Fix several formatting issues including bibliography sorting

thesis.lyx

@@ -79,6 +79,24 @@ InsetLayout "Flex:Glossary Term (Capital)"
         CustomPars            false
 End
 
+InsetLayout "Flex:Glossary Term (pl)"
+        LyxType               custom
+        LabelString           glspl
+        LatexType             command
+        LatexName             glspl*
+        InToc                 true
+        CustomPars            false
+End
+
+InsetLayout "Flex:Glossary Term (Capital, pl)"
+        LyxType               custom
+        LabelString           Glspl
+        LatexType             command
+        LatexName             Glspl*
+        InToc                 true
+        CustomPars            false
+End
+
 InsetLayout "Flex:Glossary Term (glstext)"
         LyxType               custom
         LabelString           glstext
@@ -180,9 +198,10 @@ End
 \use_package stmaryrd 1
 \use_package undertilde 1
 \cite_engine biblatex
-\cite_engine_type authoryear
+\cite_engine_type numerical
 \biblio_style plain
-\biblatex_bibstyle authoryear
+\biblio_options sorting=none
+\biblatex_bibstyle numeric
 \biblatex_citestyle numeric
 \use_bibtopic false
 \use_indices false
@@ -269,6 +288,27 @@ in partial fulfillment of the requirements for the degree of
 October 2019
 \end_layout
 
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Plain Layout
+To remove TODOs and watermark: Add 
+\begin_inset Quotes eld
+\end_inset
+
+final
+\begin_inset Quotes erd
+\end_inset
+
+ to the document class custom options.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
 [Copyright notice]
 \end_layout
@@ -583,7 +623,7 @@ Structure of the thesis
 status open
 
 \begin_layout Plain Layout
-This section might even go before the Chapter 1 header
+Put at end up intro
 \end_layout
 
 \end_inset
@@ -698,7 +738,7 @@ literal "false"
  of immune memory.
 \end_layout
 
-\begin_layout Subsubsection
+\begin_layout Subsection
 Diagnosis and treatment of allograft rejection is a major challenge
 \end_layout
 
@@ -799,7 +839,7 @@ for cause
  biopsies 
 \begin_inset CommandInset citation
 LatexCommand cite
-key "Wilkinson2006,Salomon2002,Patel2018,Zachariah2018"
+key "Salomon2002,Wilkinson2006,Patel2018,Zachariah2018"
 literal "false"
 
 \end_inset
@@ -864,7 +904,7 @@ literal "false"
  on the scale of days to weeks, rather than months.
 \end_layout
 
-\begin_layout Subsubsection
+\begin_layout Subsection
 Memory cells are resistant to immune suppression
 \end_layout
 
@@ -960,22 +1000,32 @@ literal "false"
  and regulation is required.
 \end_layout
 
-\begin_layout Subsubsection
+\begin_layout Subsection
 MSC infusion to improve transplant outcomes (prevent/delay rejection)
 \end_layout
 
 \begin_layout Standard
-\begin_inset Flex TODO Note (inline)
+One promising experimental treatment for transplant rejection involves the
+ infusion of 
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-Do I still talk about this? It's the motivation for chapter 4, but I don't
- actually present any work related to MSCs.
+MSC
 \end_layout
 
 \end_inset
 
 
+\begin_inset CommandInset nomenclature
+LatexCommand nomenclature
+symbol "MSC"
+description "mesenchymal stem cell"
+literal "true"
+
+\end_inset
+
+.
 \end_layout
 
 \begin_layout Itemize
@@ -1013,10 +1063,23 @@ RNA-seq
  at serial time points
 \end_layout
 
-\begin_layout Subsubsection
+\begin_layout Subsection
 Investigate dynamics of histone marks in CD4 T-cell activation and memory
 \end_layout
 
+\begin_layout Standard
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+Put this at end of intro as part of a description to structure of thesis
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
 \begin_layout Itemize
 Previous studies have looked at single snapshots of histone marks
 \end_layout
@@ -1025,10 +1088,23 @@ Previous studies have looked at single snapshots of histone marks
 Instead, look at changes in histone marks across activation and memory
 \end_layout
 
-\begin_layout Subsubsection
+\begin_layout Subsection
 High-throughput sequencing and microarray technologies
 \end_layout
 
+\begin_layout Standard
+\begin_inset Flex TODO Note (inline)
+status open
+
+\begin_layout Plain Layout
+This will serve as transition to bioinf
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
 \begin_layout Itemize
 Powerful methods for assaying gene expression and epigenetics across entire
  genomes
@@ -1052,19 +1128,6 @@ Overview of bioinformatic analysis methods
 \begin_inset Flex TODO Note (inline)
 status open
 
-\begin_layout Plain Layout
-Some kind of transition into bioinformatics would be good here
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Flex TODO Note (inline)
-status open
-
 \begin_layout Plain Layout
 Also cite somewhere: R, Bioconductor
 \end_layout
@@ -4059,14 +4122,11 @@ TSS
 
 .
  For genes with multiple annotated 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{TSS}
+TSS
 \end_layout
 
 \end_inset
@@ -4082,14 +4142,11 @@ TSS
 \end_inset
 
  individually, and any promoters that overlapped (due to multiple 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{TSS}
+TSS
 \end_layout
 
 \end_inset
@@ -4813,14 +4870,11 @@ noprefix "false"
 
 .
  
-\begin_inset ERT
+\begin_inset Flex Glossary Term (Capital, pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-Glspl*{LF}
+LF
 \end_layout
 
 \end_inset
@@ -6982,6 +7036,131 @@ end{landscape}
 
 \end_layout
 
+\begin_layout Standard
+We hypothesized that if naïve cells had differentiated into memory cells
+ by Day 14, then their patterns of expression and histone modification should
+ converge with those of memory cells at Day 14.
+ Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:PCoA-promoters"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+ shows the patterns of variation in all 3 histone marks in the promoter
+ regions of the genome using 
+\begin_inset Flex Glossary Term
+status open
+
+\begin_layout Plain Layout
+PCoA
+\end_layout
+
+\end_inset
+
+
+\begin_inset CommandInset nomenclature
+LatexCommand nomenclature
+symbol "PCoA"
+description "principal coordinate analysis"
+literal "false"
+
+\end_inset
+
+.
+ All 3 marks show a noticeable convergence between the naïve and memory
+ samples at day 14, visible as an overlapping of the day 14 groups on each
+ plot.
+ This is consistent with the counts of significantly differentially modified
+ promoters and estimates of the total numbers of differentially modified
+ promoters shown in Table 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "tab:Number-signif-promoters"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+.
+ For all histone marks, evidence of differential modification between naïve
+ and memory samples was detected at every time point except day 14.
+ The day 14 convergence pattern is also present in the 
+\begin_inset Flex Glossary Term
+status open
+
+\begin_layout Plain Layout
+RNA-seq
+\end_layout
+
+\end_inset
+
+ data (Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:RNA-PCA-group"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+), albeit in the 2nd and 3rd principal coordinates, indicating that it is
+ not the most dominant pattern driving gene expression.
+ Taken together, the data show that promoter histone methylation for these
+ 3 histone marks and RNA expression for naïve and memory cells are most
+ similar at day 14, the furthest time point after activation.
+ 
+\begin_inset Flex Glossary Term
+status open
+
+\begin_layout Plain Layout
+MOFA
+\end_layout
+
+\end_inset
+
+ was also able to capture this day 14 convergence pattern in 
+\begin_inset Flex Glossary Term
+status open
+
+\begin_layout Plain Layout
+LF
+\end_layout
+
+\end_inset
+
+5 (Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:mofa-lf-scatter"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+), which accounts for shared variation across all 3 histone marks and the
+ 
+\begin_inset Flex Glossary Term
+status open
+
+\begin_layout Plain Layout
+RNA-seq
+\end_layout
+
+\end_inset
+
+ data, confirming that this convergence is a coordinated pattern across
+ all 4 data sets.
+ While this observation does not prove that the naïve cells have differentiated
+ into memory cells at Day 14, it is consistent with that hypothesis.
+\end_layout
+
 \begin_layout Standard
 \begin_inset Float figure
 placement p
@@ -6994,7 +7173,7 @@ status open
 \begin_inset Float figure
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Plain Layout
 \align center
@@ -7039,7 +7218,7 @@ PCoA plot of H3K4me2 promoters, after subtracting surrogate variables
 \begin_inset Float figure
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Plain Layout
 \align center
@@ -7129,7 +7308,7 @@ PCoA plot of H3K27me3 promoters, after subtracting surrogate variables
 \begin_inset Float figure
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Plain Layout
 \align center
@@ -7194,131 +7373,6 @@ PCoA plots for promoter ChIP-seq and expression RNA-seq data
 
 \end_layout
 
-\begin_layout Standard
-We hypothesized that if naïve cells had differentiated into memory cells
- by Day 14, then their patterns of expression and histone modification should
- converge with those of memory cells at Day 14.
- Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:PCoA-promoters"
-plural "false"
-caps "false"
-noprefix "false"
-
-\end_inset
-
- shows the patterns of variation in all 3 histone marks in the promoter
- regions of the genome using 
-\begin_inset Flex Glossary Term
-status open
-
-\begin_layout Plain Layout
-PCoA
-\end_layout
-
-\end_inset
-
-
-\begin_inset CommandInset nomenclature
-LatexCommand nomenclature
-symbol "PCoA"
-description "principal coordinate analysis"
-literal "false"
-
-\end_inset
-
-.
- All 3 marks show a noticeable convergence between the naïve and memory
- samples at day 14, visible as an overlapping of the day 14 groups on each
- plot.
- This is consistent with the counts of significantly differentially modified
- promoters and estimates of the total numbers of differentially modified
- promoters shown in Table 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "tab:Number-signif-promoters"
-plural "false"
-caps "false"
-noprefix "false"
-
-\end_inset
-
-.
- For all histone marks, evidence of differential modification between naïve
- and memory samples was detected at every time point except day 14.
- The day 14 convergence pattern is also present in the 
-\begin_inset Flex Glossary Term
-status open
-
-\begin_layout Plain Layout
-RNA-seq
-\end_layout
-
-\end_inset
-
- data (Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:RNA-PCA-group"
-plural "false"
-caps "false"
-noprefix "false"
-
-\end_inset
-
-), albeit in the 2nd and 3rd principal coordinates, indicating that it is
- not the most dominant pattern driving gene expression.
- Taken together, the data show that promoter histone methylation for these
- 3 histone marks and RNA expression for naïve and memory cells are most
- similar at day 14, the furthest time point after activation.
- 
-\begin_inset Flex Glossary Term
-status open
-
-\begin_layout Plain Layout
-MOFA
-\end_layout
-
-\end_inset
-
- was also able to capture this day 14 convergence pattern in 
-\begin_inset Flex Glossary Term
-status open
-
-\begin_layout Plain Layout
-LF
-\end_layout
-
-\end_inset
-
-5 (Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:mofa-lf-scatter"
-plural "false"
-caps "false"
-noprefix "false"
-
-\end_inset
-
-), which accounts for shared variation across all 3 histone marks and the
- 
-\begin_inset Flex Glossary Term
-status open
-
-\begin_layout Plain Layout
-RNA-seq
-\end_layout
-
-\end_inset
-
- data, confirming that this convergence is a coordinated pattern across
- all 4 data sets.
- While this observation does not prove that the naïve cells have differentiated
- into memory cells at Day 14, it is consistent with that hypothesis.
-\end_layout
-
 \begin_layout Subsection
 Effect of H3K4me2 and H3K4me3 promoter coverage upstream vs downstream of
  TSS
@@ -8637,14 +8691,11 @@ TSS
  (Cluster 6).
  Referring to these opposing pairs of clusters as axes of variation is justified
 , because they correspond precisely to the first 3 
-\begin_inset ERT
-status collapsed
+\begin_inset Flex Glossary Term (pl)
+status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{PC}
+PC
 \end_layout
 
 \end_inset
@@ -9071,14 +9122,11 @@ LF
 
 5.
  Like all the 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{LF}
+LF
 \end_layout
 
 \end_inset
@@ -16802,14 +16850,11 @@ RNA-seq
 \end_inset
 
  in primate blood samples that uses complimentary 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -17035,14 +17080,11 @@ literal "false"
 .
  In the present report, we evaluated globin reduction using custom blocking
  
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -17136,14 +17178,11 @@ Globin Blocking
 
 \begin_layout Standard
 Four 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -17156,14 +17195,11 @@ glspl*{oligo}
  two hybridization sites for HBB and 2 sites for HBA (the chosen sites were
  identical in both HBA genes).
  All 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -17263,14 +17299,11 @@ mRNA
  PolyA selected RNA was then combined with 8 pmol of HBA1/2 (site 1), 8
  pmol of HBA1/2 (site 2), 12 pmol of HBB (site 1) and 12 pmol of HBB (site
  2) 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -17288,14 +17321,11 @@ glspl*{oligo}
 sher).
  A second “unblocked” library was prepared in the same way for each sample
  but replacing the blocking 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -18524,14 +18554,11 @@ GB
 \end_inset
 
  
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -19322,28 +19349,22 @@ noprefix "false"
 ).
  Other than the 3 designated alpha and beta globin genes, two other genes
  stand out as having especially large negative 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{logFC}
+logFC
 \end_layout
 
 \end_inset
 
 : HBD and LOC1021365.
  HBD, delta globin, is most likely targeted by the blocking 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -19395,14 +19416,11 @@ GB
 \end_inset
 
  
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -20269,14 +20287,11 @@ GB
  samples.
  However, given that both datasets are derived from the same biological
  samples and have nearly equal 
-\begin_inset ERT
-status collapsed
+\begin_inset Flex Glossary Term (pl)
+status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{BCV}
+BCV
 \end_layout
 
 \end_inset
@@ -20473,14 +20488,11 @@ GB
 \end_inset
 
  
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -20546,14 +20558,11 @@ RNA-seq
  the relative levels of non-globin genes.
  Based on these results, globin transcript reduction using sequence-specific,
  complementary blocking 
-\begin_inset ERT
+\begin_inset Flex Glossary Term (pl)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-glspl*{oligo}
+oligo
 \end_layout
 
 \end_inset
@@ -20648,6 +20657,7 @@ Closing remarks
 \end_layout
 
 \begin_layout Standard
+\align center
 \begin_inset ERT
 status collapsed
 
@@ -20675,20 +20685,7 @@ bibname}{References}
 LatexCommand bibtex
 btprint "btPrintCited"
 bibfiles "code-refs,refs-PROCESSED"
-options "bibtotoc,unsrt"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Flex TODO Note (inline)
-status open
-
-\begin_layout Plain Layout
-Check bib entry formatting & sort order
-\end_layout
+options "bibtotoc"
 
 \end_inset
 
@@ -20700,8 +20697,9 @@ Check bib entry formatting & sort order
 status open
 
 \begin_layout Plain Layout
-Check in-text citation format.
- Probably don't just want [1], [2], etc.
+Reference URLs that span pages have clickable links that include the page
+ numbers and watermark.
+ Try to fix that.
 \end_layout
 
 \end_inset