diff --git a/.gitignore b/.gitignore index 47e14ce..472b042 100644 --- a/.gitignore +++ b/.gitignore @@ -4,9 +4,9 @@ !*.bbl !*.glo -!src -src/* -!src/*.tex -!src/*.bib -!src/*.bbl -!src/*.glo \ No newline at end of file +!tex +tex/* +!tex/*.tex +!tex/*.bib +!tex/*.bbl +!tex/*.glo \ No newline at end of file diff --git a/proposal.bib b/tex/proposal.bib similarity index 100% rename from proposal.bib rename to tex/proposal.bib diff --git a/tex/thesis.glo b/tex/thesis.glo new file mode 100644 index 0000000..e69de29 diff --git a/tex/thesis.tex b/tex/thesis.tex new file mode 100644 index 0000000..58c3aa0 --- /dev/null +++ b/tex/thesis.tex @@ -0,0 +1,227 @@ +\documentclass[twocolumn]{article} +\usepackage[top=0.75in,left=0.75in,right=0.75in,bottom=0.9in]{geometry} +\usepackage{siunitx} +\usepackage[acronym]{glossaries} +\usepackage[T1]{fontenc} +\usepackage{enumitem} +\usepackage{titlesec} +\usepackage{titlecaps} +\usepackage{upgreek} +\usepackage{graphicx} +\usepackage{subcaption} +\usepackage{nth} +\usepackage[capitalize]{cleveref} +\usepackage[version=4]{mhchem} +\usepackage{pgfgantt} + +\titleformat{\section}[block]{\bfseries\large}{}{0pt}{\uppercase} +\titleformat{\subsection}[block]{\bfseries\large}{}{0pt}{\titlecap} +\titleformat{\subsubsection}[block]{\itshape\large}{}{0pt}{\titlecap} +\titleformat{\paragraph}[runin]{\bfseries\itshape}{}{0pt}{\titlecap} + +\setlist[description]{font=$\bullet$~\textbf\normalfont} + +\sisetup{per-mode=symbol,list-units=single} +\DeclareSIUnit\activityunit{U} +\DeclareSIUnit\carrier{carriers} +\DeclareSIUnit\cell{cells} +\DeclareSIUnit\ab{mAbs} +\DeclareSIUnit\molar{M} +\DeclareSIUnit\gforce{\times{} g} + +% add acronyms here +\renewcommand{\glossarysection}[2][]{} % remove glossary title +\makeglossaries +\newacronym{act}{ACT}{adoptive cell therapies} + +\begin{document} + +\begin{titlepage} + \begin{center} + + \huge\textbf{Optimizing T Cell Manufacturing and Quality Using + Functionalized Degradable Microscaffolds} + + \vfill + + \LARGE Nathan John Dwarshuis, B.S. \\ + + \vspace{1.5em} + + \Large PhD Thesis \\ + Doctor of Philosophy in Biomedical Engineering \\ + Georgia Institute of Technology and Emory University + + \vspace{1.5em} + + \large\today + + \vfill + + \end{center} + + \large{ + + \noindent + Committee Members + + \vspace{1.5em} + + \noindent + Dr. Krishnendu Roy (Advisor) \\ + Wallace H. Coulter Department of Biomedical Engineering, Georgia + Institute of Technology and Emory University + + \vspace{1.5em} + + \noindent + Dr. Madhav Dhodapkar \\ + Department of Hematology and Medical Oncology, Emory University + + \vspace{1.5em} + + \noindent + Dr. Melissa Kemp \\ + Wallace H. Coulter Department of Biomedical Engineering, Georgia + Institute of Technology and Emory University + + \vspace{1.5em} + + \noindent + Dr. Wilbur Lam \\ + Wallace H. Coulter Department of Biomedical Engineering, Georgia + Institute of Technology and Emory University + + \vspace{1.5em} + + \noindent + Dr. Sakis Mantalaris \\ + Wallace H. Coulter Department of Biomedical Engineering, Georgia + Institute of Technology and Emory University } +\end{titlepage} + +\onecolumn \pagenumbering{roman} +\clearpage + +% TODO +Insert witty quote here + +\clearpage + +\section*{acknowledgements} + +Thank you to Lex Fridman and Devin Townsend for being awesome and inspirational. + +\clearpage + +\section*{abstract} + +Insert abstract here. + +\clearpage + +\tableofcontents + +\clearpage + +\listoffigures + +\clearpage + +\listoftables + +\clearpage + +\twocolumn +\section*{acronyms} + +\printglossary[type=\acronymtype] + +\clearpage +\pagenumbering{arabic} + +\clearpage + +\section{introduction} + +\subsection*{overview} + +Insert overview here + +\subsection*{hypothesis} + +Insert hypothesis here + +\subsection*{specific aims} +\subsubsection*{aim 1} +\subsubsection*{aim 2} +\subsubsection*{aim 3} + +\subsection*{outline} + +\subsubsection*{Aim 1} + +Aim 1 + +\subsubsection*{Aim 2} + +Aim 2 + +\subsubsection*{Aim 3} + +Aim 3 + +\section{background and significance} +\subsubsection*{background} +\subsubsection*{current T cell manufacturing technologies} + +bla bla + +\subsection*{strategies to optimize cell manufacturing} + +bla bla + +\subsubsection*{strategies to characterize cell manufacturing} + +bla bla + +\subsection{Innovation} + +\section{aim 1} + +\subsection{introduction} +\subsection{methods} +\subsection{results} +\subsection{discussion} + +\section{Aim 2} + +\subsection{introduction} +\subsection{methods} +\subsection{results} +\subsection{discussion} + +\section{Aim 3} + +\subsection{introduction} +\subsection{methods} +\subsection{results} +\subsection{discussion} + +\section{conclusions and future work} +\subsection{conclusions} +\subsection{future work} + +\onecolumn +\clearpage + +% TODO some people put appendices here....not sure if I need to + +\section{References} +\renewcommand{\section}[2]{} % noop the original bib section header + +\bibliography{../proposal} + +\bibliographystyle{naturemag} + +\end{document}