ADD figures to aim 2b
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tex/thesis.tex
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@ -85,6 +85,9 @@
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\newacronym{a2b2}{A2B2}{integrin $\upalpha$1$\upbeta$2}
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\newacronym{til}{TIL}{tumor infiltrating lymphocytes}
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\newacronym{nsg}{NSG}{NOD scid gamma}
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\newacronym{colb}{COL-B}{collagenase B}
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\newacronym{cold}{COL-D}{collagenase D}
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\newacronym{tsne}{tSNE}{t-stochastic neighbor embedding}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% SI units for uber nerds
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@ -1063,6 +1066,8 @@ cells after \SI{14}{\day} were on the interior surface of the \glspl{dms}
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%, and this did not significantly change with initial seeding density (Supplemental Table 1).
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% FIGURE caspase/bcl2 figure
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% TODO add this to the methods section
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% TODO double check the timing of this experiment (it might not be day 14)
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% TODO provide the regression results and coefficients from this
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@ -1553,6 +1558,7 @@ provide these benefits.
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\subsection{DOE shows optimal conditions for expanded potent T cells}
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% FIGURE IL2 modulation figure
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% TODO not all of these were actually use, explain why by either adding columns
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% or marking with an asterisk
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@ -1642,6 +1648,142 @@ provide these benefits.
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\section{introduction}
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\section{methods}
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\section{results}
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\subsection{adding or removing DMSs alters expansion and phenotype}
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% TODO this figure is tall and skinny like me
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\begin{figure*}[ht!]
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\begingroup
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\includegraphics{../figures/collagenase.png}
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\endgroup
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\caption[Effects Collagenase Treatment on T cells]
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{T cells treated with either \gls{colb}, \gls{cold}, or buffer and then
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stained for various surface markers and analyzing via flow cytometry.}
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\label{fig:collagenase_fx}
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\end{figure*}
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% TODO this figure still says "carrier"
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\begin{figure*}[ht!]
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\begingroup
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\includegraphics{../figures/add_remove_endpoint.png}
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\phantomsubcaption\label{fig:add_rem_growth}
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\phantomsubcaption\label{fig:add_rem_viability}
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\phantomsubcaption\label{fig:add_rem_cd4}
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\endgroup
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\caption[Endpoint results from adding/removing \gls{dms} on day 4]
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{Changing \gls{dms} concentration on day 4 has profound effects on phenotype
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and growth.
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\subcap{fig:add_rem_growth}{Longitudinal fold change},
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\subcap{fig:add_rem_viability}{longitudinal viability}, and
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\subcap{fig:add_rem_cd4}{day 14 \pthp{}} of T cell cultures with \glspl{dms}
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added, removed, or kept the same on day 4.
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}
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\label{fig:add_rem}
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\end{figure*}
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% TODO this needs some better annotations
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\begin{figure*}[ht!]
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\begingroup
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\includegraphics{../figures/add_remove_spade.png}
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\phantomsubcaption\label{fig:spade_msts}
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\phantomsubcaption\label{fig:spade_tsne_all}
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\phantomsubcaption\label{fig:spade_tsne_stem}
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\phantomsubcaption\label{fig:spade_quant}
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\endgroup
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\caption[SPADE and tSNE analysis temporally-modified DMS concentration]
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{Removing \glspl{dms} leads to a higher fraction of potent stem-memory T
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cells compared to both adding and not changing the \gls{dms} concentration
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at day 4.
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\subcap{fig:spade_msts}{SPADE plots of CD4, CD45RA, CD27, and CD45RO
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expression on T cells. All cells from the added, removed, or no change
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groups were pooled and clustered at once.}
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\subcap{fig:spade_tsne_all}{\gls{tsne} plots of all cells pooled from all
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groups.}
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\subcap{fig:spade_tsne_stem}{\gls{tsne} plots of T cells from all groups
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manually gated on \cdp{8}\cdp{27}\cdp{45RO}.}
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\subcap{fig:spade_quant}{T cells from SPADE plots clustered by expression in
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(\subref{fig:spade_msts}) quantified against total cell number from each
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group.}
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}
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\label{fig:spade}
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\end{figure*}
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\subsection{blocking integrin binding does not alter expansion or phenotype}
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% TODO perhaps these figs should be combined
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% TODO actually make the captions for these
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% TODO add some background into why integrins are important and the proposed mechanism
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\begin{figure*}[ht!]
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\begingroup
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\includegraphics{../figures/integrin_1.png}
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\phantomsubcaption\label{fig:inegrin_1_fc}
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\phantomsubcaption\label{fig:inegrin_1_mem}
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\phantomsubcaption\label{fig:inegrin_1_cd49}
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\endgroup
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\caption[Integrin blocking I]
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{Blocking with integrin does not lead to differences in memory or growth.
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}
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\label{fig:integrin_1}
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\end{figure*}
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\begin{figure*}[ht!]
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\begingroup
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\includegraphics{../figures/integrin_2.png}
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\phantomsubcaption\label{fig:inegrin_2_fc}
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\phantomsubcaption\label{fig:inegrin_2_mem}
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\endgroup
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\caption[Integrin blocking II]
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{Blocking with integrin does not lead to differences in memory or growth.
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}
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\label{fig:integrin_2}
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\end{figure*}
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\subsection{blocking IL15 signaling does not alter expansion or phenotype}
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% TODO actually add captions
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% TODO add fold change and viability to these
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% TODO maybe combine these
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% TODO add some background into why IL15 is important and the proposed mechanism
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\begin{figure*}[ht!]
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\begingroup
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\includegraphics{../figures/il15_blockade_1.png}
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\phantomsubcaption\label{fig:il15_1_fc}
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\phantomsubcaption\label{fig:il15_1_viability}
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\phantomsubcaption\label{fig:il15_1_mem}
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\endgroup
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\caption[IL15 blocking I]
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{Blocking with IL15 does not lead to differences in memory or growth.
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}
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\label{fig:il15_1}
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\end{figure*}
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\begin{figure*}[ht!]
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\begingroup
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\includegraphics{../figures/il15_blockade_2.png}
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\phantomsubcaption\label{fig:il15_2_fc}
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\phantomsubcaption\label{fig:il15_2_viability}
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\phantomsubcaption\label{fig:il15_2_mem}
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\endgroup
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\caption[IL15 blocking II]
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{Blocking with IL15 does not lead to differences in memory or growth.
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}
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\label{fig:il15_2}
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\end{figure*}
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\section{discussion}
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\chapter{aim 3}\label{aim3}
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