From a5a9804f9753df99df206558f2d44c6f61a163ea Mon Sep 17 00:00:00 2001
From: ndwarshuis <ndwar@yavin4.ch>
Date: Wed, 4 Aug 2021 21:33:15 -0400
Subject: [PATCH] ENH say which papers I stole

---
 tex/thesis.tex | 29 ++++++++++++++++++-----------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/tex/thesis.tex b/tex/thesis.tex
index 26a5d86..f8ecda2 100644
--- a/tex/thesis.tex
+++ b/tex/thesis.tex
@@ -29,6 +29,14 @@
   urlcolor=black,
 }
 
+\newcommand{\dmspaper}{Dwarshuis et al. Functionalized microcarriers improve T
+  cell manufacturing by facilitating migratory memory T cell production and
+  increasing CD4/CD8 ratio.~2019.~biorxiv.~https://doi.org/10.1101/646760}
+
+\newcommand{\modelpaper}{Odeh-Couvertier et al. Predicting T Cell Quality During
+  Manufacturing Through an Artificial Intelligence-based Integrative Multi-Omics
+  Analytical Platform.~2019.~biorxiv.~https://doi.org/10.1101/2021.05.05.442854}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % my attempt to make MATLAB code look pretty
 
@@ -1297,7 +1305,7 @@ system to state-of-the-art T cell activation technologies for both expansion
 potential and memory cell formation. The governing hypothesis was that
 microcarriers functionalized with \acd{3} and \acd{28} \glspl{mab} will
 provide superior expansion and memory phenotype compared to state-of-the-art
-bead-based T cell expansion technology.
+bead-based T cell expansion technology\footnote{adapted from \dmspaper{}}.
 
 \section{Methods}
 
@@ -1778,8 +1786,7 @@ validity using residual plots (to assess constant variance and independence
 assumptions), QQplots and Shapiro-Wilk normality test (to assess normality
 assumptions), Box-Cox plots (to assess need for power transformations), and
 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.
+context of pure error). Significance was evaluated at $\upalpha$ = 0.05.
 
 \subsection{Flow Cytometry}\label{sec:flow_cytometry}
 
@@ -2745,7 +2752,7 @@ predict the outcome of the cultures. We should stress that the specific
 universal, as this was not performed with equipment that would normally be used
 at scale. However, the process outlined here is one that can easily be adaptable
 to any system, and the specific findings themselves offer interesting insights
-that warrant further study.
+that warrant further study\footnote{adapted from \modelpaper{}}.
 
 \section{Methods}
 
@@ -4061,13 +4068,13 @@ the early work with \il{15} in mice\cite{Lodolce1998}.
 
 The purpose of this aim was to verify that \gls{car} T cells produced using the
 \gls{dms} system will show potent anti-tumor properties in a complex \invivo{}
-system compared to state-of-the-art bead technology. We hypothesized that due to
-the increased \ptmem{} and \pth{} phenotypes as shown in \cref{aim1}, that
-\gls{dms}-expanded T cells would show longer survival and lower tumor burden
-than those expanded with beads. We explored the effect of dosing at different
-levels and the effect of harvesting T cells at early timepoints in the culture,
-which has been shown to produce lower-differentiated T cells with higher
-potency\cite{Ghassemi2018}.
+system compared to state-of-the-art bead technology\footnote{adapted from
+  \dmspaper{}}. We hypothesized that due to the increased \ptmem{} and \pth{}
+phenotypes as shown in \cref{aim1}, that \gls{dms}-expanded T cells would show
+longer survival and lower tumor burden than those expanded with beads. We
+explored the effect of dosing at different levels and the effect of harvesting T
+cells at early timepoints in the culture, which has been shown to produce
+lower-differentiated T cells with higher potency\cite{Ghassemi2018}.
 
 \section{Methods}