bowel disease}
\defacro\lps{LPS}{Lipopolysaccharide}
\defacro\lname{\textsc{l}-NAME}{nitro-\textsc{l}-arginine methyl ester}
\defacro\mco{MCO}{metal-catalysed oxidation}
\defacro\mpo{MPO}{myeloperoxidase}
\defacro\nos{NOS}{nitric oxide synthases}
\defacro\pbs{PBS}{phosphate-buffered saline}
\defacro\pgps{PG-PS}{\emph{Peptidoglycan-polysaccharide}}
\defacro\pmsf{PMSF}{phenylmethylsulfonyl fluoride}
\defacro\sds{SDS}{sodium dodecyl sulfate}
\defacro\sdspage{SDS-PAGE}{SDS polyacrylamide gel electrophoresis}
\defacro\sod{SOD}{superoxide dismutase}
\defacro\tbs{TBS}{tris-buffered saline}
\defacro\tca{TCA}{trichloroacetic acid}
\defacro\tnb{TNB}{5-thio-2-nitrobenzoic acid}
\defacro\tnbs{TNBS}{\emph{2,4,6-Trinitrobenzene sulfonic acid}}
\defacro\uc{UC}{ulcerative colitis}
%% Acronyms which don't need to be spelt out.
\def\fadh{FADH\xspace}
\def\dna{DNA\xspace}
\def\rons{RONS\xspace}
%% Acronyms for text and Equations.
\def\atp{\mathac{ATP}\xspace}
\def\GSH{\mathac{GSH}\xspace}
\def\GSSG{\mathac{GSSG}\xspace}
\def\nad{\mathac{NAD^+}\xspace}
\def\nadh{\mathac{NADH}\xspace}
\def\nadp{\mathac{NADP^+}\xspace}
\def\nadph{\mathac{NADPH}\xspace}
%% Radicals for equations and text
%% radical dot after - blah\hspace*{-.16em}\raisebox{1.15ex}{\Large .}
%% radical dot before - \raisebox{1.15ex}{\Large .}\hspace*{-.06em}blah
%% Acronyms with chemical formulae
\def\HPO{\H_2\O_2}
\defacro\hpo{\HPO}{hydrogen peroxide}
\defacro\hto{\H_2\O}{water}
\def\HOCL{\H\O\Cl}
\defacro\hocl{\HOCL}{hypochlorous acid}
\def\OH{\raisebox{1.15ex}{\Large .}\hspace*{-.06em}\O\H}
\defacro\oh{\OH}{hydroxyl radical}
\def\ONOO{\O\N\O\O^-}
\defacro\onoo{\ONOO}{peroxynitrite}
\def\NO{\raisebox{1.15ex}{\Large .}\hspace*{-.06em}\N\O}
\defacro\no{\NO}{nitric oxide}
\def\NOO{\raisebox{1.15ex}{\Large .}\hspace*{-.06em}\N\O_2}
\defacro\noo{\NOO}{nitrogen dioxide}
\def\NOOM{\N\O_2^-}
\defacro\noom{\NOOM}{nitrite}
\def\NOOO{\N\O_3^-}
\defacro\nooo{\NOOO}{nitrate}
\def\SO{\O_2\hspace*{-.45em}\raisebox{1.15ex}{\Large .}\raisebox{.77ex}{-}}
\defacro\so{\SO}{superoxide}
\def\goesto{\yi=0 \pw=300 \pht=0 \cto{}{}{1}}
%% Acronyms that are already defined -- we redefine them here with a
%% different name ("a" infront of the name), so that they can be used
%% in the abstract and again in the main body, each time having the
%% long form first time.
\defacro\ahocl{\HOCL}{hypochlorous acid}
\defacro\aoh{\OH}{hydroxyl radical}
\defacro\ano{\NO}{nitric oxide}
\defacro\alname{\textsc{l}-NAME}{nitro-\textsc{l}-arginine methyl ester}
%%
%% Other misc. macros...
%%
%% Degree symbol
\def\deg{$^\circ$}
%% Equilibrium
\def\myeq{\yi=0 \pw=300 \pht=0 \equil{}{}{1}}
%% Gravity g
\def\grav{$\times g$\xspace}
%% P value
\def\pval#1{\textsl{P} $<$ #1}
%% n for mean value
\def\num#1{\textsl{n}=#1}
%%
%% Abbreviations of complex chemtex structures.
%%
%% Double bond
\def\mydb{\hspace{-.35ex}\dbond{7}{12}}
%% Salicylate structure
\def\ssal{\sixring{\O\H}{Q}{Q}{Q}{Q}{\C\O\O\H}{D}{D}{D}}
%% Aminosalicylate structure
\def\samsal{\sixring{\O\H}{Q}{Q}{\H_2\N}{Q}{\C\O\O\H}{D}{D}{D}}
%% 5-Aminosalicylate structure
\def\sfamsal{\sixring{Q}{Q}{\N}{Q}{\C\O\O\H}{\O\H}{D}{D}{D}}
%% and rotated...
\def\sfamsalr{\sixringr{Q}{Q}{\N}{Q}{\C\O\O\H}{\O\H}{D}{D}{D}}
%% Sulfapyridine structure
\def\ssfpy{\pyridiner{Q}{Q}{Q}{Q}{\N}{\N\H\S\O_2}{D}{D}{D}\put(580,0){\sixringr{Q}{Q}{}{Q}{Q}{\N}{D}{D}{D}}}
%% Ubiquinol structure
\def\subiq{\sixringb{\C\H_3}{(\C\H_2\C\H\hspace{3.59em}\C\H)_{10}\H}{Q}{\H_3\C\O}{\H_3\C\O}{Q}{\O}{\O}{9}\put(654,-100){\cbranch{\C\H_3}{S}{}{D}{\C}{S}{}{}{}}}
%% 2,3 Dihydroxybenzoate structure
\def\sdhbt{\sixring{\O\H}{\O\H}{Q}{Q}{Q}{\C\O\O\H}{D}{D}{D}}
%% 2,5 Dihydroxybenzoate structure
\def\sdhbf{\sixring{\O\H}{Q}{Q}{\H\O}{Q}{\C\O\O\H}{D}{D}{D}}
%% Catechol structure
\def\scat{\sixring{\O\H}{Q}{Q}{Q}{Q}{\O\H}{D}{D}{D}}
%% Carbonyl structure
\def\scarb{\cleft{\R_1}{S}{\C}{S}{\R_2}{D}{\O}}
%% DNP structure
\def\sdnp{\sixringr{Q}{Q}{}{\O_2\N}{Q}{\N\O_2}{D}{D}{D}}