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