ADD inside carrier figure and phenotype figure

tex/thesis.tex

@@ -139,6 +139,8 @@
 
 \newcommand{\subcap}[2]{\subref{#1}) #2}
 
+\newcommand{\sigkey}{Significance test key: *p<0.1; **p < 0.05; ***p<0.01}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % ditto for environments
 
@@ -992,11 +994,32 @@ context of pure error). Statistical significance was evaluated at $\upalpha$ =
   \label{fig:dms_cells}
 \end{figure*}
 
-% 3-donor expansion figure
+% TODO add this to the methods section
+% TODO double check the timing of this experiment (it might not be day 14)
+% TODO provide the regression results and coefficients from this
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/dms_inside.png}
+  \phantomsubcaption\label{fig:dms_inside_bf}
+  \phantomsubcaption\label{fig:dms_inside_regression}
+
+  \endgroup
+  \caption[A subset of T cells grow in interior of \glspl{dms}]
+  {A percentage of T cells grow in the interior of \glspl{dms}.
+    \subcap{fig:dms_inside_bf}{T cells stained dark with MTT after growing on
+      either coated or uncoated \glspl{dms} for 14 days visualized with 
+      brightfield microscope.}
+    \subcap{fig:dms_inside_regression}{Linear regression performed on T cell
+      percentages harvested on the interior of the \glspl{dms} vs the initial
+      starting cell density.}
+  }
+  \label{fig:dms_inside}
+\end{figure*}
+
 
 \subsection{DMSs lead to greater expansion and memory and CD4+ phenotypes}
 
-% TODO add significance tests to this
 \begin{figure*}[ht!]
   \begingroup
 
@@ -1019,12 +1042,29 @@ context of pure error). Statistical significance was evaluated at $\upalpha$ =
     \subcap{fig:dms_exp_mem}{\ptmem{} cells},
     \subcap{fig:dms_exp_cd4}{\pth{} cells},
     \subcap{fig:dms_exp_mem4}{\ptmemh{} cells}, and
-    \subcap{fig:dms_exp_mem8}{\ptmemk{} cells}
+    \subcap{fig:dms_exp_mem8}{\ptmemk{} cells}. \sigkey{}
   }
   \label{fig:dms_exp}
 \end{figure*}
 
-% phenotype flow plots
+% TODO this figure has weird proportions
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/dms_phenotypes.png}
+  \phantomsubcaption\label{fig:dms_phenotype_mem}
+  \phantomsubcaption\label{fig:dms_phenotype_cd4}
+
+  \endgroup
+  \caption[Representative flow plots of \ptmem{} and \pth{} T cells]
+  {Representative flow plots of \ptmem{} and \pth{} T cells at day 14 of
+    expansion using either beads or \glspl{dms}. For three representative donor
+    samples, phenotypes are shown for \subcap{fig:dms_phenotype_mem}{\ptmem{}}
+    and \subcap{fig:dms_phenotype_cd4}{\pth}. Each population was also gated on
+    \cdp{3} T cells.
+  }
+  \label{fig:dms_phenotype}
+\end{figure*}
 
 \subsection*{DMSs can be used to produce functional CAR T cells}