From cd9f438d7da759135e7cf40035d9b4c6250f265f Mon Sep 17 00:00:00 2001
From: ndwarshuis <ndwar@yavin4.ch>
Date: Tue, 27 Jul 2021 12:26:45 -0400
Subject: [PATCH] REF add some notes to myself

---
 tex/thesis.tex | 29 ++++++++++++++++++++---------
 1 file changed, 20 insertions(+), 9 deletions(-)

diff --git a/tex/thesis.tex b/tex/thesis.tex
index b230661..926dffb 100644
--- a/tex/thesis.tex
+++ b/tex/thesis.tex
@@ -698,6 +698,7 @@ Therefore, the proposed microcarrier system should enable greater expansion and
 better retention of memory phenotype compared to current bead-based methods.
 
 \section{methods}
+
 \subsection{dms functionalization}
 
 \begin{figure*}[ht!]
@@ -834,6 +835,8 @@ Cells on the \glspl{dms} were visualized by adding \SI{0.5}{\ul}
 \product{\acd{45}-\gls{af647}}{\bl}{368538}, incubating for \SI{1}{\hour}, and
 imaging on a spinning disk confocal microscope.
 
+% METHOD mtt staining and interior quantification
+
 \subsection{quantification of apoptosis using Annexin-V}
 
 Apoptosis was quantified using \gls{anv} according to the manufacturer's
@@ -905,6 +908,7 @@ Briefly, cells were washed once and stained with \product{biotinylated
 BD Accuri. Readout was percent \gls{pe}+ cells as compared to secondary controls
 (\gls{pe}-\gls{stp} with no \gls{ptnl}).
 
+% TODO add BCMA-CAR stuff
 \subsection{car plasmid and lentiviral transduction}
 
 The anti-CD19-CD8-CD137-CD3z \gls{car} with the EF1$\upalpha$
@@ -924,8 +928,6 @@ plates and incubated for another \SI{24}{\hour}. Cells and beads/\glspl{dms}
 were removed from the retronectin plates using vigorous pipetting and
 transferred to another 96 well plate wherein expansion continued.
 
-
-
 \subsection{statistical analysis}
 
 For 1-way \gls{anova} analysis with Tukey multiple comparisons test,
@@ -947,7 +949,8 @@ lack-of-fit tests where replicates were present (to assess model fit in the
 context of pure error). Statistical significance was evaluated at $\upalpha$ =
 0.05.
 
-% TODO add meta-analysis section
+% METHOD add meta-analysis
+% METHOD add Grex
 
 \section{results}
 
@@ -976,9 +979,8 @@ noted that the maximal \gls{mab} binding capacity occurred near \SI{50}{\nmol}
 biotin input (which corresponded to \SI{2.5}{\nmol\per\mg\of{\dms}}) thus we
 used this in subsequent processes.
 
-% TODO add paragraph explaining the qc stuff
-
-% TODO add paragraph explaining the reaction kinetics stuff
+% RESULT add paragraph explaining the qc stuff
+% RESULT add paragraph explaining the reaction kinetics stuff
 
 % TODO flip the rows of this figure (right now the text is backward)
 \begin{figure*}[ht!]
@@ -1135,7 +1137,6 @@ cells after \SI{14}{\day} were on the interior surface of the \glspl{dms}
   \label{fig:dms_flowchart}
 \end{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!]
@@ -1290,9 +1291,17 @@ showing that migration was likely independent of \gls{car} transduction.
     \subcap{fig:car_production_migration}{Endpoint plot for transmigration assay
     with \gls{anova}.} All data is from T cells expanded for \SI{14}{\day}.
   }
-  \label{fig:dms_phenotype}
+  \label{fig:car_production}
 \end{figure*}
 
+% FIGURE bcma results
+
+\subsection{DMSs efficiently expand T cells in Grex bioreactors}
+
+% FIGURE grex
+% FIGURE luminex
+% FIGURE grex + car
+
 \subsection{DMSs do not leave antibodies attached to cell product}
 
 We asked if \glspl{mab} from the \glspl{dms} detached from the \gls{dms} surface
@@ -1625,6 +1634,8 @@ provide these benefits.
 
 \subsection{DOE shows optimal conditions for expanded potent T cells}
 
+% TABLE luminex panel used
+
 % TODO this plots proportions look dumb
 \begin{figure*}[ht!]
   \begingroup
@@ -1699,7 +1710,7 @@ provide these benefits.
   \label{fig:doe_responses}
 \end{figure*}
 
-% TODO add DOE regression tables
+% TABLE DOE regression results
 
 % TODO this section header sucks
 \subsection{AI modeling reveals highly predictive species}