ndwarshuis
/
phd_thesis
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

ENH make section headers one line and pretty

This commit is contained in:
Nathan Dwarshuis 2021-09-07 20:35:12 -04:00
parent f30399869f
commit 89baa4f970
1 changed files with 18 additions and 24 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

42
tex/thesis.tex
View File

@ -974,7 +974,7 @@ using retro- or lentiviral vectors as their means of gene-editing must be tested
for replication competent vectors\cite{Wang2013} and for contamination via
bacteria or other pathogens.
\subsection{T cell Activation Methods}\label{sec:background_activation}
\subsection{T Cell Activation Methods}\label{sec:background_activation}
In order for T cells to be expanded \exvivo{} they must be activated with a
stimulatory signal (Signal 1) and a costimulatory signal (Signal 2). \Invivo{},
@ -2067,7 +2067,7 @@ water prior to adding it to the microcarrier suspension (which itself is in
\label{fig:dms_kinetics}
\end{figure*}
\subsection{Reaction Kinetics for Coating the DMSs}
\subsection{DMS Process Has Defined Reaction Kinetics}
We investigated the reaction kinetics of all three coating steps (accompanying
MATLAB codes are provided in \cref{sec:appendix_binding}). To quantify the
@ -2154,7 +2154,7 @@ one that could be optimized).
MATLAB code and output for all the wash step calculations are given in
\cref{sec:appendix_washing}.
\subsection{DMSs can efficiently expand T cells compared to beads}
\subsection{DMSs Can Efficiently Expand T Cells Compared to Beads}
\begin{figure*}[ht!]
\begingroup
@ -2284,7 +2284,6 @@ expansion by lowering apoptosis of the cells in culture.
\input{../tables/inside_fraction_regression.tex}
\end{table}
% RESULT state the CI of what are inside the carriers
We also asked how many cells were inside the \glspl{dms} vs. free-floating in
suspension and/or loosely attached to the surface. We qualitatively verified the
presence of cells inside the \glspl{dms} using a \gls{mtt} stain to opaquely
@ -2299,7 +2298,7 @@ regression on this data revealed that the percentage of T cells inside the
\glspl{dms} does not depend on the initial starting cell density (at least when
harvested after \SI{14}{\day}) (\cref{tab:inside_regression}).
\subsection{DMSs lead to greater expansion and memory and CD4+ phenotypes}
\subsection{DMSs Lead to Greater Expansion and High-Quality Phenotypes}
\begin{figure*}[ht!]
\begingroup
@ -2388,7 +2387,7 @@ indicate the \gls{dms} platform has the capacity to expand higher numbers and
percentages of highly potent \ptmem{} and \pth{} T cells compared to
state-of-the-art bead technology.
\subsection*{DMSs can be used to produce functional CAR T cells}
\subsection{DMSs Produce Functional CAR T Cells}
After optimizing for naïve/memory and CD4 yield, we sought to determine if the
\glspl{dms} were compatible with lentiviral transduction protocols used to
@ -2489,7 +2488,7 @@ for bead (\cref{fig:car_bcma_total}).
\label{fig:car_bcma}
\end{figure*}
\subsection{DMSs efficiently expand T cells in Grex bioreactors}
\subsection{DMSs Efficiently Expand T Cells in Grex Bioreactors}
\begin{figure*}[ht!]
\begingroup
@ -2556,7 +2555,7 @@ in Grex bioreactors, although more optimization may be necessary to maximize the
media feed rate and growth area to get comparable results to those seen in
tissue-culture plates.
\subsection{DMSs do not leave antibodies attached to cell product}
\subsection{DMSs Do Not Leave Antibodies Attached to Cell Product}
\begin{figure*}[ht!]
\begingroup
@ -2581,8 +2580,7 @@ not detect the presence of either \ahcd{3} or \ahcd{28} \glspl{mab} (both of
which were \gls{igg}) on the final T cell product after \SI{14}{\day} of
expansion (\cref{fig:nonstick}).
\subsection{DMSs consistently outperform bead-based expansion compared to
beads in a variety of conditions}
\subsection{DMSs Outperform Beads in a Variety of Conditions}
In order to establish the robustness of our method, we combined all experiments
performed in our lab using beads or \glspl{dms} and combined them into one
@ -2915,7 +2913,7 @@ additional samples (\cref{fig:mod_overview_doe}). Process parameters for the
\si{\IU\per\ml}), \pdms{} (500, 1000, 1500, 2000, 2500, 3000, 3500
\si{\dms\per\ml}), and \pmab{} (\SI{100}{\percent}) (\cref{fig:mod_overview}).
\subsection{DMS fabrication}
\subsection{DMS Fabrication}
\glspl{dms} were fabricated as described in \cref{sec:dms_fab} with the
following modifications in order to obtain a variable functional \gls{mab}
@ -3119,7 +3117,7 @@ a Venn diagram from the \inlinecode{venn} R package.
\section{Results}
\subsection{T Cells Can be Grown on DMSs with Lower IL2 Concentrations}
\subsection{DMSs Grow T Cells With Lower IL2 Concentrations}
Prior to the main experiments in this aim, we performed a preliminary experiment
to assess the effect of lowering the \gls{il2} concentration on the T cells
@ -3176,7 +3174,7 @@ advantage at lower \gls{il2} concentrations compared to beads. For this reason,
we decided to investigate the lower range of \gls{il2} concentrations starting
at \SI{10}{\IU\per\ml} throughout the remainder of this aim.
\subsection{DOE Shows Optimal Conditions for Expanded Potent T Cells}
\subsection{DOE Shows Optimal Conditions for Potent T Cells}
% TABLE not all of these were actually used, explain why by either adding columns
% or marking with an asterisk
@ -3364,8 +3362,7 @@ combinations at and around this optimum were tested, the model nonetheless
showed that there were no other optimal values or regions elsewhere in the
model.
\subsection{Modeling With Artificial Intelligence Methods Reveals Potential
CQAs}
\subsection{Modeling with Machine Learning Reveals Putative CQAs}
Due to the heterogeneity of the multivariate data collected and knowing that no
single model is perfect for all applications, we implemented an agnostic
@ -3686,7 +3683,7 @@ Adding \glspl{dms} was relatively much simpler; the number of \gls{dms} used per
area on day 0 was scaled up by 3 on day 4 to match the change from a 96 well
plate to a 24 well plate, effectively producing a constant activation signal.
\subsection{Mass Wytometry and Clustering Analysis}
\subsection{Mass Cytometry and Clustering Analysis}
T cells were stained using a \product{34 \gls{cytof} marker
panel}{Fluidigm}{201322} and \product{cisplatin}{Fluidigm}{201064} which were
@ -3867,7 +3864,7 @@ leads to potentially higher expansion, lower \pthp{}, and higher fraction of
lower differentiated T cells such as \gls{tscm}, and adding \gls{dms} seems to
do the inverse.
\subsection{Blocking Integrin Binding Does not Alter Expansion or Phenotype}
\subsection{Blocking Integrin Does Not Alter Expansion or Phenotype}
One of the reasons the \gls{dms} platform might perform better than the beads is
the fact that they are composed of gelatin, which is a collagen derivative. The
@ -3957,7 +3954,7 @@ CD4, or CD8) were statistically different between groups
Taken together, these data suggest that the advantage of the \gls{dms} platform
is not due to signaling through \gls{a2b1} or \gls{a2b2}.
\subsection{Blocking IL15 Signaling does not Alter Expansion or Phenotype}
\subsection{Blocking IL15 Does Not Alter Expansion or Phenotype}
\gls{il15} is a cytokine responsible for memory T cell survival and maintenance.
Furthermore, we observed in other experiments that it is secreted to a much
@ -4175,7 +4172,6 @@ lower-differentiated T cells with higher potency\cite{Ghassemi2018}.
T cells were grown as described in \cref{sec:tcellculture}.
\subsection{\Invivo{} Therapeutic Efficacy in NSG Mice Model}
% METHOD describe how the luciferase cells were generated (eg the kwong lab)
@ -4226,8 +4222,7 @@ between survival groups.
\input{../tables/mouse_dose_car.tex}
\end{table}
\subsection{DMS-expanded T Cells Show Greater Anti-Tumor Activity \invivo{}
Compared to Beads}
\subsection{DMSs Lead to Greater \invivo{} Anti-Tumor Activity}
\begin{figure*}[ht!]
\begingroup
@ -4273,7 +4268,7 @@ between survival groups.
\subcap{fig:mouse_dosing_ivis_survival_full}{The same data as
\subref{fig:mouse_dosing_ivis_survival} except showing the full time until
euthanasia for all mice (including those that died via \gls{gvhd}). Survival
curves were statistically analyzed using the logrank test in GraphPad
curves were statistically analyzed using the Mantel-Cox test in GraphPad
Prism.}
}
\label{fig:mouse_dosing_ivis}
@ -4693,7 +4688,7 @@ cytokine is undetectable, this indicates that the blocking \gls{mab} completely
quenched all target cytokine at the time of addition and in the time between
feeding cycles.
\subsubsection{Interior cell phenotype}
\subsubsection{Interior Cell Phenotype}
Unlike the beads, the \glspl{dms} have interior and exterior surfaces. We
demonstrated that some T cell expand on the interior of the \glspl{dms}, and is
@ -4820,7 +4815,6 @@ potential mitigation strategies:
due to its automated nature.
\end{description}
\subsubsection{Surface Stiffness}
The beads and \gls{dms} are composed of different materials: iron/polymer in the