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 for replication competent vectors\cite{Wang2013} and for contamination via
bacteria or other pathogens. 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 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{}, 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} \label{fig:dms_kinetics}
\end{figure*} \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 We investigated the reaction kinetics of all three coating steps (accompanying
MATLAB codes are provided in \cref{sec:appendix_binding}). To quantify the 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 MATLAB code and output for all the wash step calculations are given in
\cref{sec:appendix_washing}. \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!] \begin{figure*}[ht!]
\begingroup \begingroup
@ -2284,7 +2284,6 @@ expansion by lowering apoptosis of the cells in culture.
\input{../tables/inside_fraction_regression.tex} \input{../tables/inside_fraction_regression.tex}
\end{table} \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 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 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 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 \glspl{dms} does not depend on the initial starting cell density (at least when
harvested after \SI{14}{\day}) (\cref{tab:inside_regression}). 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!] \begin{figure*}[ht!]
\begingroup \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 percentages of highly potent \ptmem{} and \pth{} T cells compared to
state-of-the-art bead technology. 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 After optimizing for naïve/memory and CD4 yield, we sought to determine if the
\glspl{dms} were compatible with lentiviral transduction protocols used to \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} \label{fig:car_bcma}
\end{figure*} \end{figure*}
\subsection{DMSs efficiently expand T cells in Grex bioreactors} \subsection{DMSs Efficiently Expand T Cells in Grex Bioreactors}
\begin{figure*}[ht!] \begin{figure*}[ht!]
\begingroup \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 media feed rate and growth area to get comparable results to those seen in
tissue-culture plates. 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!] \begin{figure*}[ht!]
\begingroup \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 which were \gls{igg}) on the final T cell product after \SI{14}{\day} of
expansion (\cref{fig:nonstick}). expansion (\cref{fig:nonstick}).
\subsection{DMSs consistently outperform bead-based expansion compared to \subsection{DMSs Outperform Beads in a Variety of Conditions}
beads in a variety of conditions}
In order to establish the robustness of our method, we combined all experiments 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 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{\IU\per\ml}), \pdms{} (500, 1000, 1500, 2000, 2500, 3000, 3500
\si{\dms\per\ml}), and \pmab{} (\SI{100}{\percent}) (\cref{fig:mod_overview}). \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 \glspl{dms} were fabricated as described in \cref{sec:dms_fab} with the
following modifications in order to obtain a variable functional \gls{mab} 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} \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 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 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 we decided to investigate the lower range of \gls{il2} concentrations starting
at \SI{10}{\IU\per\ml} throughout the remainder of this aim. 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 % TABLE not all of these were actually used, explain why by either adding columns
% or marking with an asterisk % 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 showed that there were no other optimal values or regions elsewhere in the
model. model.
\subsection{Modeling With Artificial Intelligence Methods Reveals Potential \subsection{Modeling with Machine Learning Reveals Putative CQAs}
CQAs}
Due to the heterogeneity of the multivariate data collected and knowing that no Due to the heterogeneity of the multivariate data collected and knowing that no
single model is perfect for all applications, we implemented an agnostic 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 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. 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 T cells were stained using a \product{34 \gls{cytof} marker
panel}{Fluidigm}{201322} and \product{cisplatin}{Fluidigm}{201064} which were 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 lower differentiated T cells such as \gls{tscm}, and adding \gls{dms} seems to
do the inverse. 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 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 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 Taken together, these data suggest that the advantage of the \gls{dms} platform
is not due to signaling through \gls{a2b1} or \gls{a2b2}. 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. \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 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}. T cells were grown as described in \cref{sec:tcellculture}.
\subsection{\Invivo{} Therapeutic Efficacy in NSG Mice Model} \subsection{\Invivo{} Therapeutic Efficacy in NSG Mice Model}
% METHOD describe how the luciferase cells were generated (eg the kwong lab) % 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} \input{../tables/mouse_dose_car.tex}
\end{table} \end{table}
\subsection{DMS-expanded T Cells Show Greater Anti-Tumor Activity \invivo{} \subsection{DMSs Lead to Greater \invivo{} Anti-Tumor Activity}
Compared to Beads}
\begin{figure*}[ht!] \begin{figure*}[ht!]
\begingroup \begingroup
@ -4273,7 +4268,7 @@ between survival groups.
\subcap{fig:mouse_dosing_ivis_survival_full}{The same data as \subcap{fig:mouse_dosing_ivis_survival_full}{The same data as
\subref{fig:mouse_dosing_ivis_survival} except showing the full time until \subref{fig:mouse_dosing_ivis_survival} except showing the full time until
euthanasia for all mice (including those that died via \gls{gvhd}). Survival 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.} Prism.}
} }
\label{fig:mouse_dosing_ivis} \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 quenched all target cytokine at the time of addition and in the time between
feeding cycles. feeding cycles.
\subsubsection{Interior cell phenotype} \subsubsection{Interior Cell Phenotype}
Unlike the beads, the \glspl{dms} have interior and exterior surfaces. We 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 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. due to its automated nature.
\end{description} \end{description}
\subsubsection{Surface Stiffness} \subsubsection{Surface Stiffness}
The beads and \gls{dms} are composed of different materials: iron/polymer in the The beads and \gls{dms} are composed of different materials: iron/polymer in the