From a3f37bece8e4c79ca4bc9afdfc7467a7ef12afd1 Mon Sep 17 00:00:00 2001
From: Blaise Thompson <blaise@untzag.com>
Date: Fri, 20 Apr 2018 13:01:25 -0500
Subject: 2018-04-20 13:01

---
 presentation.tex | 106 ++++++++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 94 insertions(+), 12 deletions(-)

(limited to 'presentation.tex')

diff --git a/presentation.tex b/presentation.tex
index 97bd9de..9f4a3f1 100644
--- a/presentation.tex
+++ b/presentation.tex
@@ -5,7 +5,6 @@
 
 \institute{University of Wisconsin--Madison}
 \date{2018-04-23}
-%\subject{}
 
 \begin{document}
 \maketitle
@@ -34,28 +33,62 @@
   What am I doing in a field so rich with fundamental studies?
   \vspace{\baselineskip} \\
   I hope to convince you that CMDS can be used for analytical work.  % TODO: better
+  \begin{itemize}
+    \item detection (selectivity)
+    \item unknown identification
+    \item quantification
+  \end{itemize}
 \end{frame}
 
 % TODO: in fact, 2DIR is already used regularly...
 
-\begin{frame}{Analytical}  
+\begin{frame}{Pakoulev et al. (2009)}  
   \fbox{\adjincludegraphics[width=\textwidth]{literature/PakoulevAndreiV2009a}}
 \end{frame}
 
-% TODO: pakoulev quotes
+\begin{frame}{Pakoulev et al. (2009)}
+  \begin{shadequote}
+    Spectroscopy forms the heart of the analytical methodology used for routine chemical
+    measurement.  %
+    Of all the analytical spectroscopic methods, NMR spectroscopy is unique in its ability to
+    \hl{correlate} spin resonances and \hl{resolve} spectral features from spectra containing
+    \hl{thousands of peaks}.  %
+    For example, heteronuclear multiple quantum coherence (HMQC) spectroscopy achieves this
+    capability by exciting $^1$H, $^{15}$N, $^{13}$ C=O, and $^{13}$C$\alpha$ spins to form a
+    multiple quantum coherence \hl{characteristic of a specific position} in a protein’s backbone.
+    Three excitations define a specific residue, and a fourth defines the coupling to an adjacent
+    residue.
+    Not only does it decongest the spectra, it defines the couplings and connectivity between the
+    different nuclear spin states.
+    Coherent multidimensional spectroscopy (CMDS) has emerged as the \hl{optical analogue} of
+    nuclear magnetic resonance (NMR), and there is great interest in using it as a \hl{general
+      analytical methodology}.
+  \end{shadequote}
+\end{frame}
 
-\begin{frame}{Proteomics}
-  \fbox{\adjincludegraphics[width=\textwidth]{literature/FournierFrederic2009a}}
+\begin{frame}{Donaldson et al. (2010)}
+  \fbox{\adjincludegraphics[width=\textwidth]{literature/DonaldsonPaulMurray2010a}}
 \end{frame}
 
-% TODO: fournier quotes
+\begin{frame}{Fournier et al. (2009)}
+  \fbox{\adjincludegraphics[width=\textwidth]{literature/FournierFrederic2009a}}
+\end{frame}
 
-\begin{frame}{Proteomics}
-  \fbox{\adjincludegraphics[width=\textwidth]{literature/DonaldsonPaulMurray2010a}}
+\begin{frame}{Fournier et al. (2009)}
+  \begin{shadequote}
+    Our protein identification strategy is based on using EVV 2DIR to quantify the amino acid
+    content of a protein.  %
+    EVV 2DIR is shown to be able to perform \hl{absolute quantification}, something of major
+    importance in the field of proteomics but rather difficult and time-consuming to achieve with
+    mass spectrometry.  %
+    Our technique can be qualified as a top-down \hl{label-free} method; it does not require
+    intensive sample preparation, the proteins are intact when analyzed, and it does not have any
+    mass restriction on the proteins to be analyzed.  %
+    Moreover, EVV 2DIR is a \hl{nondestructive} technique; the samples can be kept for reanalysis
+    in the light of further information.  %
+  \end{shadequote}
 \end{frame}
 
-% TODO: donaldson quotes
-  
 \section{Frequency domain}  % =====================================================================
 
 \begin{frame}{Domains of CMDS}
@@ -67,7 +100,8 @@
 \end{frame}
 
 \begin{frame}{Time domain}
-  Multiple broadband pulses are scanned in \emph{time} to collect a multidimensional interferogram.
+  Multiple broadband pulses are scanned in \emph{time} to collect a multidimensional interferogram
+  (analogous to FTIR, NMR).
   \vspace{\baselineskip} \\
   A local oscillator must be used to measure the \emph{phase} of the output.
   \vspace{\baselineskip} \\
@@ -139,21 +173,64 @@
 \end{frame}
 
 \begin{frame}{Universal format}
+  WrightTools defines a \emph{universal file format} for CMDS.
+  \begin{itemize}
+    \item store multiple multidimensional arrays
+    \item metadata
+  \end{itemize}
+  Import data from a variety of sources.
+  \begin{itemize}
+    \item previous Wright Group acquisition software
+    \item commercial instruments (JASCO, Shimadzu, Ocean Optics)
+  \end{itemize}
 \end{frame}
 
 \begin{frame}{Flexible data model}
+  Flexibility to transform into any desired ``projection'' on component variables.
+  \adjincludegraphics[width=\textwidth]{processing/fringes_transform}
+  % mention: including expressions
 \end{frame}
 
 \section{Acquisition}  % ==========================================================================
 
 \begin{frame}{Acquisition}
-  PyCMDS.
+  PyCMDS---unified software for controlling hardware and collecting data.
+  \adjincludegraphics[width=\textwidth]{acquisition/screenshots/000}
 \end{frame}
 
+\begin{frame}{Abstraction}
+  Hardware---something that has a \hl{position} that can be \hl{set}.
+  \vspace{\baselineskip} \\
+  Sensor---something that has a \hl{signal} that can be \hl{read}.
+\end{frame}
+  
 \begin{frame}{Modular hardware model}
+  \adjincludegraphics[scale=0.25]{acquisition/hardware_inheritance}
+\end{frame}
+
+\begin{frame}{Modular sensor model}
+  Can have as many sensors as needed.
+  \vspace{\baselineskip} \\
+  Each sensor contributes one or more channels.
+  \vspace{\baselineskip} \\
+  Sensors with size contribute new variables (dimensions).
 \end{frame}
 
+\begin{frame}{Central loop}
+  Set, wait, read, wait, repeat.
+  \vspace{\baselineskip} \\
+  Everything is multi-threaded (simultaneous motion, simultaneous read).
+\end{frame}
+  
 \begin{frame}{Acquisitions}
+  Acquisition---a particular set of actions.
+  \vspace{\baselineskip} \\
+  Acquisition modules---a GUI that accepts a user instruction.
+\end{frame}
+
+\begin{frame}{Queue}
+  Queue.
+  \adjincludegraphics[width=\textwidth]{acquisition/screenshots/004}
 \end{frame}
 
 \begin{frame}{Queue}
@@ -169,6 +246,11 @@
 \begin{frame}{Tuning}
 \end{frame}
 
+\section{Conclusion}  % ===========================================================================
+
+\begin{frame}{Conclusion}
+\end{frame}
+
 \section{Supplement}  % ===========================================================================
 
 \begin{frame}{MR-CMDS theory}
-- 
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