From 4682a2693e1591c2f96416126ec12ec8f31b5c7f Mon Sep 17 00:00:00 2001 From: ndwarshuis Date: Mon, 26 Jul 2021 15:47:11 -0400 Subject: [PATCH] ADD figs to aim 2a --- figures/doe_responses.svg | 2660 +++++++++++++++ figures/modeling_flower.svg | 5980 +++++++++++++++++++++++++++++++++ figures/modeling_overview.svg | 1572 +++++++++ tex/thesis.tex | 72 +- 4 files changed, 10283 insertions(+), 1 deletion(-) create mode 100644 figures/doe_responses.svg create mode 100644 figures/modeling_flower.svg create mode 100644 figures/modeling_overview.svg diff --git a/figures/doe_responses.svg b/figures/doe_responses.svg new file mode 100644 index 0000000..2434394 --- /dev/null +++ b/figures/doe_responses.svg @@ -0,0 +1,2660 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + Experiment + + + + + + + + + Initial DOEValidation DOE + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2e+064e+066e+068e+06 + + + + + + + + + + 10203040 + IL2 concentration(U/mL) + CD4+ cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 100020003000 + DMS concentration(DMSs/mL) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 60708090100 + Functional mAbDensity (%) + + + + + + + Experiment + + + + + + + + + Initial DOEValidation DOE + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 5.0e+061.0e+071.5e+072.0e+07 + + + + + + + + + + 10203040 + IL2 concentration(U/mL) + CCR7+CD62L+ cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 100020003000 + DMS concentration(DMSs/mL) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 60708090100 + Functional mAbDensity (%) + + + a. + b. + + diff --git a/figures/modeling_flower.svg b/figures/modeling_flower.svg new file mode 100644 index 0000000..14904b7 --- /dev/null +++ b/figures/modeling_flower.svg @@ -0,0 +1,5980 @@ + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + a. + b. + + + Secretome Only + Secretome Only + Metabolome Only + Metabolome Only + + diff --git a/figures/modeling_overview.svg b/figures/modeling_overview.svg new file mode 100644 index 0000000..4818f0b --- /dev/null +++ b/figures/modeling_overview.svg @@ -0,0 +1,1572 @@ + + + + + + + + + + + + image/svg+xml + + + + + + + + a. + b. + + diff --git a/tex/thesis.tex b/tex/thesis.tex index 890b9e0..f399ede 100644 --- a/tex/thesis.tex +++ b/tex/thesis.tex @@ -1550,6 +1550,77 @@ provide these benefits. \section{introduction} \section{methods} \section{results} + +\subsection{DOE shows optimal conditions for expanded potent T cells} + +\begin{figure*}[ht!] + \begingroup + + \includegraphics{../figures/modeling_overview.png} + \phantomsubcaption\label{fig:mod_overview_flow} + \phantomsubcaption\label{fig:mod_overview_doe} + + \endgroup + \caption[Modeling Overview] + {Overview of modeling experiments. + \subcap{fig:mod_overview_flow}{Relationship + between \gls{doe} experiments and AI driven prediction. \glspl{doe} will + be used to determine optimal process input conditions, and longitudinal + multiomics data will be used to fit predictive models. Together, these + will reveal predictive species that may be used for \glspl{cqa} and + \glspl{cpp}.} + \subcap{fig:mod_overview_doe}{Overview of the two \gls{doe} experiments; the + initial \gls{doe} is given by the blue points and the augmented \gls{doe} + is given by the blue points.} + } + \label{fig:mod_overview} +\end{figure*} + +\begin{figure*}[ht!] + \begingroup + + \includegraphics{../figures/doe_responses.png} + \phantomsubcaption\label{fig:doe_responses_mem} + \phantomsubcaption\label{fig:doe_responses_cd4} + + \endgroup + \caption[T cell optimization through Design of Experiments] + {\gls{doe} methodology reveals optimal conditions for expanding T cell + subsets. Responses vs IL2 concentration, \gls{dms} concentration, and + functional \gls{mab} percentage are shown for + \subcap{fig:doe_responses_mem}{total \ptmem{} T cells} and + \subcap{fig:doe_responses_cd4}{total \pth{} T cells}. Each point represents + one run. + } + \label{fig:doe_responses} +\end{figure*} + +% DOE regression tables + +% TODO this section header sucks +\subsection{AI modeling reveals highly predictive species} + +% model summary table + +\begin{figure*}[ht!] + \begingroup + + \includegraphics{../figures/modeling_flower.png} + \phantomsubcaption\label{fig:mod_flower_48r} + \phantomsubcaption\label{fig:mod_flower_cd4} + + \endgroup + \caption[Data-Driven \gls{cqa} identification] + {Data-driven modeling using techniques with regularization reveals species + predictive species which are candidates for \glspl{cqa}. Flower plots are + shown for \subcap{fig:mod_flower_48r}{CD4:CD8 ratio} and + \subcap{fig:mod_flower_cd4}{total \ptmemh{} cells}. The left and right + columns includes models that were trained only on the secretome and + metabolome respectively. Each flower on each plot represents one model, + moving toward the center indicates higher agreement between models.} + \label{fig:mod_flower} +\end{figure*} + \section{discussion} \chapter{aim 2b}\label{aim2b} @@ -1615,7 +1686,6 @@ between survival groups. \label{fig:mouse_dosing_overview} \end{figure*} - \begin{table}[!h] \centering \caption{Results for \gls{car} T cell \invivo{} dose study} \label{tab:mouse_dosing_results}