Skip to content

Commit

Permalink
template modifications for minimum working example
Browse files Browse the repository at this point in the history
  • Loading branch information
@alexdiem
alexdiem committed Feb 2, 2017
1 parent 99f4c08 commit 2232b45
Show file tree
Hide file tree
Showing 2 changed files with 81 additions and 95 deletions.
96 changes: 46 additions & 50 deletions phdthesis.cls
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,8 @@
%%
%% Licence: BSD 3-Clause
%%
\NeedsTeXFormat{LaTeX2e}[1996/12/01]
\ProvidesClass{ecsthesis}
[2003/25/04 v1.6
LaTeX document class]
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{phdthesis}[2017/02/02 PhD Thesis Class]
\def\baseclass{book}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{\baseclass}}
\def\@checkoptions#1#2{
Expand Down Expand Up @@ -108,7 +106,7 @@
\usepackage{booktabs}
\usepackage{rotating}
\usepackage{listings}
%\usepackage{lstpatch}
\usepackage{xspace}
\lstset{captionpos=b,
frame=tb,
basicstyle=\scriptsize\ttfamily,
Expand All @@ -126,43 +124,22 @@
\pdfstringdefDisableCommands{
\let\\\space
}
\newcommand*{\supervisor}[1]{\def\supname{#1}}
\newcommand*{\examiner}[1]{\def\examname{#1}}
\newcommand*{\degree}[1]{\def\degreename{#1}}
\newcommand*{\authors}[1]{\def\authornames{#1}}
\newcommand*{\addresses}[1]{\def\addressnames{#1}}
\newcommand*{\university}[1]{\def\univname{#1}}
\newcommand*{\UNIVERSITY}[1]{\def\UNIVNAME{#1}}
\newcommand*{\department}[1]{\def\deptname{#1}}
\newcommand*{\DEPARTMENT}[1]{\def\DEPTNAME{#1}}
\newcommand*{\group}[1]{\def\groupname{#1}}
\newcommand*{\GROUP}[1]{\def\GROUPNAME{#1}}
\newcommand*{\faculty}[1]{\def\facname{#1}}
\newcommand*{\FACULTY}[1]{\def\FACNAME{#1}}
\newcommand*{\subject}[1]{\def\subjectname{#1}}
\newcommand*{\keywords}[1]{\def\keywordnames{#1}}
\newcommand*{\atitle}{Prediction of Perivascular Drainage of \Ab from the Brain Using Computational Modelling: Implications for Alzheimer's Disease}
\supervisor {}
\examiner {}
\degree {}
\authors {}
\university {\texorpdfstring{University of Southampton}}
\UNIVERSITY {\texorpdfstring{UNIVERSITY OF SOUTHAMPTON}}
\department {\texorpdfstring{Computational Engineering and Design}}
\DEPARTMENT {\texorpdfstring{COMPUTATIONAL ENGINEERING AND DESIGN}}
\group {\texorpdfstring{Computational Engineering and Design Group}}
\GROUP {\texorpdfstring{COMPUTATIONAL ENGINEERING AND DESIGN GROUP}}
\faculty {\texorpdfstring{Faculty of Engineering and the Environment}}
\FACULTY {\texorpdfstring{FACULTY OF ENGINEERING AND THE ENVIRONMENT}}
\addresses {}
\subject {}
\keywords {}
\newcommand*{\supervisor}[1]{\gdef\@supervisor{#1}}
\newcommand*{\university}[1]{\gdef\@university{#1}}
\newcommand*{\UNIVERSITY}{\MakeUppercase\@university}
\newcommand*{\department}[1]{\gdef\@department{#1}}
\newcommand*{\DEPARTMENT}{\MakeUppercase\@department}
\newcommand*{\group}[1]{\gdef\@group{#1}}
\newcommand*{\GROUP}{\MakeUppercase\@group}
\newcommand*{\faculty}[1]{\gdef\@faculty{#1}}
\newcommand*{\FACULTY}{\MakeUppercase\@faculty}
\newcommand*{\addresses}[1]{\@group\\\@department\\\@university}
\newcommand*{\atitle}[1]{\gdef\@title{#1}}

\renewcommand\maketitle{
\btypeout{Title Page}
\hypersetup{pdftitle={\@title}}
\hypersetup{pdfsubject=\subjectname}
\hypersetup{pdfauthor=\authornames}
\hypersetup{pdfkeywords=\keywordnames}
\hypersetup{pdfauthor={\@author}}
\thispagestyle{empty}
\begin{titlepage}
\let\footnotesize\small
Expand All @@ -173,21 +150,21 @@
\vskip 60\p@
\begin{center}
\setlength{\parskip}{0pt}
{\large\textbf{\UNIVNAME}\par}
{\large\textbf{\UNIVERSITY}\par}
\vfill
{\huge \bf \atitle \par}
{\huge \bf \@title \par}
\vfill
{\LARGE by \par}
\smallskip
{\LARGE \authornames \par}
{\LARGE \@author \par}
\vfill
{\large A thesis submitted for the degree of \par}
{\large Doctor of Philosophy \par}
\bigskip
\bigskip
{\large in the \par}
{\large \facname\par \par}
{\large \deptname\par \par}
{\large \@faculty\par \par}
{\large \@department\par \par}
\bigskip
\bigskip
\bigskip
Expand Down Expand Up @@ -218,17 +195,17 @@
\null\vfil
\begin{center}
\setlength{\parskip}{0pt}
{\normalsize \UNIVNAME \par \par}
{\normalsize \UNIVERSITY \par \par}
{\underline{ABSTRACT} \par \par}
\bigskip
{\normalsize \FACNAME\par \par}
{\normalsize \DEPTNAME\par \par}
{\normalsize \FACULTY\par \par}
{\normalsize \DEPARTMENT\par \par}
\bigskip
{\normalsize \underline{Doctor of Philosophy}\par \par}
\bigskip
{\normalsize\bf Prediction of Perivascular Drainage of \Ab from the Brain Using Computational Modelling: Implications for Alzheimer's Disease \par \par}
{\normalsize\bf \@title \par \par}
\medskip
{\normalsize by \authornames \par \par}
{\normalsize by \@author \par \par}
\bigskip
\end{center}
}
Expand Down Expand Up @@ -348,7 +325,26 @@
\null\vfill
\vskip 60\p@
\begin{center}{\Large\bf \declarationname \par}\end{center}
{\normalsize #1}
{\normalsize
I, \@author, declare that this thesis entitled \@title and the work presented in it are my own and has been generated by me as the result of my own original research.

I confirm that:

\begin{enumerate}
\item This work was done wholly or mainly while in candidature for a research degree at this University;
\item Where any part of this thesis has previously been submitted for a degree or any other qualification at this University or any other institution, this has been clearly stated;
\item Where I have consulted the published work of others, this is always clearly attributed;
\item Where I have quoted from the work of tohers, the source is always given. With the exception of such quotations, this thesis is entirely my own work;
\item I have acknowledged all main sources of help;
\item Where the thesis is based on work done by myself jointly with others, I have made clear exactly what was done by others and what I have contributed myself;
\item Either none of this work has been published before submission, or parts of this work have been published as: #1.
\end{enumerate}

Signed:

Date:

}
\cleardoublepage
}
\newcommand\acknowledgementsname{Acknowledgements}
Expand Down
80 changes: 35 additions & 45 deletions thesis.tex
View file
Original file line number Diff line number Diff line change
@@ -1,74 +1,64 @@
%% ----------------------------------------------------------------
%% MiniThesis.tex
%% thesis.tex
%% ----------------------------------------------------------------
\documentclass{ecsthesis} % Use the progress Style
\graphicspath{{./figures/}} % Location of your graphics files
\documentclass[a4paper]{phdthesis}

\usepackage[round]{natbib} % Use Natbib style for the refs.
\usepackage[binary-units=true]{siunitx}
\usepackage{pgfgantt}
\usepackage{rotating}
\usepackage{verbatim}
\usepackage{tikz}
\usepackage{listings}
\usepackage{fixltx2e}
\usepackage{textgreek}

\hypersetup{colorlinks=true} % Set to false for black/white printing

\sisetup{range-phrase=--}
\sisetup{range-units=single}

\DeclareSIUnit\Molar{M}
\DeclareSIUnit\cell{cell}
\DeclareSIUnit\neuron{neuron}
\DeclareSIUnit\microglia{microglia}

\usetikzlibrary{arrows}
\graphicspath{{.}} % Location of your graphics files

\renewcommand{\bibname}{References}

\input{definitions}
\input{lstdefinitions}
%% ----------------------------------------------------------------
\begin{document}
\frontmatter
\title {Prediction of Perivascular Drainage of \Ab from the Brain Using Computational Modelling: Implications for Alzheimer's Disease}
\authors {Alexandra Katharina Diem}
\addresses {\groupname\\\deptname\\\univname}
\title {Thesis Title}
\date {November 2016}
\subject {}
\keywords {}
\supervisor {Prof. Neil W. Bressloff, Dr. Giles Richardson, Dr. Roxana O. Carare}
\author {Author Names}
\supervisor {Prof. XYZ}
\university {University of Southampton}
\department {Computational Engineering and Design}
\group {Computational Engineering and Design Group}
\faculty {Faculty of Engineering and the Environment}

\maketitle

\begin{abstract}
Alzheimer's Disease (AD) is the most common form of dementia and although it has been researched for over 100 years, to date, there is still no cure or preventive medication. Its onset and progression is closely related to the accumulation of the neuronal metabolite \Ab, raising the question of how metabolites and waste products are eliminated from the brain normally. The brain does not have conventional lymphatic vessels, which are found in other parts of the body and, therefore, has to eliminate metabolites differently. In recent years a connection between the pathology of AD and cerebrovascular diseases has been suggested and confirmed in various mice studies and this has led to the hypothesis that interstitial fluid in the basement membranes in the walls of cerebral arteries provide the pathways for perivascular drainage of \Ab with arterial pulsations as the pumping mechanism. However, perivascular drainage occurs along basement membranes towards the surface of the brain, which can not be explained solely by arterial pulsations. The aim of this thesis was to develop a coupled computational and mathematical model of perivascular drainage in the brain in order to investigate possible mechanisms for fluid drainage from the brain. In this thesis the results of coupling a computational model of a short arterial segment with a mathematical model of the perivascular space are presented. They demonstrate that the model is capable of producing net drainage of interstitial fluid in the reverse direction of the blood flow by introducing a valve mechanism. However, they also show that arterial pulsations are not strong enough to provide the driving force for perivascular drainage. This result negates one of the most cited hypotheses on perivascular drainage. Following these results the development of a network model of the brain takes a more global perspective on fluid dynamics through the brain and demonstrates the feasibility of simulating the dynamic responses of cells and the vasculature. This approach lays the foundations for a multiscale model of \Ab distribution, flow and drainage in the brain and an in silico framework for exploring related pathophysiology and therapy.
Abstract goes here.
\end{abstract}

\tableofcontents
\listoffigures
\listoftables
\lstlistoflistings
\include{listofsymbols}
\include{listofacronyms}
\include{authordeclaration}
\include{acknowledgements}
\listofsymbols{llc}{
$a$ & description & unit\\
$b$ & description & unit\\
$c$ & description & unit}
\listofacronyms{ll}{
ACR & acronym\\
ACR & acronym\\
ACR & acronym}
\declaration{Author et al. 2017}
\acknowledgements{Thanks to no one.}
\mainmatter
%% ----------------------------------------------------------------
\include{introduction} % finished
\include{perivascular} % finished
\include{diffusionpaper} % finished
\include{numerical}
\include{analytical} % finished
\include{coupling}
\include{network}
\include{discussion}
\chapter{A Chapter}
The text for a chapter goes here.

\chapter{Another Chapter}
The text for another chapter goes here.

\appendix
\include{bmanalysis}
\include{publications}
\include{glossary}
\chapter{Appendix}
The text for an appendix goes here.

%% ----------------------------------------------------------------
\backmatter
\bibliographystyle{plainnat}
\bibliography{thesis}
%\bibliographystyle{plainnat}
%\bibliography{thesis}
\end{document}
%% ----------------------------------------------------------------

0 comments on commit 2232b45

Please sign in to comment.