ENH say which papers I stole

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Nathan Dwarshuis 2021-08-04 21:33:15 -04:00
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1 changed files with 18 additions and 11 deletions

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@ -29,6 +29,14 @@
urlcolor=black, 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}
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% my attempt to make MATLAB code look pretty % 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 potential and memory cell formation. The governing hypothesis was that
microcarriers functionalized with \acd{3} and \acd{28} \glspl{mab} will microcarriers functionalized with \acd{3} and \acd{28} \glspl{mab} will
provide superior expansion and memory phenotype compared to state-of-the-art 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} \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), QQplots and Shapiro-Wilk normality test (to assess normality
assumptions), Box-Cox plots (to assess need for power transformations), and 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 lack-of-fit tests where replicates were present (to assess model fit in the
context of pure error). Statistical significance was evaluated at $\upalpha$ = context of pure error). Significance was evaluated at $\upalpha$ = 0.05.
0.05.
\subsection{Flow Cytometry}\label{sec:flow_cytometry} \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 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 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 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} \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 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{} \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 system compared to state-of-the-art bead technology\footnote{adapted from
the increased \ptmem{} and \pth{} phenotypes as shown in \cref{aim1}, that \dmspaper{}}. We hypothesized that due to the increased \ptmem{} and \pth{}
\gls{dms}-expanded T cells would show longer survival and lower tumor burden phenotypes as shown in \cref{aim1}, that \gls{dms}-expanded T cells would show
than those expanded with beads. We explored the effect of dosing at different longer survival and lower tumor burden than those expanded with beads. We
levels and the effect of harvesting T cells at early timepoints in the culture, explored the effect of dosing at different levels and the effect of harvesting T
which has been shown to produce lower-differentiated T cells with higher cells at early timepoints in the culture, which has been shown to produce
potency\cite{Ghassemi2018}. lower-differentiated T cells with higher potency\cite{Ghassemi2018}.
\section{Methods} \section{Methods}