thesis.tex.recover.bak~

\documentclass[12pt,a4paper,twoside,openright]{report}
\setcounter{secnumdepth}{6}
%\usepackage{standalone}
%\usepackage[showframe]{geometry} % Used to adjust the document margins
\usepackage{geometry} % Used to adjust the document margins

%\usepackage{fullpage}
\usepackage{multirow}
\usepackage{setspace}
\usepackage{nameref}
\usepackage{currfile}
\usepackage{grffile}


\usepackage{graphicx}
\usepackage[font=footnotesize]{caption}
\usepackage[noadjust]{cite}
\usepackage[toc,page]{appendix}
\usepackage{lineno}


\usepackage[xetex,
pdfauthor={Quentin Geissmann},
pdftitle={High-throughput Recording, Analysis and Manipulation of Sleep in Drosophila},
pdfsubject={Computational biology},
pdfkeywords={Drosophila, behaviour, sleep, high-throughput},
pdfproducer={Latex with hyperref},
pdfcreator={XeTex}]{hyperref}


\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{caption}
\usepackage{subcaption}
\usepackage{gensymb}

%\usepackage[colorinlistoftodos,disable]{todonotes}
\usepackage[colorinlistoftodos]{todonotes}
\usepackage{csquotes}
\usepackage{parskip} % Spaces between paragraphs

\usepackage[acronym]{glossaries}
% add binding margins

%\geometry{bindingoffset=1cm}
\usepackage{wasysym}
\usepackage{sidecap}
\usepackage{epigraph}

\usepackage{etoolbox}
\usepackage{titlesec}
\usepackage{fancyhdr}
\usepackage{lastpage}

\usepackage{titlesec, blindtext, color}

\definecolor{gray75}{gray}{0.75}
\newcommand{\hsp}{\hspace{20pt}}
\titleformat{\chapter}[hang]{\Huge\bfseries}{\thechapter\hsp\textcolor{gray75}{|}\hsp}{0pt}{\Huge\bfseries}


\preto\chapter\glsresetall



\makeglossaries

%~ \renewcommand*\abstractname{Summary}

% http://www.tex.ac.uk/cgi-bin/texfaq2html?label=altabcr
\setcounter{MaxMatrixCols}{50}

% package name:
\newcommand{\py}{\texttt{python}}
\newcommand{\re}{\texttt{rethomics}}
\newcommand{\ctit}{\emph}
\newcommand{\ptit}{\emph}
\newcommand{\eg}{\emph{e.g.}}
\newcommand{\ie}{\emph{i.e.}}
\newcommand{\droso}{\emph{Drosophila}}
\newcommand{\dmel}{\emph{Drosophila melanogaster}}

\newcommand{\specialcell}[2][c]{\begin{tabular}[#1]{@{}c@{}}#2\end{tabular}}
\newcommand{\FIXME}[2][]{\todo[color=cyan, #1]{\textbf{QG:} #2}}
\newcommand{\TODO}[2][]{\todo[color=red, #1]{\textbf{QG:} #2}}
\newcommand{\citationneeded}[2][]{\todo[color=brown, fancyline, #1]{\textbf{Citation Needed:} #2}}
\newcommand{\contrib}{\emph}

\newcommand*{\addthinspace}{\hskip0.16667em\relax}

\sloppy

\newcommand{\bootci}[4]{
	\def\temp{#1}\ifx\temp\empty
		${#2}$, ${\text{CI}_{95\%}=[#3,#4]}$
	\else
		${#1=#2}$, ${\text{CI}_{95\%}=[#3,#4]}$
	\fi
} 
\newcommand{\emd}{\,---\,}

%\newcommand{\sectionbreak}{\clearpage}

\begin{document}


\pagenumbering{roman}

\title{High-throughput Recording, Analysis and Manipulation of Sleep in \emph{Drosophila}}
\author{Quentin Geissmann\\
\href{mailto:quentin.geissmann13@imperial.ac.uk}{quentin.geissmann13@imperial.ac.uk}\\	
\\
\\
Supervisor: Giorgio Gilestro\\
Co-supervisor: Stefanos Zafeiriou\\
\\
\\
Imperial College London
\\
\\
\\
\\
\\
}

\date{\today}

\clearpage\maketitle
\thispagestyle{empty}
\newpage{}
\listoftodos
\newpage
\input{./acronyms}

\begin{abstract}
%
%The fruit fly (\dmel) has recently proven very valuable for understanding the genetic basis of sleep.
%In this model organism, sleep is inferred and quantified from the lack of movement.
%Despite attempts to provide alternative accurate motion classifiers, most results to date have relied on \gls{dam}, a minimalist movement detection device that is only sensitive to flies that are walking several times their body length.
%This latter approach has been shown to overestimate sleep, as fruit flies can be active without walking long distances (\eg{} when feeding and grooming).
%
%In the study herein, I present a working prototype of the ethoscope platform, a novel behavioural monitoring system.
%I thoroughly validate it and demonstrate great position accuracy as well as very reliable motion classification.
%As a proof of principle, I compare sleep patterns between males and females.
%I discover that improving quality of motion classification can considerably change the nature of biological results. 
%For instance, I show that females sleep less than males during the day, but also, surprisingly, during the night. 
%I extend the analysis of baseline sleep by studying its variability. 
%I discover that sleep patterns are very variables within animals, even though they are environmentally and genetically controlled.
%Despite this large variability in the population, I show a strong temporal individual redundancy of sleep patterns.
%
%To take full advantage of real time analysis, I couple video tracking with a novel ethoscope module that allows me to dynamically sleep deprive fruit flies; a paradigm that had not been automatised before.
%I show that my device can very effectively elicit a moving response. 
%Then, I apply it to socially naive animals and show a robust rebound in males, but very surprisingly no effect in females.
%
%These very promising results indicate that my methods will allow experimenters to observe phenotypic differences that may have otherwise been overlooked.
%In conclusion, I foresee great potential for adoption of my platform in \droso{} sleep research.
%The ethoscope system has a very modular architecture, which makes if very flexible, robust, inexpensive, scalable and user-friendly.
%Therefore, it has potential to transcend inter-disciplinary boundaries and to be applied to several model organisms.



\end{abstract}
\setcounter{tocdepth}{5}

\newpage

Acknowledgments
%
%C'est pas sorcier
%
%Yazour 
%Jancosky
%
%FXDCM
%
%Gerard Chazal
%
%Jean-Claude Ameisen
%
%
%
%

\newpage

%\tableofcontents
%\listoffigures
%\listoftables

%\newpage
\\begin{environment-name}
content
\end{environment-name}

\onehalfspacing
\input{1-intro/1-intro}
\input{2-ethoscopes/2-ethoscopes}
\input{3-rethomics/3-rethomics}
\input{4-baseline/4-baseline}
\input{5-sleep-deprivation/5-sleep-deprivation}
\input{6-discussion/6-discussion}
\newpage
\singlespacing
\bibliography{thesis.bib}{}
\bibliographystyle{ieeetr}


\end{document}