-
Notifications
You must be signed in to change notification settings - Fork 0
/
dissertation.tex
237 lines (175 loc) · 6.22 KB
/
dissertation.tex
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
\documentclass[11pt,oneside]{book}
\usepackage[left=1in,right=1in,top=1in,bottom=1in]{geometry}
\usepackage{amsmath}
\usepackage[title,titletoc]{appendix}
\usepackage{multicol}
\usepackage[nottoc,notlot,notlof]{tocbibind}
\usepackage{cite}
\usepackage{siunitx}
\usepackage{textgreek}
\usepackage{booktabs}
\usepackage{setspace}
\usepackage{fancyhdr}
\pagestyle{fancy}
%\usepackage{wrapfig}
\usepackage{textcomp}
\usepackage[T1]{fontenc}
\usepackage{subfigure}
\usepackage[font=small,labelfont=bf]{caption}
\usepackage{multirow}
\usepackage{graphicx}
\usepackage{hyperref}
\hypersetup{
pdffitwindow=false, % window fit to page when opened
pdfstartview={FitH}, % fits the width of the page to the window
pdftitle={2012 QE Outline}, % title
pdfauthor={Adam Coster}, % author
pdfsubject={2012 QE Outline}, % subject of the document
pdfcreator={Adam Coster}, % creator of the document
pdfproducer={Adam Coster}, % producer of the document
pdfnewwindow=true, % links in new window
colorlinks=true, % false: boxed links; true: colored links
linkcolor=black, % color of internal links
citecolor=black, % color of links to bibliography
filecolor=green, % color of file links
urlcolor=blue % color of external links
}
\usepackage[all]{hypcap}
\onehalfspacing
\usepackage[toc=true,xindy,nonumberlist,nopostdot,acronym]{glossaries}
\usepackage{glossary-mcols}
\renewcommand*{\glspostdescription}{}
\makeglossary
\newcommand{\myTitle}{Quantitative single-cell imaging
reveals insulation of morphogenic signal transduction}
\newcommand{\tgfbsf}{TGFB$_\text{sf}$}
\newcommand{\tgf}{TGF\textbeta}
\newcommand{\bcat}{\textbeta-catenin}
\newcommand{\gsk}{GSK3\textbeta}
\newcommand{\frog}{\textit{Xenopus laevis}}
\newcommand{\fly}{\textit{Drosophila}}
\newcommand{\ta}{\textit{Trichoplax adhaerens}}
\newcommand{\fz}{Frizzled}
\newcommand{\ubn}{ubiquitination}
\newcommand{\pn}{phosphorylation}
\newcommand{\p}{phosphorylate}
\newcommand{\ue}{microenvironment}
\newcommand{\C}[1]{#1$^{\circ}$C}
\newcommand{\micro}[1]{\hbox{\textmu}#1}
\newcommand{\uL}[1]{#1\hbox{\textmu}L}
\newcommand{\ug}[1]{#1\hbox{\textmu}g}
\newcommand{\uM}[1]{#1\hbox{\textmu}M}
\newcommand{\e}[1]{\ensuremath{\times 10^{#1}}}
\newcommand{\ar}[1]{\autoref{#1}}
\newcommand{\arp}[1]{(\autoref{#1})}
\renewcommand{\i}[1]{\textit{#1}}
\renewcommand{\b}[1]{\textbf{#1}}
\newcommand{\E}{\mathrm{E}}
\newcommand{\Var}{\mathrm{Var}}
\newcommand{\Cov}{\mathrm{Cov}}
\renewcommand{\vec}[1]{\mathbf{#1}}
\def\sectionautorefname{Section}
\def\subsectionautorefname{Section}
\def\subsubsectionautorefname{Section}
\def\chapterautorefname{Chapter}
\def\figureautorefname{Fig.}
\begin{document}
\setlength{\textfloatsep}{6.0pt plus 2.0pt minus 4.0pt}
\setlength{\floatsep} {6.0pt plus 2.0pt minus 2.0pt}
\setlength{\intextsep} {6.0pt plus 2.0pt minus 2.0pt}
\setlength{\abovecaptionskip}{6pt plus 2pt minus 0pt}
\belowdisplayskip=12pt plus 4pt
\abovedisplayskip=12pt plus 4pt
% DEFAULT SPACING FOR FLOATS
%\textfloatsep — distance between floats on the top or the bottom and the text;
%\floatsep — distance between two floats;
%\intextsep — distance between floats inserted inside the page text (using h) and the text proper.
%\textfloatsep: 20.0pt plus 2.0pt minus 4.0pt;
%\floatsep: 12.0pt plus 2.0pt minus 2.0pt;
%\intextsep: 12.0pt plus 2.0pt minus 2.0pt.
\input{glossary}
\input{acronym}
\fancyhead{}
\fancyfoot{}
\renewcommand{\headrulewidth}{0pt}
\pagestyle{empty}
\include{FRONT/title}
\pagestyle{plain}
\pagenumbering{roman}
\setcounter{page}{5}
\include{FRONT/abstract}
%%%%%%%% TABLES %%%%%%%
% TOC
\tableofcontents
\newpage
\vspace*{\fill}
\addcontentsline{toc}{chapter}{Prior Publications}
\section*{\Huge Prior Publications}
\begin{enumerate}
\item \textit{Coster}, Thorne, Wu, Altschuler. ``Disentangling signaling from transcriptional crosstalk in morphogenic
pathways.'' (\textit{Manucript in preparation}).
\item Thorne, Wichaidit, \textbf{Coster}, Wu, Altschuler. ``GSK-3 is a gatekeeper for kinase-targeted drug response.'' \textit{Nature Chemical Biology}. (\textit{in press}).
\item \textbf{Coster}, Wichaidit, Rajaram, Altschuler, Wu. ``A simple image correction method for high-throughput microscopy.'' \textit{Nature Methods}, 11(2014): 602.
\item Xiong, Brunson, Huh, Huang, \textbf{Coster}, Wendt, Fay, Qin. ``The Role of Surface Chemistry on the Toxicity of Ag Nanoparticles.'' \textit{Small} 9(2013): 2628-38.
\item Marjanovic, Chalupska, Patenode, \textbf{Coster}, Arnold, Ye, Anesi, Lu, Okun, Tkachenko, Haselkorn, Gornicki. ``Recombinant yeast screen for new inhibitors of human acetyl-CoA carboxylase 2 identifies potential drugs to treat obesity.'' \textit{PNAS} 107(2010): 9093-9088.
\end{enumerate}
\vspace*{\fill}
% list of figures/tables/equations/appendices
%{\listoffigures \let\cleardoublepage\clearpage \listoftables}
%\newpage
\cleardoublepage
\addcontentsline{toc}{chapter}{\listfigurename}
\listoffigures
\cleardoublepage
\addcontentsline{toc}{chapter}{\listtablename}
\listoftables
% List of abbreviations goes HERE
\printglossary[type=acronym,style=mcolindex,title=List of Abbreviations]
\newpage
% MAINMATTER
\pagestyle{fancy}
\pagenumbering{arabic}
\setcounter{page}{1}
\fancyhf{}
%\fancyfoot[RO,LE]{\thepage}
%\fancyhead[LE]{\leftmark}
%\fancyhead[RO]{\rightmark}
\fancyhead[LO]{\leftmark}
\fancyhead[RO]{\thepage}
%\fancyfoot{} % clear all footer fields
%\renewcommand{\headrulewidth}{0.4pt}
% NOW FOR THE CONTENT
\input{TEXT/introduction/introductionMain}
\input{TEXT/pathways/pathwaysMain}
\input{TEXT/insulation/insulationMain}
\input{TEXT/imaging/imagingMain}
\input{TEXT/conclusion/conclusionMain}
% BACKMATTER
% Appendices
\glsaddall
\begin{appendices}
\input{TEXT/pseg/pseg}
\end{appendices}
%\glossarystyle{listhypergroup}
\footnotesize{
\printglossary[style=mcolindex,title=Glossary]
}
% Bibliography
\singlespacing
\small{
\renewcommand{\chapter}[2]{}
\clearpage
\begin{multicols}{2}
\bibliographystyle{ieeetr}
\bibliography{REFS/library}
\end{multicols}
}
\end{document}
%% FIGURE TEMPLATE
%\begin{figure}[ht!]
%\centering
%\includegraphics[width=6in]{FIGS/figure.pdf}
%{\singlespacing
%\caption{ The caption.}
%\label{fig:figure ref}}
%\end{figure}