final final

8 files changed, 31 insertions, 27 deletions

diff --git a/deliverable/main.acn b/deliverable/main.acn
index 494713e..a604578 100644
--- a/deliverable/main.acn
+++ b/deliverable/main.acn
@@ -20,5 +20,5 @@
 \glossaryentry{GMT?\glossentry{gmt}|setentrycounter[]{page}\glsnumberformat}{17}
 \glossaryentry{GMT?\glossentry{gmt}|setentrycounter[]{page}\glsnumberformat}{17}
 \glossaryentry{GMT?\glossentry{gmt}|setentrycounter[]{page}\glsnumberformat}{18}
-\glossaryentry{GMT?\glossentry{gmt}|setentrycounter[]{page}\glsnumberformat}{18}
+\glossaryentry{GMT?\glossentry{gmt}|setentrycounter[]{page}\glsnumberformat}{19}
 \glossaryentry{GMT?\glossentry{gmt}|setentrycounter[]{page}\glsnumberformat}{25}
diff --git a/deliverable/main.acr b/deliverable/main.acr
index 44f807a..14d7cde 100644
--- a/deliverable/main.acr
+++ b/deliverable/main.acr
@@ -5,7 +5,7 @@
 		\setentrycounter[]{page}\glsnumberformat{4}\delimN 
 		\setentrycounter[]{page}\glsnumberformat{7}\delimN 
 		\setentrycounter[]{page}\glsnumberformat{17\delimR 19}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{23}}}\glsgroupskip
+		\setentrycounter[]{page}\glsnumberformat{25}}}\glsgroupskip
 \glsgroupheading{H}\relax \glsresetentrylist %
 \glossentry{ha}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{3}\delimN 
diff --git a/deliverable/main.bsd b/deliverable/main.bsd
index fa1b082..a164daf 100644
--- a/deliverable/main.bsd
+++ b/deliverable/main.bsd
@@ -11,14 +11,14 @@
 \glossentry{bu:bcell}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{4}\delimN 
 		\setentrycounter[]{page}\glsnumberformat{8}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{29\delimN 30}}}\glsgroupskip
+		\setentrycounter[]{page}\glsnumberformat{29}}}\glsgroupskip
 \glsgroupheading{C}\relax \glsresetentrylist %
 \glossentry{bu:cd4pos}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{8}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{29\delimN 30}}}%
+		\setentrycounter[]{page}\glsnumberformat{29}}}%
 \glossentry{bu:cd8pos}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{8}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{30}}}%
+		\setentrycounter[]{page}\glsnumberformat{29}}}%
 \glossentry{bu:cmv}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{13}\delimN 
 		\setentrycounter[]{page}\glsnumberformat{17}\delimN 
@@ -39,19 +39,22 @@
 		\setentrycounter[]{page}\glsnumberformat{7\delimR 9}\delimN 
 		\setentrycounter[]{page}\glsnumberformat{17\delimN 18}\delimN 
 		\setentrycounter[]{page}\glsnumberformat{21}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{23}}}\glsgroupskip
+		\setentrycounter[]{page}\glsnumberformat{24}}}\glsgroupskip
 \glsgroupheading{L}\relax \glsresetentrylist %
 \glossentry{bu:lymphocyte}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{4}}}\glsgroupskip
 \glsgroupheading{M}\relax \glsresetentrylist %
 \glossentry{bu:monocyte}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{4}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{30}}}%
+		\setentrycounter[]{page}\glsnumberformat{29}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{33}}}%
 \glossentry{bu:mutation}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{7}}}\glsgroupskip
 \glsgroupheading{P}\relax \glsresetentrylist %
 \glossentry{bu:pbmc}{\glossaryentrynumbers{\relax 
-		\setentrycounter[]{page}\glsnumberformat{8}}}\glsgroupskip
+		\setentrycounter[]{page}\glsnumberformat{8}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{33}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{45}}}\glsgroupskip
 \glsgroupheading{R}\relax \glsresetentrylist %
 \glossentry{bu:rnaVirus}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{7}}}\glsgroupskip
@@ -59,11 +62,11 @@
 \glossentry{bu:seropc}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{7}\delimN 
 		\setentrycounter[]{page}\glsnumberformat{17\delimR 19}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{23}}}%
+		\setentrycounter[]{page}\glsnumberformat{25}}}%
 \glossentry{bu:stat}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{8}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{29\delimN 30}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{32\delimN 33}}}\glsgroupskip
+		\setentrycounter[]{page}\glsnumberformat{29}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{33\delimR 35}}}\glsgroupskip
 \glsgroupheading{T}\relax \glsresetentrylist %
 \glossentry{bu:tcell}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{3\delimN 4}\delimN 
diff --git a/deliverable/main.bsg b/deliverable/main.bsg
index f1adc43..a2fab3d 100644
--- a/deliverable/main.bsg
+++ b/deliverable/main.bsg
@@ -1,7 +1,7 @@
 This is makeindex, version 2.15 [TeX Live 2020] (kpathsea + Thai support).
 Scanning style file ./main.ist.............................done (29 attributes redefined, 0 ignored).
-Scanning input file main.bsn....done (103 entries accepted, 0 rejected).
-Sorting entries....done (763 comparisons).
-Generating output file main.bsd....done (79 lines written, 0 warnings).
+Scanning input file main.bsn....done (128 entries accepted, 0 rejected).
+Sorting entries....done (1006 comparisons).
+Generating output file main.bsd....done (82 lines written, 0 warnings).
 Output written in main.bsd.
 Transcript written in main.bsg.
diff --git a/deliverable/main.dmd b/deliverable/main.dmd
index 2fb21b4..1dc7f71 100644
--- a/deliverable/main.dmd
+++ b/deliverable/main.dmd
@@ -6,16 +6,17 @@
 		\setentrycounter[]{page}\glsnumberformat{5}\delimN 
 		\setentrycounter[]{page}\glsnumberformat{8\delimR 13}\delimN 
 		\setentrycounter[]{page}\glsnumberformat{15\delimR 17}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{20\delimN 21}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{23}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{32\delimR 34}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{43}}}\glsgroupskip
+		\setentrycounter[]{page}\glsnumberformat{20\delimR 22}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{24}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{33\delimN 34}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{36}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{44\delimN 45}}}\glsgroupskip
 \glsgroupheading{S}\relax \glsresetentrylist %
 \glossentry{d:simon}{\glossaryentrynumbers{\relax 
 		\setentrycounter[]{page}\glsnumberformat{2}\delimN 
 		\setentrycounter[]{page}\glsnumberformat{9\delimR 12}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{23}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{25\delimR 28}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{32\delimN 33}\delimN 
-		\setentrycounter[]{page}\glsnumberformat{37}}}%
+		\setentrycounter[]{page}\glsnumberformat{24\delimR 27}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{29}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{33\delimN 34}\delimN 
+		\setentrycounter[]{page}\glsnumberformat{39}}}%
 \end{theglossary}\glossarypostamble
diff --git a/deliverable/main.dmg b/deliverable/main.dmg
index 54fc825..568e3c3 100644
--- a/deliverable/main.dmg
+++ b/deliverable/main.dmg
@@ -1,7 +1,7 @@
 This is makeindex, version 2.15 [TeX Live 2020] (kpathsea + Thai support).
 Scanning style file ./main.ist.............................done (29 attributes redefined, 0 ignored).
-Scanning input file main.dmn....done (81 entries accepted, 0 rejected).
-Sorting entries....done (487 comparisons).
-Generating output file main.dmd....done (21 lines written, 0 warnings).
+Scanning input file main.dmn....done (83 entries accepted, 0 rejected).
+Sorting entries....done (516 comparisons).
+Generating output file main.dmd....done (22 lines written, 0 warnings).
 Output written in main.dmd.
 Transcript written in main.dmg.
diff --git a/deliverable/main.pdf b/deliverable/main.pdf
index c1524d9..a1fd73a 100644
--- a/deliverable/main.pdf
+++ b/deliverable/main.pdf
diff --git a/deliverable/main.tex b/deliverable/main.tex
index 7968fa8..44fc77e 100644
--- a/deliverable/main.tex
+++ b/deliverable/main.tex
@@ -41,7 +41,7 @@ Nevertheless, overall per age influenza burdens varied per season.
 Seasonal age variability was shown in \cite{greenMortalityAttributableInfluenza2013}, where an age shift in Wales and England seasonal influenza burden was observed following the 2009 swine flue pandemic.
 It is also estimated that globally 291.243–645.832 influenza associated seasonal deaths occur annually \citep{iulianoEstimatesGlobalSeasonal2018}.
 These varying demographic statistics and the volume of influenza patients can confound decision making on national and international public health policies.
-Rapid knowledge extraction of vaccine efficacy data from clinical datasets and implementation of that knowledge can be a valuable asset for fighting future seasonal influenza outbreaks.
+Rapid knowledge extraction of vaccine efficacy from clinical datasets and implementation of that knowledge can be a valuable asset for fighting future seasonal influenza outbreaks.
 
 \subsection{Vaccine success criteria}
 
@@ -66,7 +66,7 @@ These pathways are important for viral entry, replication, and propagation, and
 The activation of these pathways is commonly meditated by the phosphorylation and dephosphorylation of several proteins, including \gls{bu:stat}.
 One example is the JAK-STAT signaling pathway in \gls{bu:bcell}s, where a large set of \gls{bu:bcell} receptors is known to bind \gls{bu:cytokine}s produced by \gls{bu:cd4pos}s and this results in downstream biological processes that make the immune response to a vaccination \citep{Papin_2004}.
 Further, these pathways are found in all \gls{bu:pbmc} and control a great amount of biological programs  \citep{Cantrell_2015}.
-In general, the phosphorylation pattern of these pathways in \gls{bu:pbmc}s are used in clinical studies as a measure of cell activation in response to \gls{bu:cytokine} stimulation  \citep{Toapanta_2012,tomicFluPRINTDatasetMultidimensional2019}.
+In general, the phosphorylation pattern of these pathways in \gls{bu:pbmc}s are used in clinical studies as a measure of cell activation in response to \gls{bu:cytokine} stimulation or absence thereof \citep{Toapanta_2012,tomicFluPRINTDatasetMultidimensional2019}.
 
 Machine learning has been applied to clinical datasets to find influenza protection markers, such as the described \gls{bu:tcell} populations, \gls{bu:titer}s of \gls{bu:pbmc}s and related molecules, or \gls{bu:cytokine} signalling related activity \citep{furmanApoptosisOtherImmune2013, sobolevAdjuvantedInfluenzaH1N1Vaccination2016, tsangGlobalAnalysesHuman2014}.
 However, these studies suffer from multiple issues, such as: inconsistencies between findings depending on the epidemic season, only focussing on one type of biological assay to get data, and a low amount of donors/samples.