From 957f09821cee8d9cb6fdf703ab69c9f42b22ec91 Mon Sep 17 00:00:00 2001 From: ndwarshuis Date: Tue, 7 Sep 2021 21:09:06 -0400 Subject: [PATCH] ENH make figure and table captions sane --- tex/thesis.tex | 107 +++++++++++++++++++++++++------------------------ 1 file changed, 54 insertions(+), 53 deletions(-) diff --git a/tex/thesis.tex b/tex/thesis.tex index 933fb24..4415035 100644 --- a/tex/thesis.tex +++ b/tex/thesis.tex @@ -1426,7 +1426,8 @@ bead-based T cell expansion technology\footnote{adapted from \dmspaper{}}. \includegraphics{../figures/dms_flowchart.png} \endgroup - \caption[\Acrshort{dms} Flowchart]{Overview of \gls{dms} manufacturing process.} + \caption[\Acrshort{dms} Manufacturin Flowchart] + {Overview of \gls{dms} manufacturing process.} \label{fig:dms_flowchart} \end{figure*} @@ -1468,7 +1469,7 @@ step to remove excess \gls{stp}. They were washed once again in the cell culture media to be used for the T cell expansion. \begin{table}[!h] \centering - \caption{Properties of the microcarriers used} + \caption{Microcarrier properties} \label{tab:carrier_props} \input{../tables/carrier_properties.tex} \end{table} @@ -1833,7 +1834,7 @@ that was under-range (`OOR <' in output spreadsheet) was set to zero. All values that were extrapolated from the standard curve were left unchanged. \begin{table}[!h] \centering - \caption{Luminex Panel} + \caption{Luminex panel} \label{tab:luminex_panel} \input{../tables/luminex_panel.tex} \end{table} @@ -1894,7 +1895,7 @@ context of pure error). Significance was evaluated at $\upalpha$ = 0.05. \end{figure*} \begin{table}[!h] \centering - \caption{\glspl{mab} used for flow cytometry} + \caption{Antibodies used for flow cytometry} \label{tab:flow_mabs} \input{../tables/flow_mabs.tex} \end{table} @@ -1919,7 +1920,7 @@ respective sections. Cells were gated according to \cref{fig:gating_strategy}. \phantomsubcaption\label{fig:mab_carrier_fitc} \endgroup - \caption[\gls{dms} Coating] + \caption[\acrshort{dms} Coating] {\gls{dms} functionalization results. \subcap{fig:cug_vs_cus}{Bound \gls{stp} surface density on either \gls{cus} or \gls{cug} microcarriers. Surface density @@ -1977,7 +1978,7 @@ the T cells receive downstream. \phantomsubcaption\label{fig:dms_snb_decay_curves} \endgroup - \caption[\gls{dms} Process Parameters] + \caption[\acrshort{dms} Process Parameters] {Investigation of influential parameters for the \gls{dms} process. \subcap{fig:dms_qc_doe}{\gls{doe} investigating the effect of initial mass of microcarriers, reaction temperature, and biotin concentration on @@ -2054,7 +2055,7 @@ water prior to adding it to the microcarrier suspension (which itself is in \phantomsubcaption\label{fig:dms_biotin_washed} \endgroup - \caption[\gls{dms} Reaction kinetics] + \caption[\acrshort{dms} Reaction Kinetics] {Reaction kinetics for microcarrier functionalization. \subcap{fig:dms_biotin_rxn_mass}{Biotin mass bound per time} \subcap{fig:dms_biotin_rxn_frac}{Fraction of input biotin bound per time} @@ -2164,7 +2165,7 @@ MATLAB code and output for all the wash step calculations are given in \phantomsubcaption\label{fig:dms_cells_fluor} \endgroup - \caption[T cells growing on \glspl{dms}] + \caption[T Cells Growing on \acrshortpl{dms}] {Cells grow in tight clusters in and around functionalized \gls{dms}. \subcap{fig:dms_cells_phase}{Phase-contrast image of T cells growing on \glspl{dms}} @@ -2184,7 +2185,7 @@ MATLAB code and output for all the wash step calculations are given in \phantomsubcaption\label{fig:dms_expansion_isotype} \endgroup - \caption[\glspl{dms} selectively expand T cells] + \caption[\acrshortpl{dms} Selectively Expand T Cells] {T cells are selectively expanded on \gls{dms}. \subcap{fig:dms_expansion_bead}{T cells expanded with either \glspl{dms} or bead for 12 days. Significance was assessed using a two-tailed @@ -2221,7 +2222,7 @@ due to the \acd{3} and \acd{28} \glspl{mab}\cite{Waysbort2013}. \phantomsubcaption\label{fig:apoptosis_bcl2} \endgroup - \caption[Apoptosis Quantification for \glspl{dms}] + \caption[Apoptosis Quantification for \acrshortpl{dms}] {\glspl{dms} produce cells with lower apoptosis marker expression on average compared to bead. \subcap{fig:apoptosis_annV}{Quantification of apoptosis and necrosis by @@ -2266,7 +2267,7 @@ expansion by lowering apoptosis of the cells in culture. \phantomsubcaption\label{fig:dms_inside_regression} \endgroup - \caption[A subset of T cells grow in interior of \glspl{dms}] + \caption[T Cells Growing on Interior of \acrshortpl{dms}] {A percentage of T cells grow in the interior of \glspl{dms}. \subcap{fig:dms_inside_bf}{T cells stained dark with \gls{mtt} after growing on either coated or uncoated \glspl{dms} for 15 days visualized @@ -2279,7 +2280,7 @@ expansion by lowering apoptosis of the cells in culture. \end{figure*} \begin{table}[!h] \centering - \caption{Regression for fraction of cells in \gls{dms} at day 14} + \caption{Regression for fraction of cells in \acrshortpl{dms} at day 14} \label{tab:inside_regression} \input{../tables/inside_fraction_regression.tex} \end{table} @@ -2311,7 +2312,7 @@ harvested after \SI{14}{\day}) (\cref{tab:inside_regression}). \phantomsubcaption\label{fig:dms_exp_mem8} \endgroup - \caption[\gls{dms} vs bead expansion] + \caption[\acrshort{dms} vs Bead Expansion] {\gls{dms} lead to superior expansion of T cells compared to beads across multiple donors. \subcap{fig:dms_exp_fold_change}{Longitudinal fold change of T cells grown @@ -2357,7 +2358,7 @@ true when observing the CD4+ and CD8+ fractions of the naïve/memory subset \phantomsubcaption\label{fig:dms_phenotype_cd4} \endgroup - \caption[Representative flow plots of \ptmem{} and \pth{} T cells] + \caption[Representative Flow Plots of \ptmem{} and \pth{} T Cells] {Representative flow plots of \ptmem{} and \pth{} T cells at day 14 of expansion using either beads or \glspl{dms}. For three representative donor samples, phenotypes are shown for \subcap{fig:dms_phenotype_mem}{\ptmem{}} @@ -2431,7 +2432,7 @@ showing that migration was likely independent of \gls{car} transduction. \phantomsubcaption\label{fig:car_cd19_endpoint} \endgroup - \caption[\glspl{dms} lead to efficient CD19 transduction] + \caption[CD19 Transduction] {\glspl{dms} lead to efficient CD19 transduction. \subcap{fig:car_cd19_flow}{Representative flow cytometry plot for transduced or untransduced T cells stained with \gls{ptnl}.} @@ -2451,7 +2452,7 @@ showing that migration was likely independent of \gls{car} transduction. \phantomsubcaption\label{fig:car_degran_migration} \endgroup - \caption[\glspl{dms} produce functional \gls{car} T cells] + \caption[\acrshort{car} T Cell Functionality] {\glspl{dms} produce functional \gls{car} T cells. \subcap{fig:car_degran_flow}{Representative flow plot for degenerating T cells.} @@ -2479,7 +2480,7 @@ for bead (\cref{fig:car_bcma_total}). \phantomsubcaption\label{fig:car_bcma_total} \endgroup - \caption[BMCA Transduction Results] + \caption[\acrshort{bcma} Transduction] {\glspl{dms} produce larger numbers of \gls{bcma} \gls{car} T cells compared to beads. \subcap{fig:car_bcma_percent}{\ptcarp{} at day 14.} @@ -2500,7 +2501,7 @@ for bead (\cref{fig:car_bcma_total}). \phantomsubcaption\label{fig:grex_cd4} \endgroup - \caption[Grex bioreactor results] + \caption[Grex Expansion] {\glspl{dms} expand T cells robustly in Grex bioreactors. \subcap{fig:grex_results_fc}{Fold change of T cells over time.} \subcap{fig:grex_results_viability}{Viability of T cells over time.} @@ -2538,7 +2539,7 @@ area could mean higher signaling and higher differentiation rate to \includegraphics{../figures/grex_luminex.png} \endgroup - \caption[Grex luminex results] + \caption[Grex Luminex Results] {\gls{dms} lead to higher cytokine production in Grex bioreactors.} \label{fig:grex_luminex} \end{figure*} @@ -2563,7 +2564,7 @@ tissue-culture plates. \includegraphics{../figures/nonstick.png} \endgroup - \caption[\acrshort{mab} do not detach from \glspl{dms}] + \caption[\acrshort{dms} \acrshort{mab} Detachment] {\glspl{mab} do not detach from microcarriers onto T cells in a detectable manner. Plots are representative manufacturing runs harvest after \SI{14}{\day} of expansion and stained with \anti{\gls{igg}}. @@ -2630,20 +2631,19 @@ this modification as removing conditioned media as the cell are expanding could disrupt signaling pathways. \begin{table}[!h] \centering - \caption{Causal Inference on treatment variables only} + \caption{Causal inference on treatment variables} \label{tab:ci_treat} \input{../tables/causal_inference_treat.tex} \end{table} \begin{table}[!h] \centering - \caption{Causal Inference on treatment variables and control variables} + \caption{Causal inference on all variables} \label{tab:ci_controlled} \input{../tables/causal_inference_control.tex} \end{table} \begin{table}[!h] \centering - \caption{Causal Inference on treatment variables and control variables (single - donor)} + \caption{Causal inference on all variables (single donor)} \label{tab:ci_single} \input{../tables/causal_inference_single.tex} \end{table} @@ -2657,7 +2657,7 @@ disrupt signaling pathways. \phantomsubcaption\label{fig:metaanalysis_fx_cd4} \endgroup - \caption[Meta-analysis effect sizes] + \caption[Meta-analysis Effect Sizes] {\glspl{dms} exhibit superior performance compared to beads controlling for many experimental and process conditions. Effect sizes for \subcap{fig:metaanalysis_fx_exp}{fold change}, @@ -3137,7 +3137,7 @@ were true. \phantomsubcaption\label{fig:il2_mod_flow} \endgroup - \caption[T cells grown at varying IL2 concentrations] + \caption[T Cells Grown at Varying IL2 Concentrations] {\glspl{dms} grow T cells effectively at lower IL2 concentrations. \subcap{fig:il2_mod_timecourse}{Longitudinal cell counts of T cells grown with either bead or \glspl{dms} using varying IL2 concentrations} @@ -3192,7 +3192,7 @@ at \SI{10}{\IU\per\ml} throughout the remainder of this aim. \phantomsubcaption\label{fig:doe_response_first_cd4} \endgroup - \caption[Response plots for first DOE] + \caption[Response Plots for First \acrshort{doe}] {Response plots from the first \gls{doe} experiment for \subcap{fig:doe_response_first_mem}{\ptmemp{}} and \subcap{fig:doe_response_first_cd4}{\pthp{}}. Each point is one run. @@ -3243,7 +3243,7 @@ this bias in our data, these runs were not used.}. \phantomsubcaption\label{fig:doe_responses_ratio} \endgroup - \caption[T cell optimization through Design of Experiments] + \caption[T Cell Optimization Through \acrshortpl{doe}] {\gls{doe} methodology reveals optimal conditions for expanding T cell subsets. Responses vs IL2 concentration, \gls{dms} concentration, and functional \gls{mab} percentage are shown for @@ -3257,31 +3257,31 @@ this bias in our data, these runs were not used.}. \end{figure*} \begin{table}[!h] \centering - \caption{Total CD62L+CCR7+ T cell response (first order regression)} + \caption{Regression for total \ptmem{} cells (first order)} \label{tab:doe_mem1.tex} \input{../tables/doe_mem1.tex} \end{table} \begin{table}[!h] \centering - \caption{Total CD62L+CCR7+ T cell response (third order regression)} + \caption{Regression for total \ptmem{} cells (third order)} \label{tab:doe_mem2.tex} \input{../tables/doe_mem2.tex} \end{table} \begin{table}[!h] \centering - \caption{Total CD4+ T cell response} + \caption{Regression for total \pth{} cells} \label{tab:doe_cd4.tex} \input{../tables/doe_cd4.tex} \end{table} \begin{table}[!h] \centering - \caption{Linear regression for total \ptmemh{} cells} + \caption{Regression for total \ptmemh{} cells} \label{tab:doe_mem4.tex} \input{../tables/doe_mem4.tex} \end{table} \begin{table}[!h] \centering - \caption{Linear regression for CD4:CD8 ratio in the \ptmem{} compartment} + \caption{Regression for \ptmem{} CD4:CD8 ratio} \label{tab:doe_ratio.tex} \input{../tables/doe_ratio.tex} \end{table} @@ -3345,7 +3345,7 @@ significant predictors. \phantomsubcaption\label{fig:doe_sr_contour_ratio} \endgroup - \caption[Contour plots for DOE responses] + \caption[Contour Plots for \acrshort{doe} Responses] {Symbolic regression and contour plots reveal optimal conditions for \subcap{fig:doe_sr_contour_mem4}{\ptmemh{} cells} and \subcap{fig:doe_sr_contour_ratio}{CD4:CD8 ratio in the \ptmem{} @@ -3378,7 +3378,7 @@ features of quality early in their expansion process. \includegraphics{../figures/doe_luminex.png} \endgroup - \caption[Cytokine release profile of T cells from DOE] + \caption[Cytokine Release Profile of T Cells from \acrshort{doe}] {T cells show robust and varying cytokine responses over time} \label{fig:doe_luminex} \end{figure*} @@ -3394,8 +3394,8 @@ data were collected in plates) (\cref{fig:grex_luminex}). % TABLE this table looks like crap, break it up into smaller tables \begin{table}[!h] \centering - \caption[Results for data-driven modeling] - {Results for data-driven modeling using process parameters (PP) with + \caption[Machine Learning Model Results] + {Results for \gls{ml} modeling using process parameters (PP) with only \gls{nmr} on day 4 (N4), only \gls{nmr} on day 6 (N6), only secretome on day 6 (S6), or various combindation of each for all seven \gls{ml} techniques} @@ -3444,7 +3444,7 @@ others showed maximum \rmemh{} predictions (\cref{fig:sr_omics}). \phantomsubcaption\label{fig:mod_flower_cd4} \endgroup - \caption[Data-Driven \gls{cqa} identification] + \caption[\acrshort{cqa} Consensus Plots] {Data-driven modeling using techniques with regularization reveals species predictive species which are candidates for \glspl{cqa}. Flower plots are shown for \subcap{fig:mod_flower_48r}{CD4:CD8 ratio} and @@ -3485,7 +3485,7 @@ lactate. \phantomsubcaption\label{fig:nmr_cors_matrix} \endgroup - \caption[NMR Day 4 correlations] + \caption[NMR Day 4 Correlations] {\gls{nmr} features at day 4 are strongly correlated with each other and the response variables. Highly correlated relationships are shown for \subcap{fig:nmr_cors_lactate}{lactate}, @@ -3750,7 +3750,7 @@ used \gls{cold} moving forward. \includegraphics{../figures/collagenase.png} \endgroup - \caption[Effects Collagenase Treatment on T cells] + \caption[Effects of Collagenase Treatment on T cells] {T cells treated with either \gls{colb}, \gls{cold}, or buffer and then stained for various surface markers and analyzing via flow cytometry.} \label{fig:collagenase_fx} @@ -3781,7 +3781,7 @@ are fundamentally altered by changing the number of \glspl{dms} temporally. \phantomsubcaption\label{fig:add_rem_cd4} \endgroup - \caption[Endpoint results from adding/removing \gls{dms} on day 4] + \caption[Results of Adding/Removing \acrshort{dms} on Day 4] {Changing \gls{dms} concentration on day 4 has profound effects on phenotype and growth. \subcap{fig:add_rem_growth}{Longitudinal fold change}, @@ -3798,7 +3798,7 @@ are fundamentally altered by changing the number of \glspl{dms} temporally. \includegraphics{../figures/spade_gates.png} \endgroup - \caption[SPADE Gating Strategy] + \caption[\acrshort{spade} Gating Strategy] {Gating strategy for quantifying early-differentiated T cells via \gls{spade}.} \label{fig:spade_gates} @@ -3814,7 +3814,8 @@ are fundamentally altered by changing the number of \glspl{dms} temporally. \phantomsubcaption\label{fig:spade_tsne_stem} \endgroup - \caption[SPADE and tSNE analysis temporally-modified DMS concentration] + \caption[\acrshort{spade} and \acrshort{tsne} Analysis of Temporally Modulated + \acrshort{dms} Cultures] {Removing \glspl{dms} leads to a higher fraction of potent stem-memory T cells compared to both adding and not changing the \gls{dms} concentration at day 4. @@ -3884,7 +3885,7 @@ T cells through \gls{a2b1} and \gls{a2b2}, causing them to grow better in the \phantomsubcaption\label{fig:inegrin_1_cd49} \endgroup - \caption[Integrin blocking I] + \caption[Integrin Blocking I] {Blocking with integrin does not lead to differences in memory or growth. \subcap{fig:inegrin_1_overview}{Experimental overview} \subcap{fig:inegrin_1_fc}{Fold change of \gls{dms}-activated T cell over @@ -3898,7 +3899,7 @@ T cells through \gls{a2b1} and \gls{a2b2}, causing them to grow better in the \end{figure*} \begin{table}[!h] \centering - \caption{Linear regression for day 14 phenotype shown in \cref{fig:integrin_1}} + \caption{Regression for day 14 phenotype shown in \cref{fig:integrin_1}} \label{tab:integrin_1_reg} \input{../tables/integrin_1_reg.tex} \end{table} @@ -3924,7 +3925,7 @@ T cells at day 6, showing that the target we wished to block was present \phantomsubcaption\label{fig:inegrin_2_mem} \endgroup - \caption[Integrin blocking II] + \caption[Integrin Blocking II] {Blocking with integrin does not lead to differences in memory or growth. \subcap{fig:inegrin_1_fc}{Fold change of \gls{dms}-activated T cell over time with each blocking condition.} @@ -3936,7 +3937,7 @@ T cells at day 6, showing that the target we wished to block was present \end{figure*} \begin{table}[!h] \centering - \caption{Linear regression for day 14 phenotype shown in \cref{fig:integrin_2}} + \caption{Regression for day 14 phenotype shown in \cref{fig:integrin_2}} \label{tab:integrin_2_reg} \input{../tables/integrin_2_reg.tex} \end{table} @@ -3976,7 +3977,7 @@ density. \phantomsubcaption\label{fig:il15_1_mem} \endgroup - \caption[IL15 blocking I] + \caption[IL15 Blocking I] {Blocking IL15Ra does not lead to differences in memory or growth. \subcap{fig:il15_1_overview}{Experimental overview} Longitudinal measurements of @@ -4011,7 +4012,7 @@ the markers, and by extension showing no difference in phenotype \phantomsubcaption\label{fig:il15_2_mem} \endgroup - \caption[IL15 blocking II] + \caption[IL15 Blocking II] {Blocking soluble IL15 does not lead to differences in memory or growth. \subcap{fig:il15_2_overview}{Experimental overview} Longitudinal measurements of @@ -4217,7 +4218,7 @@ between survival groups. \end{figure*} \begin{table}[!h] \centering - \caption{Results for \gls{car} T cell \invivo{} dose study} + \caption{Cells injected for \acrshort{car} T cell \invivo{} dose study} \label{tab:mouse_dosing_results} \input{../tables/mouse_dose_car.tex} \end{table} @@ -4233,7 +4234,7 @@ between survival groups. \phantomsubcaption\label{fig:mouse_dosing_qc_growth} \endgroup - \caption[Mouse Dosing T cell Characteristics] + \caption[Mouse Dosing T Cell Characteristics] {Characteristics of T cells harvested at day 14 injected into NSG mice at varying doses. Fractions of T cell subtypes in the day 14 product including @@ -4383,7 +4384,7 @@ at day 14 despite the overall \ptmemp{} decreasing with time as shown elsewhere \phantomsubcaption\label{fig:mouse_timecourse_qc_mem} \endgroup - \caption[Mouse Timecourse T cell Characteristics] + \caption[Mouse Timecourse T Cell Characteristics] {Characteristics of T cells harvested at varying timepoints injected into NSG mice. \subcap{fig:mouse_timecourse_qc_growth}{Fold change of T cells (each @@ -4896,7 +4897,7 @@ hosted using \gls{aws} using their proprietary Aurora implementation. \includegraphics{../figures/metaanalysis.png} \endgroup - \caption[Meta-analysis overview] + \caption[Meta-analysis Overview] {Overview of strategy used for meta-analysis. Colors: notebook (pink), input files (green), analysis framework (blue), data store (cyan), analysis pipeline (orange).}