ENH add citations where needed

tex/references.bib

@@ -2475,6 +2475,75 @@ CONCLUSIONS: We developed a simplified, semi-closed system for the initial selec
   publisher = {Springer Science and Business Media {LLC}},
 }
 
+@Article{Kamholz2001,
+  author          = {Kamholz, A. E. and Schilling, E. A. and Yager, P.},
+  journal         = {Biophysical journal},
+  title           = {Optical measurement of transverse molecular diffusion in a microchannel.},
+  year            = {2001},
+  issn            = {0006-3495},
+  month           = apr,
+  pages           = {1967--1972},
+  volume          = {80},
+  abstract        = {Quantitative analysis of molecular diffusion is a necessity for the efficient design of most microfluidic devices as well as an important biophysical method in its own right. This study demonstrates the rapid measurement of diffusion coefficients of large and small molecules in a microfluidic device, the T-sensor, by means of conventional epifluorescence microscopy. Data were collected by monitoring the transverse flux of analyte from a sample stream into a second stream flowing alongside it. As indicated by the low Reynolds numbers of the system (< 1), flow is laminar, and molecular transport between streams occurs only by diffusion. Quantitative determinations were made by fitting data with predictions of a one-dimensional model. Analysis was made of the flow development and its effect on the distribution of diffusing analyte using a three-dimensional modeling software package. Diffusion coefficients were measured for four fluorescently labeled molecules: fluorescein-biotin, insulin, ovalbumin, and streptavidin. The resulting values differed from accepted results by an average of 2.4%. Microfluidic system parameters can be selected to achieve accurate diffusion coefficient measurements and to optimize other microfluidic devices that rely on precise transverse transport of molecules.},
+  chemicals       = {Biotin},
+  citation-subset = {IM},
+  completed       = {2001-06-21},
+  country         = {United States},
+  doi             = {10.1016/S0006-3495(01)76166-8},
+  issn-linking    = {0006-3495},
+  issue           = {4},
+  keywords        = {Biochemistry, instrumentation; Biotin, pharmacology; Computer Simulation; Diffusion; Microscopy, Fluorescence, instrumentation, methods; Models, Theoretical},
+  nlm-id          = {0370626},
+  owner           = {NLM},
+  pii             = {S0006-3495(01)76166-8},
+  pmc             = {PMC1301385},
+  pmid            = {11259309},
+  pubmodel        = {Print},
+  pubstate        = {ppublish},
+  revised         = {2018-11-13},
+}
+
+@Article{Niether2020,
+  author    = {Doreen Niether and Mona Sarter and Bernd W. Koenig and Jörg Fitter and Andreas M. Stadler and Simone Wiegand},
+  journal   = {Polymers},
+  title     = {Thermophoresis: The Case of Streptavidin and Biotin},
+  year      = {2020},
+  month     = {feb},
+  number    = {2},
+  pages     = {376},
+  volume    = {12},
+  doi       = {10.3390/polym12020376},
+  publisher = {{MDPI} {AG}},
+}
+
+@Article{Kerwin2008,
+  author          = {Kerwin, Bruce A.},
+  journal         = {Journal of pharmaceutical sciences},
+  title           = {Polysorbates 20 and 80 used in the formulation of protein biotherapeutics: structure and degradation pathways.},
+  year            = {2008},
+  issn            = {1520-6017},
+  month           = aug,
+  pages           = {2924--2935},
+  volume          = {97},
+  abstract        = {Polysorbates 20 and 80 (Tween 20 and Tween 80) are used in the formulation of biotherapeutic products for both preventing surface adsorption and as stabilizers against protein aggregation. The polysorbates are amphipathic, nonionic surfactants composed of fatty acid esters of polyoxyethylene sorbitan being polyoxyethylene sorbitan monolaurate for polysorbate 20 and polyoxyethylene sorbitan monooleate for polysorbate 80. The polysorbates used in the formulation of biopharmaceuticals are mixtures of different fatty acid esters with the monolaurate fraction of polysorbate 20 making up only 40-60% of the mixture and the monooleate fraction of polysorbate 80 making up >58% of the mixture. The polysorbates undergo autooxidation, cleavage at the ethylene oxide subunits and hydrolysis of the fatty acid ester bond. Autooxidation results in hydroperoxide formation, side-chain cleavage and eventually formation of short chain acids such as formic acid all of which could influence the stability of a biopharmaceutical product. Oxidation of the fatty acid moiety while well described in the literature has not been specifically investigated for polysorbate. This review focuses on the chemical structure of the polysorbates, factors influencing micelle formation and factors and excipients influencing stability and degradation of the polyoxyethylene and fatty acid ester linkages.},
+  chemicals       = {Polysorbates, Proteins, Surface-Active Agents},
+  citation-subset = {IM},
+  completed       = {2008-11-04},
+  country         = {United States},
+  doi             = {10.1002/jps.21190},
+  issn-linking    = {0022-3549},
+  issue           = {8},
+  keywords        = {Chemistry, Pharmaceutical; Molecular Structure; Oxidation-Reduction; Polysorbates, chemistry; Proteins, administration & dosage, chemical synthesis, therapeutic use; Surface Tension; Surface-Active Agents, chemistry},
+  nlm-id          = {2985195R},
+  owner           = {NLM},
+  pii             = {S0022-3549(16)32657-0},
+  pmid            = {17973307},
+  pubmodel        = {Print},
+  pubstate        = {ppublish},
+  references      = {91},
+  revised         = {2008-07-28},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping:

tex/thesis.tex

@@ -485,8 +485,8 @@ such as bioreactors.
 % TODO probably need to address some of the modeling stuff here as well
 
 This thesis describes a novel degradable microscaffold-based method derived from
-porous microcarriers functionalized with \acd{3} and \acd{28} \glspl{mab}
+porous microcarriers functionalized with \acd{3} and \acd{28} \glspl{mab} for
-for use in T cell expansion cultures. Microcarriers have historically been used
+use in T cell expansion cultures. Microcarriers have historically been used
 throughout the bioprocess industry for adherent cultures such as stem cells and
 \gls{cho} cells, but not with suspension cells such as T
 cells\cite{Heathman2015, Sart2011}. The microcarriers chosen to make the DMSs in
@@ -499,17 +499,17 @@ larger contact area for T cells to interact with the \glspl{mab} relative to
 beads; this may better emulate the large contact surface area that occurs
 between T cells and \glspl{dc}. These microcarriers are readily available in
 over 30 countries and are used in an FDA fast-track-approved combination retinal
-pigment epithelial cell product (Spheramine, Titan Pharmaceuticals) {\#}[Purcell
+pigment epithelial cell product (Spheramine, Titan
-documentation]. This regulatory history will aid in clinical translation. We
+Pharmaceuticals)\cite{purcellmain}. This regulatory history will aid in clinical
-show that compared to traditional microbeads, \gls{dms}-expanded T cells not
+translation. We show that compared to traditional microbeads, \gls{dms}-expanded
-only provide superior expansion, but consistently provide a higher frequency of
+T cells not only provide superior expansion, but consistently provide a higher
-naïve/memory and CD4 T cells (CCR7+CD62L+) across multiple donors. We also
+frequency of naïve/memory and CD4 T cells (CCR7+CD62L+) across multiple donors.
-demonstrate functional cytotoxicity using a CD19 \gls{car} and a superior
+We also demonstrate functional cytotoxicity using a CD19 \gls{car} and a
-performance, even at a lower \gls{car} T cell dose, of \gls{dms}-expanded
+superior performance, even at a lower \gls{car} T cell dose, of
-\gls{car}-T cells \invivo{} in a mouse xenograft model of human B cell
+\gls{dms}-expanded \gls{car}-T cells \invivo{} in a mouse xenograft model of
-\gls{all}. Our results indicate that \glspl{dms} provide a robust and scalable
+human B cell \gls{all}. Our results indicate that \glspl{dms} provide a robust
-platform for manufacturing therapeutic T cells with higher naïve/memory
+and scalable platform for manufacturing therapeutic T cells with higher
-phenotype and more balanced CD4+ T cell content.
+naïve/memory phenotype and more balanced CD4+ T cell content.
 
 \section*{hypothesis}
 
@@ -1569,10 +1569,9 @@ diffusion coefficient of \gls{stp} in water. This model was given by
 \item $n$ is the number of microcarriers in the reaction volume
 \end{itemize}
 
-% TODO cite the diffusion rate of stp
 The diffusion rate of \gls{stp} was assumed to be
-\SI{3.89e-7}{\cm\squared\per\second} {\#}{diffusion rate citation}. Since all
+\SI{6.2e-7}{\cm\squared\per\second}\cite{Kamholz2001}. Since all but $\beta$ was
-but $\beta$ was known, the experimental data was fit using these equations using
+known, the experimental data was fit using these equations using
 \inlinecode{ode45} in MATLAB and least squares as the fitting error.
 
 % TODO this diffusion rate isn't actually reflected in the code
@@ -1582,6 +1581,9 @@ These equations were then used analogously to describe the reaction profile of
 
 % METHOD add the equation governing the washing steps
 
+The diffusion coefficient used for biotin was
+\SI{5e-6}{\cm\squared\per\second}\cite{Niether2020}
+
 \subsection{Luminex Analysis}\label{sec:luminex_analysis}
 
 Luminex was performed using a \product{ProcartaPlex kit}{\thermo}{custom} for
@@ -1685,25 +1687,25 @@ context of pure error). Statistical significance was evaluated at $\upalpha$ =
 Two types of gelatin-based microcariers, \gls{cus} and \gls{cug}, were
 covalently conjugated with varying concentration of \gls{snb} and then coated
 with \gls{stp} and \glspl{mab} to make \glspl{dms}. Aside from slight
-differences in swelling ratio and crosslinking chemistry {\#}[Purcell
+differences in swelling ratio and crosslinking chemistry\cite{purcellmain} the
-documentation], the properties of \gls{cus} and \gls{cug} were the same
+properties of \gls{cus} and \gls{cug} were the same (\cref{tab:carrier_props}).
-(\cref{tab:carrier_props}). We chose to continue with the \gls{cus}-based
+We chose to continue with the \gls{cus}-based \glspl{dms}, which showed higher
-\glspl{dms}, which showed higher overall \gls{stp} binding compared to
+overall \gls{stp} binding compared to \gls{cug}-based \glspl{dms}
-\gls{cug}-based \glspl{dms} (\cref{fig:cug_vs_cus}). We showed that by varying
+(\cref{fig:cug_vs_cus}). We showed that by varying the concentration of
-the concentration of \gls{snb}, we were able to precisely control the amount of
+\gls{snb}, we were able to precisely control the amount of attached biotin
-attached biotin (\cref{fig:biotin_coating}), mass of attached \gls{stp}
+(\cref{fig:biotin_coating}), mass of attached \gls{stp}
 (\cref{fig:stp_coating}), and mass of attached \glspl{mab}
 (\cref{fig:mab_coating}). Furthermore, we showed that the microcarriers were
 evenly coated with \gls{stp} on the surface and throughout the interior as
-evidenced by the presence of biotin-binding sites occupied with \gls{stp}-\gls{fitc}
+evidenced by the presence of biotin-binding sites occupied with
-on the microcarrier surfaces after the \gls{stp}-coating step
+\gls{stp}-\gls{fitc} on the microcarrier surfaces after the \gls{stp}-coating
-(\cref{fig:stp_carrier_fitc}). Finally, we confirmed that biotinylated
+step (\cref{fig:stp_carrier_fitc}). Finally, we confirmed that biotinylated
 \glspl{mab} were bound to the \glspl{dms} by staining either \gls{stp} or
-\gls{stp} and \gls{mab}-coated carriers with \antim{\gls{igg}-\gls{fitc}} and imaging
+\gls{stp} and \gls{mab}-coated carriers with \antim{\gls{igg}-\gls{fitc}} and
-on a confocal microscope (\cref{fig:mab_carrier_fitc}). Taking this together, we
+imaging on a confocal microscope (\cref{fig:mab_carrier_fitc}). Taking this
-noted that the maximal \gls{mab} binding capacity occurred near \SI{50}{\nmol}
+together, we noted that the maximal \gls{mab} binding capacity occurred near
-biotin input (which corresponded to \SI{2.5}{\nmol\per\mg\of{\dms}}) thus we
+\SI{50}{\nmol} biotin input (which corresponded to
-used this in subsequent processes.
+\SI{2.5}{\nmol\per\mg\of{\dms}}) thus we used this in subsequent processes.
 
 % TODO flip the rows of this figure (right now the text is backward)
 \begin{figure*}[ht!]
@@ -1872,7 +1874,7 @@ using the \gls{bca} assay to indirectly quantify the amount of attached
 (\cref{fig:dms_stp_per_time}). Assuming a quasi-steady-state paradigm, we used
 this experimental binding data to fit a continuous model for the \gls{stp}
 binding reaction. Using the diffusion rate of the \gls{stp}, we then calculated
-the effective diffusivity of the microcarriers to be {\#}.
+the effective diffusivity of the microcarriers to be 0.2.
 
 Using this effective diffusivity and the known diffusion coefficient of a
 \gls{mab} protein in water, we calculated predict the binding of \glspl{mab} per
@@ -2002,9 +2004,9 @@ membrane. When staining for these two markers and assessing via flow cytometry,
 we observe that the \gls{dms}-expanded T cells have lower frequencies of
 apoptotic and necrotic cells (\cref{fig:apoptosis_annV}). Furthermore, we
 stained our cultures with CellEvent dye, which is an indicator of \gls{cas37},
-which is activated in apoptotic cells {\#}{cas37 activation}. In line with the
+which is activated in apoptotic cells. In line with the \gls{pi}/\gls{anv}
-\gls{pi}/\gls{anv} results, we observed that the \gls{dms} T cells had lower
+results, we observed that the \gls{dms} T cells had lower frequency of
-frequency of \gls{cas37} expression, indicating less apoptosis for our method
+\gls{cas37} expression, indicating less apoptosis for our method
 (\cref{fig:apoptosis_cas}). Finally, we lysed our cells and stained for
 \gls{bcl2}, which is also upregulated in apoptosis. In this case, some (but not
 all) of the bead-expanded cultures showed higher \gls{bcl2} expression, which
@@ -3642,8 +3644,8 @@ them to grow better in the \gls{dms} system.
 We tested this hypothesis by adding blocking \glspl{mab} against \gls{a2b1}
 and/or \gls{a2b2} to running T cell cultures activated using the \glspl{dms}.
 These block \glspl{mab} were added at day 6 of culture when \gls{a2b1} and
-\gls{a2b2} were known to be expressed {\#}. We found that the fold expansion was
+\gls{a2b2} were known to be expressed\cite{Hemler1990}. We found that the fold
-identical in all the blocked groups vs the unblocked control group
+expansion was identical in all the blocked groups vs the unblocked control group
 (\cref{fig:inegrin_1_fc}). Furthermore, we observed that the \ptmemp{} (total
 and across the CD4/CD8 compartments) was not significantly different between any
 of the groups (\cref{fig:inegrin_1_mem,tab:integrin_1_reg}). We also noted that
@@ -3808,13 +3810,13 @@ receptors may simply be irrelevant for our system.
 
 On the first point, we did not verify that these \glspl{mab} indeed blocked the
 receptor we were targeting. There has been evidence from other groups that these
-particular clones work at the concentrations we used {\#}. This does not
+particular clones work at the concentrations we used\cite{MirandaCarus2005}.
-necessarily mean that the \glspl{mab} we obtained were functional in blocking
+This does not necessarily mean that the \glspl{mab} we obtained were functional
-their intended targets (although they were from a reputable manufacturer, \bl).
+in blocking their intended targets (although they were from a reputable
-Furthermore, we can safely rule out the possibility that the \glspl{mab} never
+manufacturer, \bl). Furthermore, we can safely rule out the possibility that the
-reached their targets, as they were added immediately after the T cells were
+\glspl{mab} never reached their targets, as they were added immediately after
-resuspended as required for cell counting, hence their resting clustered state
+the T cells were resuspended as required for cell counting, hence their resting
-was disrupted.
+clustered state was disrupted.
 
 % TODO define Bite
 On the second point, the collagen domains may not even be relevant to our system
@@ -4046,15 +4048,15 @@ case of beads (\cref{fig:mouse_dosing_qc_mem}).
 \subsection{Beads and DMSs perform similarly at earlier timepoints}
 
 We then asked how T cells harvested using either beads or \gls{dms} performed
-when harvested at earlier timepoints {\#}{levine paper with early timepoints}.
+when harvested at earlier timepoints\cite{Ghassemi2018}. We performed the same
-We performed the same experiments as described in
+experiments as described in \cref{fig:mouse_dosing_overview} with the
-\cref{fig:mouse_dosing_overview} with the modification that T cells were only
+modification that T cells were only grown and harvested after \SI{6}{\day},
-grown and harvested after \SI{6}{\day}, \SI{10}{\day}, or \SI{14}{\day} of
+\SI{10}{\day}, or \SI{14}{\day} of expansion
-expansion (\cref{fig:mouse_timecourse_overview}). T cells were frozen after
+(\cref{fig:mouse_timecourse_overview}). T cells were frozen after harvest, and
-harvest, and all timepoints were thawed at the same time prior to injection. The
+all timepoints were thawed at the same time prior to injection. The dose of T
-dose of T cells injected was \num{1.25e6} cells per mouse (the same as the high
+cells injected was \num{1.25e6} cells per mouse (the same as the high dose in
-dose in the first experiment). All other characteristics of the experiment were
+the first experiment). All other characteristics of the experiment were the
-the same.
+same.
 
 \begin{figure*}[ht!]
   \begingroup
@@ -4083,7 +4085,7 @@ untransduced cells. The \pthp{} of the harvested T cells was higher overall in
 (\cref{fig:mouse_timecourse_qc_cd4}). The \ptmemp{} was similar at day 6
 between bead and \gls{dms} groups but the \gls{dms} group had higher \ptmemp{}
 at day 14 despite the overall \ptmemp{} decreasing with time as shown elsewhere
-(\cref{fig:mouse_timecourse_qc_mem}) {\#}{levine paper mem over time}.
+(\cref{fig:mouse_timecourse_qc_mem})\cite{Ghassemi2018}.
 
 \begin{figure*}[ht!]
   \begingroup
@@ -4265,17 +4267,17 @@ for the patient, while also minimizing cost for the manufacturer. Second,
 \glspl{cqa} can be used to define process control schemes as well as release
 criteria. Process control, and with it the ability to predict future outcomes
 based on data obtained at the present, is highly important for cell therapies
-given that batch failures are extremely expensive {\#}, and predicting a batch
+given that batch failures are extremely expensive\cite{Harrison2019}, and
-failure would allow manufacturers to restart the batch in a timely manner
+predicting a batch failure would allow manufacturers to restart the batch in a
-without wasting resources. Furthermore, \glspl{cqa} can be used to define what a
+timely manner without wasting resources. Furthermore, \glspl{cqa} can be used to
-`good' vs `bad' product is, which will important help anticipate dosing and
+define what a `good' vs `bad' product is, which will important help anticipate
-followup procedures in the clinic if the T cells are administered. In the aim,
+dosing and followup procedures in the clinic if the T cells are administered. In
-we cannot claim to have found the ultimate set of \glspl{cqa} and \glspl{cpp},
+the aim, we cannot claim to have found the ultimate set of \glspl{cqa} and
-as we used tissue culture plates instead of a bioreactor and we only used one
+\glspl{cpp}, as we used tissue culture plates instead of a bioreactor and we
-donor. However, we have indeed outlined a process that others may use to find
+only used one donor. However, we have indeed outlined a process that others may
-these for their process. In particular, the 2-phase modeling process we used
+use to find these for their process. In particular, the 2-phase modeling process
-(starting with a \gls{doe} and collecting data longitudinally) is a strategy
+we used (starting with a \gls{doe} and collecting data longitudinally) is a
-that manufacturers can easily implement. Also, collecting secretome and
+strategy that manufacturers can easily implement. Also, collecting secretome and
 metabolome is easily generalized to any setting and to most bioreactors and
 expansion systems, as they can be obtained with relatively inexpensive equipment
 (Luminex assay, benchtop \gls{nmr}, etc) without disturbing the cell culture.
@@ -4285,12 +4287,13 @@ to control and optimize the \gls{dms} system. We determined that altering the
 \gls{dms} concentration temporally has profound effects on the phenotype and
 expansion rate. This agrees with other data we obtained in \cref{aim2a} and with
 what others have generally reported about signal strength and T cell
-differentiation {\#}. We did not find any mechanistic relationship between
+differentiation\cite{Gattinoni2012}. We did not find any mechanistic
-either integrin signaling or \gls{il15} signaling. In the case of the former, it
+relationship between either integrin signaling or \gls{il15} signaling. In the
-may be more likely that the \glspl{dms} surfaces are saturated to the point of
+case of the former, it may be more likely that the \glspl{dms} surfaces are
-sterically hindering any integrin interactions with the collagen surface. In the
+saturated to the point of sterically hindering any integrin interactions with
-case of \gls{il15} more experiments likely need to be done in order to plausibly
+the collagen surface. In the case of \gls{il15} more experiments likely need to
-rule out this mechanism and/or determine if it is involved at all.
+be done in order to plausibly rule out this mechanism and/or determine if it is
+involved at all.
 
 % TODO make this tighter and cite paper showing that this makes at least some
 % sense
@@ -4327,11 +4330,11 @@ tubes. A human carrier protein such as \gls{hsa} could be used in its place to
 eliminate the non-human animal origin material, but this could be much more
 expensive. Alternatively, the use of protein could be replaced altogether by a
 non-ionic detergent such as Tween-20 or Tween-80, which are already used for
-commercial \gls{mab} formulations for precisely this purpose {\#}. Validating
+commercial \gls{mab} formulations for precisely this purpose\cite{Kerwin2008}.
-the process with Tween would be the best next step to eliminate \gls{bsa} from
+Validating the process with Tween would be the best next step to eliminate
-the process. The \gls{stp} and \glspl{mab} in this process were not
+\gls{bsa} from the process. The \gls{stp} and \glspl{mab} in this process were
-\gls{gmp}-grade; however, they are commonly used in clinical technology such as
+not \gls{gmp}-grade; however, they are commonly used in clinical technology such
-dynabeads and thus the research-grade proteins used here could be easily
+as dynabeads and thus the research-grade proteins used here could be easily
 replaced. The \gls{snb} is a synthetic small molecule and thus does not have any
 animal-origin concerns.