thesis.tex

\documentclass[12pt,letterpaper,titlepage,twoside,openright]{report} 

\usepackage{fourier}
\usepackage{setspace}
\usepackage{natbib}
\usepackage[inner=1.25in,outer=1.25in,top=1.25in,bottom=1.25in]{geometry}
\doublespacing
\usepackage{amsmath}
\usepackage{bibentry}
\nobibliography*   % This is necessary for bibentry to work
\usepackage{amssymb}
\usepackage{graphicx}
\usepackage{dpfloat}
\usepackage{chngcntr}
\counterwithout{figure}{chapter}
\renewcommand{\theequation}{\arabic{equation}}
\renewcommand{\thefigure}{\arabic{figure}}



%%%%%%%% Declarations %%%%%%%%%%%%%%%
\DeclareMathOperator{\Tr}{tr}
\newcommand{\loss}[1]{\mathcal L\left(#1\right)}
\newcommand{\T}{{\sf T}}
\newcommand{\E}[2][]{\mathbb E_{#1}\left[ #2\right]}    % expected value
\DeclareMathOperator*{\argmin}{arg\,min}

\newcommand{\sq}[1]{\lq#1\rq}
\newcommand{\ie}{\emph{i.e.}\ }
\newcommand{\eg}{\emph{e.g.}\ }

\begin{document}

\begin{titlepage}
\begin{center}

\vspace*{2cm}
\textbf{\uppercase{\large Functional connectivity in cortical circuits}}

\vspace{1.5cm}
A Dissertation Submitted to the Faculty of

\medskip
The Graduate School 

Baylor College of Medicine

\vspace{1.5cm}
In Partial Fulfillment of the 

Requirements for the Degree

of 

Doctor of Philosophy

by 

\bigskip
{\large Dimitri Yatsenko}

\vfill
Houston, Texas

December 2014

\end{center}
\end{titlepage}


%%%%%%%%% SIGNATURE PAGE

\begin{center}
\textbf{\uppercase{\large Approved by the dissertation committee}}

\vspace{9pt}
Signed \underline{\hspace{3in}}

\vspace{-9pt}
Andreas S.\ Tolias, Ph.D.

\vspace{-9pt}
Chairperson


Signed \underline{\hspace{3in}}

\vspace{-9pt}
Fabrizio Gabbiani, Ph.D.


Signed \underline{\hspace{3in}}

\vspace{-9pt}
Kre\v{s}imir Josi\`{c}, Ph.D.

Signed \underline{\hspace{3in}}

\vspace{-9pt}
Daoyun Ji, Ph.D.

Signed \underline{\hspace{3in}}

\vspace{-9pt}
Athanassios G.\ Siapas, Ph.D.


\vspace{24pt}
\textbf{\uppercase{\large Approved by the department of neuroscience}}

\vspace{9pt}
Signed \underline{\hspace{3in}}

\vspace{-9pt}
Paul J.\ Pfaffinger, Ph.D.

\vspace{-9pt}
Director of Graduate Studies

Signed \underline{\hspace{3in}}

\vspace{-9pt}
Dora E.\ Angelaki, Ph.D.

\vspace{-9pt}
Chairman of Department

\vspace{24pt}
\textbf{\uppercase{\large Approved by the dean of graduate sciences}}

\vspace{9pt}
Signed \underline{\hspace{3in}}

\vspace{-9pt}
Hiram F.\ Gilbert, Ph.D.

\vspace{6pt}
Date \underline{\hspace{3in}}

\end{center}

\chapter*{Acknowledgments}
\addcontentsline{toc}{chapter}{\numberline{}Acknowledgments}
\input{acknowledgments.tex}

\chapter*{Abstract}
\addcontentsline{toc}{chapter}{\numberline{}Abstract}
\input{abstract.tex}

\tableofcontents

\listoffigures

%\listoftables

\chapter{Introduction}
\clearpage 
\input{intro.tex}

\chapter{Improved estimation and interpretation of correlations in neural circuits}
This work has been submitted for publication in \bibentry{Yatsenko:2014}.
\clearpage

\input{pcorr-abstract.tex}
\input{pcorr-intro.tex}
\input{pcorr-results-theory.tex}
\input{pcorr-results-simulation.tex}
\input{pcorr-results-empirical.tex}
\input{pcorr-discussion.tex}
\input{pcorr-methods.tex}

\chapter{Differential functional connectivity of parvalbumin-positive interneurons}
\clearpage

\input{pv-intro.tex}
\input{pv-results.tex}
\input{pv-discussion.tex}
\input{pv-methods.tex}

\chapter{Conclusions and future directions}
\clearpage
\input{future.tex}

\bibliographystyle{dy-thesis-style}
\bibliography{biblio}
\addcontentsline{toc}{chapter}{\numberline{}Bibliography}

\end{document}