Initial commit
authorFabio Zanini <fabio.zanini@tuebingen.mpg.de>
Wed, 28 Nov 2012 02:24:12 +0000 (18:24 -0800)
committerFabio Zanini <fabio.zanini@tuebingen.mpg.de>
Wed, 28 Nov 2012 02:24:12 +0000 (18:24 -0800)
23 files changed:
bib.bib [new file with mode: 0644]
figures/Bunnik2008_fixmid_syn_ShankanonShanka.pdf [new file with mode: 0644]
figures/Henn_density_polymorphisms.pdf [new file with mode: 0644]
figures/Henn_density_polymorphisms_syn_over_chances.pdf [new file with mode: 0644]
figures/Shankarappa_allele_freqs_trajectories_syn_nonsynp8.png [new file with mode: 0644]
figures/Shankarappa_fixmid_syn_V_regions.pdf [new file with mode: 0644]
figures/fixation_loss_shortgenome_area_ada_frac_del_eff_coi_0_01_nescepi_6_heat.pdf [new file with mode: 0644]
figures/fixation_loss_shortgenome_area_ada_frac_del_eff_coi_0_01_nescepi_6_nonsyn_heat.pdf [new file with mode: 0644]
figures/fixation_probability_N_1e4_3ingredients_3rddel_envnonenv_stopall.pdf [new file with mode: 0644]
figures/fixation_probability_shortgenome_N_1e4_epitopes_example_longer.pdf [new file with mode: 0644]
figures/mixed_Shankarappa_Bunnik2008_Liu_fixation_reactivity_Vandflanking_fromSHAPE.pdf [new file with mode: 0644]
figures/mixed_Shankarappa_Bunnik2008_Liu_fixation_reactivity_nonVandflanking.pdf [new file with mode: 0644]
natbib.bst [new file with mode: 0644]
natbib.sty [new file with mode: 0644]
synmut.aux [new file with mode: 0644]
synmut.bbl [new file with mode: 0644]
synmut.blg [new file with mode: 0644]
synmut.fdb_latexmk [new file with mode: 0644]
synmut.fls [new file with mode: 0644]
synmut.log [new file with mode: 0644]
synmut.out [new file with mode: 0644]
synmut.pdf [new file with mode: 0644]
synmut.tex [new file with mode: 0644]

diff --git a/bib.bib b/bib.bib
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--- /dev/null
+++ b/bib.bib
@@ -0,0 +1,20 @@
+
+@article{watts_architecture_2009,
+       title = {Architecture and secondary structure of an entire {HIV-1} {RNA} genome},
+       volume = {460},
+       copyright = {© 2009 Nature Publishing Group},
+       issn = {0028-0836},
+       url = {http://www.nature.com/nature/journal/v460/n7256/full/nature08237.html},
+       doi = {10.1038/nature08237},
+       abstract = {Single-stranded {RNA} viruses encompass broad classes of infectious agents and cause the common cold, cancer, {AIDS} and other serious health threats. Viral replication is regulated at many levels, including the use of conserved genomic {RNA} structures. Most potential regulatory elements in viral {RNA} genomes are uncharacterized. Here we report the structure of an entire {HIV-1} genome at single nucleotide resolution using {SHAPE}, a high-throughput {RNA} analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between {RNA} and protein primary sequences, a correlation exists between high levels of {RNA} structure and sequences that encode inter-domain loops in {HIV} proteins. This correlation suggests that {RNA} structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger {RNA} motifs. We also identify organizational principles for unstructured {RNA} regions, including splice site acceptors and hypervariable regions. These results emphasize that the {HIV-1} genome and, potentially, many coding {RNAs} are punctuated by previously unrecognized regulatory motifs and that extensive {RNA} structure constitutes an important component of the genetic code.},
+       language = {en},
+       number = {7256},
+       urldate = {2012-07-01},
+       journal = {Nature},
+       author = {Watts, Joseph M. and Dang, Kristen K. and Gorelick, Robert J. and Leonard, Christopher W. and Jr, Julian W. Bess and Swanstrom, Ronald and Burch, Christina L. and Weeks, Kevin M.},
+       month = aug,
+       year = {2009},
+       keywords = {astronomy, astrophysics, biochemistry, bioinformatics, biology, biotechnology, cancer, cell cycle, cell signalling, climate change, computational biology, development, developmental biology, {DNA}, drug discovery, earth science, ecology, environmental science, Evolution, evolutionary biology, functional genomics, genetics, genomics, geophysics, Immunology, interdisciplinary science, life, marine biology, materials science, Medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, physics, proteomics, quantum physics, {RNA}, science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics},
+       pages = {711--716},
+       file = {Full Text PDF:/home/fabio/university/papers/zotero/storage/T7UGN8ID/Watts et al. - 2009 - Architecture and secondary structure of an entire .pdf:application/pdf}
+}
\ No newline at end of file
diff --git a/figures/Bunnik2008_fixmid_syn_ShankanonShanka.pdf b/figures/Bunnik2008_fixmid_syn_ShankanonShanka.pdf
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diff --git a/figures/Henn_density_polymorphisms_syn_over_chances.pdf b/figures/Henn_density_polymorphisms_syn_over_chances.pdf
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diff --git a/figures/Shankarappa_allele_freqs_trajectories_syn_nonsynp8.png b/figures/Shankarappa_allele_freqs_trajectories_syn_nonsynp8.png
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diff --git a/figures/Shankarappa_fixmid_syn_V_regions.pdf b/figures/Shankarappa_fixmid_syn_V_regions.pdf
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diff --git a/figures/fixation_loss_shortgenome_area_ada_frac_del_eff_coi_0_01_nescepi_6_heat.pdf b/figures/fixation_loss_shortgenome_area_ada_frac_del_eff_coi_0_01_nescepi_6_heat.pdf
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diff --git a/figures/fixation_loss_shortgenome_area_ada_frac_del_eff_coi_0_01_nescepi_6_nonsyn_heat.pdf b/figures/fixation_loss_shortgenome_area_ada_frac_del_eff_coi_0_01_nescepi_6_nonsyn_heat.pdf
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diff --git a/figures/fixation_probability_N_1e4_3ingredients_3rddel_envnonenv_stopall.pdf b/figures/fixation_probability_N_1e4_3ingredients_3rddel_envnonenv_stopall.pdf
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diff --git a/figures/fixation_probability_shortgenome_N_1e4_epitopes_example_longer.pdf b/figures/fixation_probability_shortgenome_N_1e4_epitopes_example_longer.pdf
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diff --git a/figures/mixed_Shankarappa_Bunnik2008_Liu_fixation_reactivity_Vandflanking_fromSHAPE.pdf b/figures/mixed_Shankarappa_Bunnik2008_Liu_fixation_reactivity_Vandflanking_fromSHAPE.pdf
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diff --git a/figures/mixed_Shankarappa_Bunnik2008_Liu_fixation_reactivity_nonVandflanking.pdf b/figures/mixed_Shankarappa_Bunnik2008_Liu_fixation_reactivity_nonVandflanking.pdf
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diff --git a/natbib.bst b/natbib.bst
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--- /dev/null
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+%% \r
+%% This is file `natbib.bst', generated \r
+%% on <1994/9/16> with the docstrip utility (2.2h).\r
+%% \r
+%% The original source files were:\r
+%% \r
+%% genbst.mbs  (with options: `ay,nat,seq-lab,nm-rev,dt-beg,yr-par,vol-bf,\r
+%%                             volp-com,etal-it')\r
+%% ---------------------------------------- \r
+%% *** Personal bib style, PWD *** \r
+%% \r
+%% (Here are the specifications of the source file)\r
+%% \ProvidesFile{genbst.mbs}[1994/09/16 1.5 (PWD)]\r
+%%   For use with BibTeX version 0.99a or later\r
+%%     and with LaTeX 2.09 or 2e\r
+%%-------------------------------------------------------------------\r
+%% NOTICE:\r
+%% This file may be used for non-profit purposes.\r
+%% It may not be distributed in exchange for money,\r
+%%   other than distribution costs.\r
+%%\r
+%% The author provides it `as is' and does not guarantee it in any way.\r
+%%\r
+%% Copyright (C) 1994 Patrick W. Daly\r
+%% Max-Planck-Institut f\"ur Aeronomie\r
+%% Postfach 20\r
+%% D-37189 Katlenburg-Lindau\r
+%% Germany\r
+%%\r
+%% E-mail:\r
+%% SPAN--     nsp::linmpi::daly    (note nsp also known as ecd1)\r
+%% Internet-- daly@linmpi.dnet.gwdg.de\r
+%%-----------------------------------------------------------\r
+%% \CharacterTable\r
+%%  {Upper-case    \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z\r
+%%   Lower-case    \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z\r
+%%   Digits        \0\1\2\3\4\5\6\7\8\9\r
+%%   Exclamation   \!     Double quote  \"     Hash (number) \#\r
+%%   Dollar        \$     Percent       \%     Ampersand     \&\r
+%%   Acute accent  \'     Left paren    \(     Right paren   \)\r
+%%   Asterisk      \*     Plus          \+     Comma         \,\r
+%%   Minus         \-     Point         \.     Solidus       \/\r
+%%   Colon         \:     Semicolon     \;     Less than     \<\r
+%%   Equals        \=     Greater than  \>     Question mark \?\r
+%%   Commercial at \@     Left bracket  \[     Backslash     \\\r
+%%   Right bracket \]     Circumflex    \^     Underscore    \_\r
+%%   Grave accent  \`     Left brace    \{     Vertical bar  \|\r
+%%   Right brace   \}     Tilde         \~}\r
+%%---------------------------------------------------------------------\r
+ % This is an author-year citation style bibliography. As such, it is\r
+ % non-standard LaTeX, and requires a special package file to function properly.\r
+ % Such a package is    natbib.sty   by Patrick W. Daly\r
+ % The form of the \bibitem entries is\r
+ %   \bibitem[Jones et al.(1990)]{key}...\r
+ %   \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}...\r
+ % The essential feature is that the label (the part in brackets) consists\r
+ % of the author names, as they should appear in the citation, with the year\r
+ % in parentheses following. There must be no space before the opening\r
+ % parenthesis!\r
+ % With natbib v5.3, a full list of authors may also follow the year.\r
+ % In natbib.sty, it is possible to define the type of enclosures that is\r
+ % really wanted (brackets or parentheses), but in either case, there must\r
+ % be parentheses in the label.\r
+ % The \cite command functions as follows:\r
+ %   \cite{key} ==>>                Jones et al. (1990)\r
+ %   \cite[]{key} ==>>              (Jones et al., 1990)\r
+ %   \cite[chap. 2]{key} ==>>       (Jones et al., 1990, chap. 2)\r
+ %   \cite[e.g.][]{key} ==>>        (e.g. Jones et al., 1990)\r
+ %   \cite[e.g.][p. 32]{key} ==>>   (e.g. Jones et al., p. 32)\r
+ %   \citeauthor{key}               Jones et al.\r
+ %   \citefullauthor{key}           Jones, Baker, and Smith\r
+ %   \citeyear{key}                 1990\r
+%%---------------------------------------------------------------------\r
+\r
+ENTRY\r
+  { address\r
+    author\r
+    booktitle\r
+    chapter\r
+    edition\r
+    editor\r
+    howpublished\r
+    institution\r
+    journal\r
+    key\r
+    month\r
+    note\r
+    number\r
+    organization\r
+    pages\r
+    publisher\r
+    school\r
+    series\r
+    title\r
+    type\r
+    volume\r
+    year\r
+  }\r
+  {}\r
+  { label extra.label sort.label }\r
+\r
+INTEGERS { output.state before.all mid.sentence after.sentence after.block }\r
+\r
+FUNCTION {init.state.consts}\r
+{ #0 'before.all :=\r
+  #1 'mid.sentence :=\r
+  #2 'after.sentence :=\r
+  #3 'after.block :=\r
+}\r
+\r
+STRINGS { s t }\r
+\r
+FUNCTION {output.nonnull}\r
+{ 's :=\r
+  output.state mid.sentence =\r
+    { ", " * write$ }\r
+    { output.state after.block =\r
+        { add.period$ write$\r
+          newline$\r
+          "\newblock " write$\r
+        }\r
+        { output.state before.all =\r
+            'write$\r
+            { add.period$ " " * write$ }\r
+          if$\r
+        }\r
+      if$\r
+      mid.sentence 'output.state :=\r
+    }\r
+  if$\r
+  s\r
+}\r
+\r
+FUNCTION {output}\r
+{ duplicate$ empty$\r
+    'pop$\r
+    'output.nonnull\r
+  if$\r
+}\r
+\r
+FUNCTION {output.check}\r
+{ 't :=\r
+  duplicate$ empty$\r
+    { pop$ "empty " t * " in " * cite$ * warning$ }\r
+    'output.nonnull\r
+  if$\r
+}\r
+\r
+FUNCTION {fin.entry}\r
+{ add.period$\r
+  write$\r
+  newline$\r
+}\r
+\r
+FUNCTION {new.block}\r
+{ output.state before.all =\r
+    'skip$\r
+    { after.block 'output.state := }\r
+  if$\r
+}\r
+\r
+FUNCTION {new.sentence}\r
+{ output.state after.block =\r
+    'skip$\r
+    { output.state before.all =\r
+        'skip$\r
+        { after.sentence 'output.state := }\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {not}\r
+{   { #0 }\r
+    { #1 }\r
+  if$\r
+}\r
+\r
+FUNCTION {and}\r
+{   'skip$\r
+    { pop$ #0 }\r
+  if$\r
+}\r
+\r
+FUNCTION {or}\r
+{   { pop$ #1 }\r
+    'skip$\r
+  if$\r
+}\r
+\r
+FUNCTION {non.stop}\r
+{ duplicate$\r
+   "}" * add.period$\r
+   #-1 #1 substring$ "." =\r
+}\r
+\r
+FUNCTION {new.block.checkb}\r
+{ empty$\r
+  swap$ empty$\r
+  and\r
+    'skip$\r
+    'new.block\r
+  if$\r
+}\r
+\r
+FUNCTION {field.or.null}\r
+{ duplicate$ empty$\r
+    { pop$ "" }\r
+    'skip$\r
+  if$\r
+}\r
+\r
+FUNCTION {emphasize}\r
+{ duplicate$ empty$\r
+    { pop$ "" }\r
+    { "{\em " swap$ * non.stop\r
+        { "\/}" * }\r
+        { "}" * }\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {bolden}\r
+{ duplicate$ empty$\r
+    { pop$ "" }\r
+    { "{\bf " swap$ * "}" * }\r
+  if$\r
+}\r
+\r
+INTEGERS { nameptr namesleft numnames }\r
+\r
+FUNCTION {format.names}\r
+{ 's :=\r
+  #1 'nameptr :=\r
+  s num.names$ 'numnames :=\r
+  numnames 'namesleft :=\r
+    { namesleft #0 > }\r
+    { s nameptr\r
+      "{vv~}{ll}{, jj}{, f.}" format.name$ 't :=\r
+      nameptr #1 >\r
+        {\r
+          namesleft #1 >\r
+            { ", " * t * }\r
+            {\r
+              numnames #2 >\r
+                { "," * }\r
+                'skip$\r
+              if$\r
+              t "others" =\r
+                { " " * "et~al." emphasize * }\r
+                { " and " * t * }\r
+              if$\r
+            }\r
+          if$\r
+        }\r
+        't\r
+      if$\r
+      nameptr #1 + 'nameptr :=\r
+      namesleft #1 - 'namesleft :=\r
+    }\r
+  while$\r
+}\r
+\r
+FUNCTION {format.names.ed}\r
+{ 's :=\r
+  #1 'nameptr :=\r
+  s num.names$ 'numnames :=\r
+  numnames 'namesleft :=\r
+    { namesleft #0 > }\r
+    { s nameptr\r
+      "{f.~}{vv~}{ll}{, jj}"\r
+      format.name$ 't :=\r
+      nameptr #1 >\r
+        {\r
+          namesleft #1 >\r
+            { ", " * t * }\r
+            {\r
+              numnames #2 >\r
+                { "," * }\r
+                'skip$\r
+              if$\r
+              t "others" =\r
+                { " " * "et~al." emphasize * }\r
+                { " and " * t * }\r
+              if$\r
+            }\r
+          if$\r
+        }\r
+        't\r
+      if$\r
+      nameptr #1 + 'nameptr :=\r
+      namesleft #1 - 'namesleft :=\r
+    }\r
+  while$\r
+}\r
+\r
+FUNCTION {format.key}\r
+{ empty$\r
+    { key field.or.null }\r
+    { "" }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.authors}\r
+{ author empty$\r
+    { "" }\r
+    { author format.names }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.editors}\r
+{ editor empty$\r
+    { "" }\r
+    { editor format.names\r
+      editor num.names$ #1 >\r
+        { ", editors" * }\r
+        { ", editor" * }\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.in.editors}\r
+{ editor empty$\r
+    { "" }\r
+    { editor format.names.ed\r
+      editor num.names$ #1 >\r
+        { ", editors" * }\r
+        { ", editor" * }\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.title}\r
+{ title empty$\r
+    { "" }\r
+    { title "t" change.case$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.full.names}\r
+{'s :=\r
+  #1 'nameptr :=\r
+  s num.names$ 'numnames :=\r
+  numnames 'namesleft :=\r
+    { namesleft #0 > }\r
+    { s nameptr\r
+      "{vv~}{ll}" format.name$ 't :=\r
+      nameptr #1 >\r
+        {\r
+          namesleft #1 >\r
+            { ", " * t * }\r
+            {\r
+              numnames #2 >\r
+                { "," * }\r
+                'skip$\r
+              if$\r
+              t "others" =\r
+                { " " * "et~al." emphasize * }\r
+                { " and " * t * }\r
+              if$\r
+            }\r
+          if$\r
+        }\r
+        't\r
+      if$\r
+      nameptr #1 + 'nameptr :=\r
+      namesleft #1 - 'namesleft :=\r
+    }\r
+  while$\r
+}\r
+\r
+FUNCTION {author.editor.key.full}\r
+{ author empty$\r
+    { editor empty$\r
+        { key empty$\r
+            { cite$ #1 #3 substring$ }\r
+            'key\r
+          if$\r
+        }\r
+        { editor format.full.names }\r
+      if$\r
+    }\r
+    { author format.full.names }\r
+  if$\r
+}\r
+\r
+FUNCTION {author.key.full}\r
+{ author empty$\r
+    { key empty$\r
+         { cite$ #1 #3 substring$ }\r
+          'key\r
+      if$\r
+    }\r
+    { author format.full.names }\r
+  if$\r
+}\r
+\r
+FUNCTION {editor.key.full}\r
+{ editor empty$\r
+    { key empty$\r
+         { cite$ #1 #3 substring$ }\r
+          'key\r
+      if$\r
+    }\r
+    { editor format.full.names }\r
+  if$\r
+}\r
+\r
+FUNCTION {make.full.names}\r
+{ type$ "book" =\r
+  type$ "inbook" =\r
+  or\r
+    'author.editor.key.full\r
+    { type$ "proceedings" =\r
+        'editor.key.full\r
+        'author.key.full\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {output.bibitem}\r
+{ newline$\r
+  "\bibitem[" write$\r
+  label write$\r
+  ")" make.full.names * "]{" * write$\r
+  cite$ write$\r
+  "}" write$\r
+  newline$\r
+  ""\r
+  before.all 'output.state :=\r
+}\r
+\r
+FUNCTION {n.dashify}\r
+{ 't :=\r
+  ""\r
+    { t empty$ not }\r
+    { t #1 #1 substring$ "-" =\r
+        { t #1 #2 substring$ "--" = not\r
+            { "--" *\r
+              t #2 global.max$ substring$ 't :=\r
+            }\r
+            {   { t #1 #1 substring$ "-" = }\r
+                { "-" *\r
+                  t #2 global.max$ substring$ 't :=\r
+                }\r
+              while$\r
+            }\r
+          if$\r
+        }\r
+        { t #1 #1 substring$ *\r
+          t #2 global.max$ substring$ 't :=\r
+        }\r
+      if$\r
+    }\r
+  while$\r
+}\r
+\r
+FUNCTION {word.in}\r
+{ "In " }\r
+\r
+FUNCTION {format.date}\r
+{ year duplicate$ empty$\r
+    { "empty year in " cite$ * "; set to ????" * warning$\r
+       pop$ "????" }\r
+    'skip$\r
+  if$\r
+  before.all 'output.state :=\r
+  " (" swap$ * extra.label * ")" *\r
+}\r
+\r
+FUNCTION {format.btitle}\r
+{ title emphasize\r
+}\r
+\r
+FUNCTION {tie.or.space.connect}\r
+{ duplicate$ text.length$ #3 <\r
+    { "~" }\r
+    { " " }\r
+  if$\r
+  swap$ * *\r
+}\r
+\r
+FUNCTION {either.or.check}\r
+{ empty$\r
+    'pop$\r
+    { "can't use both " swap$ * " fields in " * cite$ * warning$ }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.bvolume}\r
+{ volume empty$\r
+    { "" }\r
+    { "volume" volume tie.or.space.connect\r
+      series empty$\r
+        'skip$\r
+        { " of " * series emphasize * }\r
+      if$\r
+      "volume and number" number either.or.check\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.number.series}\r
+{ volume empty$\r
+    { number empty$\r
+        { series field.or.null }\r
+        { output.state mid.sentence =\r
+            { "number" }\r
+            { "Number" }\r
+          if$\r
+          number tie.or.space.connect\r
+          series empty$\r
+            { "there's a number but no series in " cite$ * warning$ }\r
+            { " in " * series * }\r
+          if$\r
+        }\r
+      if$\r
+    }\r
+    { "" }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.edition}\r
+{ edition empty$\r
+    { "" }\r
+    { output.state mid.sentence =\r
+        { edition "l" change.case$ " edition" * }\r
+        { edition "t" change.case$ " edition" * }\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+INTEGERS { multiresult }\r
+\r
+FUNCTION {multi.page.check}\r
+{ 't :=\r
+  #0 'multiresult :=\r
+    { multiresult not\r
+      t empty$ not\r
+      and\r
+    }\r
+    { t #1 #1 substring$\r
+      duplicate$ "-" =\r
+      swap$ duplicate$ "," =\r
+      swap$ "+" =\r
+      or or\r
+        { #1 'multiresult := }\r
+        { t #2 global.max$ substring$ 't := }\r
+      if$\r
+    }\r
+  while$\r
+  multiresult\r
+}\r
+\r
+FUNCTION {format.pages}\r
+{ pages empty$\r
+    { "" }\r
+    { pages multi.page.check\r
+        { "pages" pages n.dashify tie.or.space.connect }\r
+        { "page" pages tie.or.space.connect }\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.vol.num.pages}\r
+{ volume field.or.null\r
+  bolden\r
+  number empty$\r
+    'skip$\r
+    { "(" number * ")" * *\r
+      volume empty$\r
+        { "there's a number but no volume in " cite$ * warning$ }\r
+        'skip$\r
+      if$\r
+    }\r
+  if$\r
+  pages empty$\r
+    'skip$\r
+    { duplicate$ empty$\r
+        { pop$ format.pages }\r
+        { ", " * pages n.dashify * }\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.chapter.pages}\r
+{ chapter empty$\r
+    'format.pages\r
+    { type empty$\r
+        { "chapter" }\r
+        { type "l" change.case$ }\r
+      if$\r
+      chapter tie.or.space.connect\r
+      pages empty$\r
+        'skip$\r
+        { ", " * format.pages * }\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.in.ed.booktitle}\r
+{ booktitle empty$\r
+    { "" }\r
+    { editor empty$\r
+        { word.in booktitle emphasize * }\r
+        { word.in format.in.editors * ", " * booktitle emphasize * }\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.thesis.type}\r
+{ type empty$\r
+    'skip$\r
+    { pop$\r
+      type "t" change.case$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.tr.number}\r
+{ type empty$\r
+    { "Technical Report" }\r
+    'type\r
+  if$\r
+  number empty$\r
+    { "t" change.case$ }\r
+    { number tie.or.space.connect }\r
+  if$\r
+}\r
+\r
+FUNCTION {format.article.crossref}\r
+{\r
+  word.in\r
+  "\cite{" * crossref * "}" *\r
+}\r
+\r
+FUNCTION {format.book.crossref}\r
+{ volume empty$\r
+    { "empty volume in " cite$ * "'s crossref of " * crossref * warning$\r
+      word.in\r
+    }\r
+    { "Volume" volume tie.or.space.connect\r
+      " of " *\r
+    }\r
+  if$\r
+  "\cite{" * crossref * "}" *\r
+}\r
+\r
+FUNCTION {format.incoll.inproc.crossref}\r
+{\r
+  word.in\r
+  "\cite{" * crossref * "}" *\r
+}\r
+\r
+FUNCTION {article}\r
+{ output.bibitem\r
+  format.authors "author" output.check\r
+  author format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.title "title" output.check\r
+  new.block\r
+  crossref missing$\r
+    { journal emphasize "journal" output.check\r
+      format.vol.num.pages output\r
+    }\r
+    { format.article.crossref output.nonnull\r
+      format.pages output\r
+    }\r
+  if$\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {book}\r
+{ output.bibitem\r
+  author empty$\r
+    { format.editors "author and editor" output.check\r
+      editor format.key output\r
+    }\r
+    { format.authors output.nonnull\r
+      crossref missing$\r
+        { "author and editor" editor either.or.check }\r
+        'skip$\r
+      if$\r
+    }\r
+  if$\r
+  format.date "year" output.check\r
+  new.block\r
+  format.btitle "title" output.check\r
+  crossref missing$\r
+    { format.bvolume output\r
+      new.block\r
+      format.number.series output\r
+      new.sentence\r
+      publisher "publisher" output.check\r
+      address output\r
+    }\r
+    {\r
+      new.block\r
+      format.book.crossref output.nonnull\r
+    }\r
+  if$\r
+  format.edition output\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {booklet}\r
+{ output.bibitem\r
+  format.authors output\r
+  author format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.title "title" output.check\r
+  new.block\r
+  howpublished output\r
+  address output\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {inbook}\r
+{ output.bibitem\r
+  author empty$\r
+    { format.editors "author and editor" output.check\r
+      editor format.key output\r
+    }\r
+    { format.authors output.nonnull\r
+      crossref missing$\r
+        { "author and editor" editor either.or.check }\r
+        'skip$\r
+      if$\r
+    }\r
+  if$\r
+  format.date "year" output.check\r
+  new.block\r
+  format.btitle "title" output.check\r
+  crossref missing$\r
+    { format.bvolume output\r
+      format.chapter.pages "chapter and pages" output.check\r
+      new.block\r
+      format.number.series output\r
+      new.sentence\r
+      publisher "publisher" output.check\r
+      address output\r
+    }\r
+    { format.chapter.pages "chapter and pages" output.check\r
+      new.block\r
+      format.book.crossref output.nonnull\r
+    }\r
+  if$\r
+  format.edition output\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {incollection}\r
+{ output.bibitem\r
+  format.authors "author" output.check\r
+  author format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.title "title" output.check\r
+  new.block\r
+  crossref missing$\r
+    { format.in.ed.booktitle "booktitle" output.check\r
+      format.bvolume output\r
+      format.number.series output\r
+      format.chapter.pages output\r
+      new.sentence\r
+      publisher "publisher" output.check\r
+      address output\r
+      format.edition output\r
+    }\r
+    { format.incoll.inproc.crossref output.nonnull\r
+      format.chapter.pages output\r
+    }\r
+  if$\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {inproceedings}\r
+{ output.bibitem\r
+  format.authors "author" output.check\r
+  author format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.title "title" output.check\r
+  new.block\r
+  crossref missing$\r
+    { format.in.ed.booktitle "booktitle" output.check\r
+      format.bvolume output\r
+      format.number.series output\r
+      format.pages output\r
+      address output\r
+      new.sentence\r
+      organization output\r
+      publisher output\r
+    }\r
+    { format.incoll.inproc.crossref output.nonnull\r
+      format.pages output\r
+    }\r
+  if$\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {conference} { inproceedings }\r
+\r
+FUNCTION {manual}\r
+{ output.bibitem\r
+  format.authors output\r
+  author format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.btitle "title" output.check\r
+  organization address new.block.checkb\r
+  organization output\r
+  address output\r
+  format.edition output\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {mastersthesis}\r
+{ output.bibitem\r
+  format.authors "author" output.check\r
+  author format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.btitle "title" output.check\r
+  new.block\r
+  "Master's thesis" format.thesis.type output.nonnull\r
+  school "school" output.check\r
+  address output\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {misc}\r
+{ output.bibitem\r
+  format.authors output\r
+  author format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.title output\r
+  new.block\r
+  howpublished output\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {phdthesis}\r
+{ output.bibitem\r
+  format.authors "author" output.check\r
+  author format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.btitle "title" output.check\r
+  new.block\r
+  "Ph.D. thesis" format.thesis.type output.nonnull\r
+  school "school" output.check\r
+  address output\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {proceedings}\r
+{ output.bibitem\r
+  format.editors output\r
+  editor format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.btitle "title" output.check\r
+  format.bvolume output\r
+  format.number.series output\r
+  address output\r
+  new.sentence\r
+  organization output\r
+  publisher output\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {techreport}\r
+{ output.bibitem\r
+  format.authors "author" output.check\r
+  author format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.title "title" output.check\r
+  new.block\r
+  format.tr.number output.nonnull\r
+  institution "institution" output.check\r
+  address output\r
+  new.block\r
+  note output\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {unpublished}\r
+{ output.bibitem\r
+  format.authors "author" output.check\r
+  author format.key output\r
+  format.date "year" output.check\r
+  new.block\r
+  format.title "title" output.check\r
+  new.block\r
+  note "note" output.check\r
+  fin.entry\r
+}\r
+\r
+FUNCTION {default.type} { misc }\r
+\r
+MACRO {jan} {"January"}\r
+\r
+MACRO {feb} {"February"}\r
+\r
+MACRO {mar} {"March"}\r
+\r
+MACRO {apr} {"April"}\r
+\r
+MACRO {may} {"May"}\r
+\r
+MACRO {jun} {"June"}\r
+\r
+MACRO {jul} {"July"}\r
+\r
+MACRO {aug} {"August"}\r
+\r
+MACRO {sep} {"September"}\r
+\r
+MACRO {oct} {"October"}\r
+\r
+MACRO {nov} {"November"}\r
+\r
+MACRO {dec} {"December"}\r
+\r
+MACRO {acmcs} {"ACM Computing Surveys"}\r
+\r
+MACRO {acta} {"Acta Informatica"}\r
+\r
+MACRO {cacm} {"Communications of the ACM"}\r
+\r
+MACRO {ibmjrd} {"IBM Journal of Research and Development"}\r
+\r
+MACRO {ibmsj} {"IBM Systems Journal"}\r
+\r
+MACRO {ieeese} {"IEEE Transactions on Software Engineering"}\r
+\r
+MACRO {ieeetc} {"IEEE Transactions on Computers"}\r
+\r
+MACRO {ieeetcad}\r
+ {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"}\r
+\r
+MACRO {ipl} {"Information Processing Letters"}\r
+\r
+MACRO {jacm} {"Journal of the ACM"}\r
+\r
+MACRO {jcss} {"Journal of Computer and System Sciences"}\r
+\r
+MACRO {scp} {"Science of Computer Programming"}\r
+\r
+MACRO {sicomp} {"SIAM Journal on Computing"}\r
+\r
+MACRO {tocs} {"ACM Transactions on Computer Systems"}\r
+\r
+MACRO {tods} {"ACM Transactions on Database Systems"}\r
+\r
+MACRO {tog} {"ACM Transactions on Graphics"}\r
+\r
+MACRO {toms} {"ACM Transactions on Mathematical Software"}\r
+\r
+MACRO {toois} {"ACM Transactions on Office Information Systems"}\r
+\r
+MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"}\r
+\r
+MACRO {tcs} {"Theoretical Computer Science"}\r
+\r
+READ\r
+\r
+FUNCTION {sortify}\r
+{ purify$\r
+  "l" change.case$\r
+}\r
+\r
+INTEGERS { len }\r
+\r
+FUNCTION {chop.word}\r
+{ 's :=\r
+  'len :=\r
+  s #1 len substring$ =\r
+    { s len #1 + global.max$ substring$ }\r
+    's\r
+  if$\r
+}\r
+\r
+FUNCTION {format.lab.names}\r
+{ 's :=\r
+  s #1 "{vv~}{ll}" format.name$\r
+  s num.names$ duplicate$\r
+  #2 >\r
+    { pop$ " " * "et~al." emphasize * }\r
+    { #2 <\r
+        'skip$\r
+        { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =\r
+            { " " * "et~al." emphasize * }\r
+            { " and " * s #2 "{vv~}{ll}" format.name$ * }\r
+          if$\r
+        }\r
+      if$\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {author.key.label}\r
+{ author empty$\r
+    { key empty$\r
+        { cite$ #1 #3 substring$ }\r
+        'key\r
+      if$\r
+    }\r
+    { author format.lab.names }\r
+  if$\r
+}\r
+\r
+FUNCTION {author.editor.key.label}\r
+{ author empty$\r
+    { editor empty$\r
+        { key empty$\r
+            { cite$ #1 #3 substring$ }\r
+            'key\r
+          if$\r
+        }\r
+        { editor format.lab.names }\r
+      if$\r
+    }\r
+    { author format.lab.names }\r
+  if$\r
+}\r
+\r
+FUNCTION {editor.key.label}\r
+{ editor empty$\r
+    { key empty$\r
+        { cite$ #1 #3 substring$ }\r
+        'key\r
+      if$\r
+    }\r
+    { editor format.lab.names }\r
+  if$\r
+}\r
+\r
+FUNCTION {calc.label}\r
+{ type$ "book" =\r
+  type$ "inbook" =\r
+  or\r
+    'author.editor.key.label\r
+    { type$ "proceedings" =\r
+        'editor.key.label\r
+        'author.key.label\r
+      if$\r
+    }\r
+  if$\r
+  "("\r
+  *\r
+  year duplicate$ empty$\r
+     { pop$ "????" }\r
+     { purify$ #-1 #4 substring$ }\r
+  if$\r
+  *\r
+  'label :=\r
+}\r
+\r
+FUNCTION {sort.format.names}\r
+{ 's :=\r
+  #1 'nameptr :=\r
+  ""\r
+  s num.names$ 'numnames :=\r
+  numnames 'namesleft :=\r
+    { namesleft #0 > }\r
+    { nameptr #1 >\r
+        { "   " * }\r
+        'skip$\r
+      if$\r
+      s nameptr\r
+      "{vv{ } }{ll{ }}{  f{ }}{  jj{ }}"\r
+      format.name$ 't :=\r
+      nameptr numnames = t "others" = and\r
+        { "et al" * }\r
+        { numnames #2 > nameptr #2 = and\r
+          { "zzzzzz" * #1 'namesleft := }\r
+          { t sortify * }\r
+        if$\r
+        }\r
+      if$\r
+      nameptr #1 + 'nameptr :=\r
+      namesleft #1 - 'namesleft :=\r
+    }\r
+  while$\r
+}\r
+\r
+FUNCTION {sort.format.title}\r
+{ 't :=\r
+  "A " #2\r
+    "An " #3\r
+      "The " #4 t chop.word\r
+    chop.word\r
+  chop.word\r
+  sortify\r
+  #1 global.max$ substring$\r
+}\r
+\r
+FUNCTION {author.sort}\r
+{ author empty$\r
+    { key empty$\r
+        { "to sort, need author or key in " cite$ * warning$\r
+          ""\r
+        }\r
+        { key sortify }\r
+      if$\r
+    }\r
+    { author sort.format.names }\r
+  if$\r
+}\r
+\r
+FUNCTION {author.editor.sort}\r
+{ author empty$\r
+    { editor empty$\r
+        { key empty$\r
+            { "to sort, need author, editor, or key in " cite$ * warning$\r
+              ""\r
+            }\r
+            { key sortify }\r
+          if$\r
+        }\r
+        { editor sort.format.names }\r
+      if$\r
+    }\r
+    { author sort.format.names }\r
+  if$\r
+}\r
+\r
+FUNCTION {editor.sort}\r
+{ editor empty$\r
+    { key empty$\r
+        { "to sort, need editor or key in " cite$ * warning$\r
+          ""\r
+        }\r
+        { key sortify }\r
+      if$\r
+    }\r
+    { editor sort.format.names }\r
+  if$\r
+}\r
+\r
+FUNCTION {presort}\r
+{ calc.label\r
+  label sortify\r
+  "    "\r
+  *\r
+  type$ "book" =\r
+  type$ "inbook" =\r
+  or\r
+    'author.editor.sort\r
+    { type$ "proceedings" =\r
+        'editor.sort\r
+        'author.sort\r
+      if$\r
+    }\r
+  if$\r
+  #1 entry.max$ substring$\r
+  'sort.label :=\r
+  sort.label\r
+  *\r
+  "    "\r
+  *\r
+  title field.or.null\r
+  sort.format.title\r
+  *\r
+  #1 entry.max$ substring$\r
+  'sort.key$ :=\r
+}\r
+\r
+ITERATE {presort}\r
+\r
+SORT\r
+\r
+STRINGS { last.label next.extra }\r
+\r
+INTEGERS { last.extra.num }\r
+\r
+FUNCTION {initialize.extra.label.stuff}\r
+{ #0 int.to.chr$ 'last.label :=\r
+  "" 'next.extra :=\r
+  #0 'last.extra.num :=\r
+}\r
+\r
+FUNCTION {forward.pass}\r
+{ last.label label =\r
+    { last.extra.num #1 + 'last.extra.num :=\r
+      last.extra.num int.to.chr$ 'extra.label :=\r
+    }\r
+    { "a" chr.to.int$ 'last.extra.num :=\r
+      "" 'extra.label :=\r
+      label 'last.label :=\r
+    }\r
+  if$\r
+}\r
+\r
+FUNCTION {reverse.pass}\r
+{ next.extra "b" =\r
+    { "a" 'extra.label := }\r
+    'skip$\r
+  if$\r
+  extra.label 'next.extra :=\r
+  label extra.label * 'label :=\r
+}\r
+\r
+EXECUTE {initialize.extra.label.stuff}\r
+\r
+ITERATE {forward.pass}\r
+\r
+REVERSE {reverse.pass}\r
+\r
+FUNCTION {bib.sort.order}\r
+{ sort.label\r
+  "    "\r
+  *\r
+  year field.or.null sortify\r
+  *\r
+  "    "\r
+  *\r
+  title field.or.null\r
+  sort.format.title\r
+  *\r
+  #1 entry.max$ substring$\r
+  'sort.key$ :=\r
+}\r
+\r
+ITERATE {bib.sort.order}\r
+\r
+SORT\r
+\r
+FUNCTION {begin.bib}\r
+{ preamble$ empty$\r
+    'skip$\r
+    { preamble$ write$ newline$ }\r
+  if$\r
+  "\begin{thebibliography}{}" write$ newline$\r
+}\r
+\r
+EXECUTE {begin.bib}\r
+\r
+EXECUTE {init.state.consts}\r
+\r
+ITERATE {call.type$}\r
+\r
+FUNCTION {end.bib}\r
+{ newline$\r
+  "\end{thebibliography}" write$ newline$\r
+}\r
+\r
+EXECUTE {end.bib}\r
+%% End of customized bst file \r
+\r
diff --git a/natbib.sty b/natbib.sty
new file mode 100644 (file)
index 0000000..4c8c948
--- /dev/null
@@ -0,0 +1,803 @@
+%%\r
+%% This is file `natbib.sty',\r
+%% generated with the docstrip utility.\r
+%%\r
+%% The original source files were:\r
+%%\r
+%% natbib.dtx  (with options: `package,all')\r
+%% =============================================\r
+%% IMPORTANT NOTICE:\r
+%% \r
+%% This program can be redistributed and/or modified under the terms\r
+%% of the LaTeX Project Public License Distributed from CTAN\r
+%% archives in directory macros/latex/base/lppl.txt; either\r
+%% version 1 of the License, or any later version.\r
+%% \r
+%% This is a generated file.\r
+%% It may not be distributed without the original source file natbib.dtx.\r
+%% \r
+%% Full documentation can be obtained by LaTeXing that original file.\r
+%% Only a few abbreviated comments remain here to describe the usage.\r
+%% =============================================\r
+%% Copyright 1993-2000 Patrick W Daly\r
+%% Max-Planck-Institut f\"ur Aeronomie\r
+%% Max-Planck-Str. 2\r
+%% D-37191 Katlenburg-Lindau\r
+%% Germany\r
+%% E-mail: daly@linmpi.mpg.de\r
+\NeedsTeXFormat{LaTeX2e}[1995/06/01]\r
+\ProvidesPackage{natbib}\r
+        [2000/07/24 7.0a (PWD)]\r
+ % This package reimplements the LaTeX \cite command to be used for various\r
+ % citation styles, both author-year and numerical. It accepts BibTeX\r
+ % output intended for many other packages, and therefore acts as a\r
+ % general, all-purpose citation-style interface.\r
+ %\r
+ % With standard numerical .bst files, only numerical citations are\r
+ % possible. With an author-year .bst file, both numerical and\r
+ % author-year citations are possible.\r
+ %\r
+ % If author-year citations are selected, \bibitem must have one of the\r
+ %   following forms:\r
+ %   \bibitem[Jones et al.(1990)]{key}...\r
+ %   \bibitem[Jones et al.(1990)Jones, Baker, and Williams]{key}...\r
+ %   \bibitem[Jones et al., 1990]{key}...\r
+ %   \bibitem[\protect\citeauthoryear{Jones, Baker, and Williams}{Jones\r
+ %       et al.}{1990}]{key}...\r
+ %   \bibitem[\protect\citeauthoryear{Jones et al.}{1990}]{key}...\r
+ %   \bibitem[\protect\astroncite{Jones et al.}{1990}]{key}...\r
+ %   \bibitem[\protect\citename{Jones et al., }1990]{key}...\r
+ %   \harvarditem[Jones et al.]{Jones, Baker, and Williams}{1990}{key}...\r
+ %\r
+ % This is either to be made up manually, or to be generated by an\r
+ % appropriate .bst file with BibTeX.\r
+ %                            Author-year mode     ||   Numerical mode\r
+ % Then, \citet{key}  ==>>  Jones et al. (1990)    ||   Jones et al. [21]\r
+ %       \citep{key}  ==>> (Jones et al., 1990)    ||   [21]\r
+ % Multiple citations as normal:\r
+ % \citep{key1,key2}  ==>> (Jones et al., 1990; Smith, 1989) || [21,24]\r
+ %                           or  (Jones et al., 1990, 1991)  || [21,24]\r
+ %                           or  (Jones et al., 1990a,b)     || [21,24]\r
+ % \cite{key} is the equivalent of \citet{key} in author-year mode\r
+ %                         and  of \citep{key} in numerical mode\r
+ % Full author lists may be forced with \citet* or \citep*, e.g.\r
+ %       \citep*{key}      ==>> (Jones, Baker, and Williams, 1990)\r
+ % Optional notes as:\r
+ %   \citep[chap. 2]{key}    ==>> (Jones et al., 1990, chap. 2)\r
+ %   \citep[e.g.,][]{key}    ==>> (e.g., Jones et al., 1990)\r
+ %   \citep[see][pg. 34]{key}==>> (see Jones et al., 1990, pg. 34)\r
+ %  (Note: in standard LaTeX, only one note is allowed, after the ref.\r
+ %   Here, one note is like the standard, two make pre- and post-notes.)\r
+ %   \citealt{key}          ==>> Jones et al. 1990\r
+ %   \citealt*{key}         ==>> Jones, Baker, and Williams 1990\r
+ %   \citealp{key}          ==>> Jones et al., 1990\r
+ %   \citealp*{key}         ==>> Jones, Baker, and Williams, 1990\r
+ % Additional citation possibilities (both author-year and numerical modes)\r
+ %   \citeauthor{key}       ==>> Jones et al.\r
+ %   \citeauthor*{key}      ==>> Jones, Baker, and Williams\r
+ %   \citeyear{key}         ==>> 1990\r
+ %   \citeyearpar{key}      ==>> (1990)\r
+ %   \citetext{priv. comm.} ==>> (priv. comm.)\r
+ % Note: full author lists depends on whether the bib style supports them;\r
+ %       if not, the abbreviated list is printed even when full requested.\r
+ %\r
+ % For names like della Robbia at the start of a sentence, use\r
+ %   \Citet{dRob98}         ==>> Della Robbia (1998)\r
+ %   \Citep{dRob98}         ==>> (Della Robbia, 1998)\r
+ %   \Citeauthor{dRob98}    ==>> Della Robbia\r
+ %\r
+ %\r
+ % Citation aliasing is achieved with\r
+ %   \defcitealias{key}{text}\r
+ %   \citetalias{key}  ==>> text\r
+ %   \citepalias{key}  ==>> (text)\r
+ %\r
+ % Defining the citation style of a given bib style:\r
+ % Use \bibpunct (in the preamble only) with 6 mandatory arguments:\r
+ %    1. opening bracket for citation\r
+ %    2. closing bracket\r
+ %    3. citation separator (for multiple citations in one \cite)\r
+ %    4. the letter n for numerical styles, s for superscripts\r
+ %        else anything for author-year\r
+ %    5. punctuation between authors and date\r
+ %    6. punctuation between years (or numbers) when common authors missing\r
+ % One optional argument is the character coming before post-notes. It\r
+ %   appears in square braces before all other arguments. May be left off.\r
+ % Example (and default) \bibpunct[, ]{(}{)}{;}{a}{,}{,}\r
+ %\r
+ % To make this automatic for a given bib style, named newbib, say, make\r
+ % a local configuration file, natbib.cfg, with the definition\r
+ %   \newcommand{\bibstyle@newbib}{\bibpunct...}\r
+ % Then the \bibliographystyle{newbib} will cause \bibstyle@newbib to\r
+ % be called on THE NEXT LATEX RUN (via the aux file).\r
+ %\r
+ % Such preprogrammed definitions may be invoked in the text (preamble only)\r
+ %  by calling \citestyle{newbib}. This is only useful if the style specified\r
+ %  differs from that in \bibliographystyle.\r
+ %\r
+ % With \citeindextrue and \citeindexfalse, one can control whether the\r
+ % \cite commands make an automatic entry of the citation in the .idx\r
+ % indexing file. For this, \makeindex must also be given in the preamble.\r
+ %\r
+ % LaTeX2e Options: (for selecting punctuation)\r
+ %   round  -  round parentheses are used (default)\r
+ %   square -  square brackets are used   [option]\r
+ %   curly  -  curly braces are used      {option}\r
+ %   angle  -  angle brackets are used    <option>\r
+ %   colon  -  multiple citations separated by colon (default)\r
+ %   comma  -  separated by comma\r
+ %   authoryear - selects author-year citations (default)\r
+ %   numbers-  selects numerical citations\r
+ %   super  -  numerical citations as superscripts\r
+ %   sort   -  sorts multiple citations according to order in ref. list\r
+ %   sort&compress   -  like sort, but also compresses numerical citations\r
+ %   longnamesfirst  -  makes first citation full author list\r
+ %   sectionbib - puts bibliography in a \section* instead of \chapter*\r
+ % Punctuation so selected dominates over any predefined ones.\r
+ % LaTeX2e options are called as, e.g.\r
+ %        \usepackage[square,comma]{natbib}\r
+ % LaTeX the source file natbib.dtx to obtain more details\r
+ % or the file natnotes.tex for a brief reference sheet.\r
+ %-----------------------------------------------------------\r
+\@ifclassloaded{aguplus}{\PackageError{natbib}\r
+  {The aguplus class already includes natbib coding,\MessageBreak\r
+   so you should not add it explicitly}\r
+  {Type <Return> for now, but then later remove\MessageBreak\r
+   the command \protect\usepackage{natbib} from the document}\r
+  \endinput}{}\r
+\@ifclassloaded{nlinproc}{\PackageError{natbib}\r
+  {The nlinproc class already includes natbib coding,\MessageBreak\r
+   so you should not add it explicitly}\r
+  {Type <Return> for now, but then later remove\MessageBreak\r
+   the command \protect\usepackage{natbib} from the document}\r
+  \endinput}{}\r
+\@ifclassloaded{egs}{\PackageError{natbib}\r
+  {The egs class already includes natbib coding,\MessageBreak\r
+   so you should not add it explicitly}\r
+  {Type <Return> for now, but then later remove\MessageBreak\r
+   the command \protect\usepackage{natbib} from the document}\r
+  \endinput}{}\r
+ % Define citation punctuation for some author-year styles\r
+ % One may add and delete at this point\r
+ % Or put additions into local configuration file natbib.cfg\r
+\newcommand\bibstyle@chicago{\bibpunct{(}{)}{;}{a}{,}{,}}\r
+\newcommand\bibstyle@named{\bibpunct{[}{]}{;}{a}{,}{,}}\r
+\newcommand\bibstyle@agu{\bibpunct{[}{]}{;}{a}{,}{,~}}%Amer. Geophys. Union\r
+\newcommand\bibstyle@egs{\bibpunct{(}{)}{;}{a}{,}{,}}%Eur. Geophys. Soc.\r
+\newcommand\bibstyle@agsm{\bibpunct{(}{)}{,}{a}{}{,}\gdef\harvardand{\&}}\r
+\newcommand\bibstyle@kluwer{\bibpunct{(}{)}{,}{a}{}{,}\gdef\harvardand{\&}}\r
+\newcommand\bibstyle@dcu{\bibpunct{(}{)}{;}{a}{;}{,}\gdef\harvardand{and}}\r
+\newcommand\bibstyle@aa{\bibpunct{(}{)}{;}{a}{}{,}} %Astronomy & Astrophysics\r
+\newcommand\bibstyle@pass{\bibpunct{(}{)}{;}{a}{,}{,}}%Planet. & Space Sci\r
+\newcommand\bibstyle@anngeo{\bibpunct{(}{)}{;}{a}{,}{,}}%Annales Geophysicae\r
+\newcommand\bibstyle@nlinproc{\bibpunct{(}{)}{;}{a}{,}{,}}%Nonlin.Proc.Geophys.\r
+ % Define citation punctuation for some numerical styles\r
+\newcommand\bibstyle@cospar{\bibpunct{/}{/}{,}{n}{}{}%\r
+     \gdef\NAT@biblabelnum##1{##1.}}\r
+\newcommand\bibstyle@esa{\bibpunct{(Ref.~}{)}{,}{n}{}{}%\r
+     \gdef\NAT@biblabelnum##1{##1.\hspace{1em}}}\r
+\newcommand\bibstyle@nature{\bibpunct{}{}{,}{s}{}{\textsuperscript{,}}%\r
+     \gdef\NAT@biblabelnum##1{##1.}}\r
+ % The standard LaTeX styles\r
+\newcommand\bibstyle@plain{\bibpunct{[}{]}{,}{n}{}{,}}\r
+\let\bibstyle@alpha=\bibstyle@plain\r
+\let\bibstyle@abbrv=\bibstyle@plain\r
+\let\bibstyle@unsrt=\bibstyle@plain\r
+ % The author-year modifications of the standard styles\r
+\newcommand\bibstyle@plainnat{\bibpunct{[}{]}{,}{a}{,}{,}}\r
+\let\bibstyle@abbrvnat=\bibstyle@plainnat\r
+\let\bibstyle@unsrtnat=\bibstyle@plainnat\r
+\newif\ifNAT@numbers \NAT@numbersfalse\r
+\newif\ifNAT@super \NAT@superfalse\r
+\DeclareOption{numbers}{\NAT@numberstrue\r
+   \ExecuteOptions{square,comma,nobibstyle}}\r
+\DeclareOption{super}{\NAT@supertrue\NAT@numberstrue\r
+   \renewcommand\NAT@open{}\renewcommand\NAT@close{}\r
+   \ExecuteOptions{nobibstyle}}\r
+\DeclareOption{authoryear}{\NAT@numbersfalse\r
+   \ExecuteOptions{round,colon,bibstyle}}\r
+\DeclareOption{round}{%\r
+      \renewcommand\NAT@open{(} \renewcommand\NAT@close{)}\r
+   \ExecuteOptions{nobibstyle}}\r
+\DeclareOption{square}{%\r
+      \renewcommand\NAT@open{[} \renewcommand\NAT@close{]}\r
+   \ExecuteOptions{nobibstyle}}\r
+\DeclareOption{angle}{%\r
+      \renewcommand\NAT@open{$<$} \renewcommand\NAT@close{$>$}\r
+   \ExecuteOptions{nobibstyle}}\r
+\DeclareOption{curly}{%\r
+      \renewcommand\NAT@open{\{} \renewcommand\NAT@close{\}}\r
+   \ExecuteOptions{nobibstyle}}\r
+\DeclareOption{comma}{\renewcommand\NAT@sep{,}\r
+   \ExecuteOptions{nobibstyle}}\r
+\DeclareOption{colon}{\renewcommand\NAT@sep{;}\r
+   \ExecuteOptions{nobibstyle}}\r
+\DeclareOption{nobibstyle}{\let\bibstyle=\@gobble}\r
+\DeclareOption{bibstyle}{\let\bibstyle=\@citestyle}\r
+\newif\ifNAT@openbib \NAT@openbibfalse\r
+\DeclareOption{openbib}{\NAT@openbibtrue}\r
+\DeclareOption{sectionbib}{\def\NAT@sectionbib{on}}\r
+\def\NAT@sort{0}\r
+\DeclareOption{sort}{\def\NAT@sort{1}}\r
+\DeclareOption{sort&compress}{\def\NAT@sort{2}}\r
+\@ifpackageloaded{cite}{\PackageWarningNoLine{natbib}\r
+  {The `cite' package should not be used\MessageBreak\r
+   with natbib. Use option `sort' instead}\ExecuteOptions{sort}}{}\r
+\newif\ifNAT@longnames\NAT@longnamesfalse\r
+\DeclareOption{longnamesfirst}{\NAT@longnamestrue}\r
+\DeclareOption{nonamebreak}{\def\NAT@nmfmt#1{\mbox{\NAT@up#1}}}\r
+\def\NAT@nmfmt#1{{\NAT@up#1}}\r
+\renewcommand\bibstyle[1]{\@ifundefined{bibstyle@#1}{\relax}\r
+     {\csname bibstyle@#1\endcsname}}\r
+\AtBeginDocument{\global\let\bibstyle=\@gobble}\r
+\let\@citestyle\bibstyle\r
+\newcommand\citestyle[1]{\@citestyle{#1}\let\bibstyle\@gobble}\r
+\@onlypreamble{\citestyle}\@onlypreamble{\@citestyle}\r
+\newcommand\bibpunct[7][, ]%\r
+  {\gdef\NAT@open{#2}\gdef\NAT@close{#3}\gdef\r
+   \NAT@sep{#4}\global\NAT@numbersfalse\ifx #5n\global\NAT@numberstrue\r
+   \else\r
+   \ifx #5s\global\NAT@numberstrue\global\NAT@supertrue\r
+   \fi\fi\r
+   \gdef\NAT@aysep{#6}\gdef\NAT@yrsep{#7}%\r
+   \gdef\NAT@cmt{#1}%\r
+   \global\let\bibstyle\@gobble\r
+  }\r
+\@onlypreamble{\bibpunct}\r
+\newcommand\NAT@open{(} \newcommand\NAT@close{)}\r
+\newcommand\NAT@sep{;}\r
+\ProcessOptions\r
+\newcommand\NAT@aysep{,} \newcommand\NAT@yrsep{,}\r
+\newcommand\NAT@cmt{, }\r
+\newcommand\NAT@cite%\r
+    [3]{\ifNAT@swa\NAT@@open\if*#2*\else#2\ \fi\r
+        #1\if*#3*\else\NAT@cmt#3\fi\NAT@@close\else#1\fi\endgroup}\r
+\newcommand\NAT@citenum%\r
+    [3]{\ifNAT@swa\NAT@@open\if*#2*\else#2\ \fi\r
+        #1\if*#3*\else\NAT@cmt#3\fi\NAT@@close\else#1\fi\endgroup}\r
+\newcommand\NAT@citesuper[3]{\ifNAT@swa\r
+\unskip\hspace{1\p@}\textsuperscript{#1}%\r
+   \if*#3*\else\ (#3)\fi\else #1\fi\endgroup}\r
+\providecommand\r
+  \textsuperscript[1]{\mbox{$^{\mbox{\scriptsize#1}}$}}\r
+\providecommand\@firstofone[1]{#1}\r
+\newcommand\NAT@citexnum{}\r
+\def\NAT@citexnum[#1][#2]#3{%\r
+ \NAT@sort@cites{#3}%\r
+ \let\@citea\@empty\r
+  \@cite{\def\NAT@num{-1}\let\NAT@last@yr\relax\let\NAT@nm\@empty\r
+    \@for\@citeb:=\NAT@cite@list\do\r
+    {\edef\@citeb{\expandafter\@firstofone\@citeb}%\r
+     \if@filesw\immediate\write\@auxout{\string\citation{\@citeb}}\fi\r
+     \@ifundefined{b@\@citeb\@extra@b@citeb}{%\r
+       {\reset@font\bfseries?}\r
+        \NAT@citeundefined\PackageWarning{natbib}%\r
+       {Citation `\@citeb' on page \thepage \space undefined}}%\r
+     {\let\NAT@last@num\NAT@num\let\NAT@last@nm\NAT@nm\r
+      \NAT@parse{\@citeb}%\r
+      \ifNAT@longnames\@ifundefined{bv@\@citeb\@extra@b@citeb}{%\r
+        \let\NAT@name=\NAT@all@names\r
+        \global\@namedef{bv@\@citeb\@extra@b@citeb}{}}{}%\r
+      \fi\r
+      \ifNAT@full\let\NAT@nm\NAT@all@names\else\r
+        \let\NAT@nm\NAT@name\fi\r
+      \ifNAT@swa\r
+       \ifnum\NAT@ctype>1\relax\@citea\r
+        \hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+            \ifnum\NAT@ctype=2\relax\NAT@test{\NAT@ctype}%\r
+            \else\NAT@alias\r
+            \fi\hyper@natlinkend\else\r
+       \ifnum\NAT@sort>1\r
+         \begingroup\catcode`\_=8\r
+            \ifcat _\ifnum\z@<0\NAT@num _\else A\fi\r
+              \global\let\NAT@nm=\NAT@num \else \gdef\NAT@nm{-2}\fi\r
+            \ifcat _\ifnum\z@<0\NAT@last@num _\else A\fi\r
+              \global\@tempcnta=\NAT@last@num \global\advance\@tempcnta by\@ne\r
+              \else \global\@tempcnta\m@ne\fi\r
+         \endgroup\r
+         \ifnum\NAT@nm=\@tempcnta\r
+           \ifx\NAT@last@yr\relax\r
+             \edef\NAT@last@yr{\@citea \mbox{\noexpand\citenumfont{\NAT@num}}}%\r
+           \else\r
+             \edef\NAT@last@yr{--\penalty\@m\mbox{\noexpand\citenumfont{\NAT@num}}}%\r
+           \fi\r
+         \else\r
+           \NAT@last@yr \@citea \mbox{\citenumfont{\NAT@num}}%\r
+           \let\NAT@last@yr\relax\r
+         \fi\r
+       \else\r
+         \@citea \mbox{\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+           {\citenumfont{\NAT@num}}\hyper@natlinkend}%\r
+       \fi\r
+       \fi\r
+       \def\@citea{\NAT@sep\penalty\@m\NAT@space}%\r
+      \else\r
+        \ifcase\NAT@ctype\relax\r
+          \ifx\NAT@last@nm\NAT@nm \NAT@yrsep\penalty\@m\NAT@space\else\r
+          \@citea \NAT@test{1}\ \NAT@@open\r
+          \if*#1*\else#1\ \fi\fi \NAT@mbox{%\r
+          \hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+          {\citenumfont{\NAT@num}}\hyper@natlinkend}%\r
+          \def\@citea{\NAT@@close\NAT@sep\penalty\@m\ }%\r
+        \or\@citea\r
+          \hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+           \NAT@test{\NAT@ctype}\hyper@natlinkend\r
+          \def\@citea{\NAT@sep\penalty\@m\ }%\r
+        \or\@citea\r
+          \hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+           \NAT@test{\NAT@ctype}\hyper@natlinkend\r
+          \def\@citea{\NAT@sep\penalty\@m\ }%\r
+        \or\@citea\r
+          \hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+           \NAT@alias\hyper@natlinkend\r
+          \def\@citea{\NAT@sep\penalty\@m\ }%\r
+        \fi\r
+      \fi\r
+      }}%\r
+      \ifnum\NAT@sort>1\relax\NAT@last@yr\fi\r
+      \ifNAT@swa\else\ifnum\NAT@ctype=0\if*#2*\else\r
+      \NAT@cmt#2\fi \NAT@@close\fi\fi}{#1}{#2}}\r
+\newcommand\NAT@test[1]{\ifnum#1=1 \ifx\NAT@nm\NAT@noname\r
+  {\reset@font\bfseries(author?)}\PackageWarning{natbib}\r
+  {Author undefined for citation`\@citeb'\r
+   \MessageBreak\r
+   on page \thepage}\else \NAT@nm \fi\r
+  \else \if\relax\NAT@date\relax\r
+  {\reset@font\bfseries(year?)}\PackageWarning{natbib}\r
+  {Year undefined for citation`\@citeb'\r
+   \MessageBreak\r
+   on page \thepage}\else \NAT@date \fi \fi}\r
+\let\citenumfont=\relax\r
+\newcommand\NAT@citex{}\r
+\def\NAT@citex%\r
+  [#1][#2]#3{%\r
+  \NAT@sort@cites{#3}%\r
+  \let\@citea\@empty\r
+  \@cite{\let\NAT@nm\@empty\let\NAT@year\@empty\r
+    \@for\@citeb:=\NAT@cite@list\do\r
+    {\edef\@citeb{\expandafter\@firstofone\@citeb}%\r
+     \if@filesw\immediate\write\@auxout{\string\citation{\@citeb}}\fi\r
+     \@ifundefined{b@\@citeb\@extra@b@citeb}{\@citea%\r
+       {\reset@font\bfseries ?}\NAT@citeundefined\r
+                 \PackageWarning{natbib}%\r
+       {Citation `\@citeb' on page \thepage \space undefined}\def\NAT@date{}}%\r
+     {\let\NAT@last@nm=\NAT@nm\let\NAT@last@yr=\NAT@year\r
+     \NAT@parse{\@citeb}%\r
+      \ifNAT@longnames\@ifundefined{bv@\@citeb\@extra@b@citeb}{%\r
+        \let\NAT@name=\NAT@all@names\r
+        \global\@namedef{bv@\@citeb\@extra@b@citeb}{}}{}%\r
+      \fi\r
+     \ifNAT@full\let\NAT@nm\NAT@all@names\else\r
+       \let\NAT@nm\NAT@name\fi\r
+     \ifNAT@swa\ifcase\NAT@ctype\r
+       \if\relax\NAT@date\relax\r
+         \@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+         \NAT@nmfmt{\NAT@nm}\NAT@date\hyper@natlinkend\r
+       \else\r
+         \ifx\NAT@last@nm\NAT@nm\NAT@yrsep\r
+            \ifx\NAT@last@yr\NAT@year\r
+              \hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@exlab\r
+              \hyper@natlinkend\r
+            \else\unskip\\r
+              \hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@date\r
+              \hyper@natlinkend\r
+            \fi\r
+         \else\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+           \NAT@nmfmt{\NAT@nm}%\r
+           \hyper@natlinkbreak{\NAT@aysep\ }{\@citeb\@extra@b@citeb}%\r
+           \NAT@date\hyper@natlinkend\r
+         \fi\r
+       \fi\r
+     \or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+         \NAT@nmfmt{\NAT@nm}\hyper@natlinkend\r
+     \or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+         \NAT@date\hyper@natlinkend\r
+     \or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+         \NAT@alias\hyper@natlinkend\r
+     \fi \def\@citea{\NAT@sep\ }%\r
+     \else\ifcase\NAT@ctype\r
+        \if\relax\NAT@date\relax\r
+          \@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+          \NAT@nmfmt{\NAT@nm}\hyper@natlinkend\r
+        \else\r
+         \ifx\NAT@last@nm\NAT@nm\NAT@yrsep\r
+            \ifx\NAT@last@yr\NAT@year\r
+              \hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@exlab\r
+              \hyper@natlinkend\r
+            \else\unskip\\r
+              \hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@date\r
+              \hyper@natlinkend\r
+            \fi\r
+         \else\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+           \NAT@nmfmt{\NAT@nm}%\r
+           \hyper@natlinkbreak{\ \NAT@@open\if*#1*\else#1\ \fi}%\r
+              {\@citeb\@extra@b@citeb}%\r
+           \NAT@date\hyper@natlinkend\fi\r
+        \fi\r
+       \or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+         \NAT@nmfmt{\NAT@nm}\hyper@natlinkend\r
+       \or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+         \NAT@date\hyper@natlinkend\r
+       \or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%\r
+         \NAT@alias\hyper@natlinkend\r
+       \fi \if\relax\NAT@date\relax\def\@citea{\NAT@sep\ }%\r
+           \else\def\@citea{\NAT@@close\NAT@sep\ }\fi\r
+     \fi\r
+     }}\ifNAT@swa\else\if*#2*\else\NAT@cmt#2\fi\r
+     \if\relax\NAT@date\relax\else\NAT@@close\fi\fi}{#1}{#2}}\r
+\newif\ifNAT@par \NAT@partrue\r
+\newcommand\NAT@@open{\ifNAT@par\NAT@open\fi}\r
+\newcommand\NAT@@close{\ifNAT@par\NAT@close\fi}\r
+\newcommand\NAT@alias{\@ifundefined{al@\@citeb\@extra@b@citeb}{%\r
+  {\reset@font\bfseries(alias?)}\PackageWarning{natbib}\r
+  {Alias undefined for citation `\@citeb'\r
+  \MessageBreak on page \thepage}}{\@nameuse{al@\@citeb\@extra@b@citeb}}}\r
+\let\NAT@up\relax\r
+\newcommand\NAT@Up[1]{{\let\protect\@unexpandable@protect\let~\relax\r
+  \expandafter\NAT@deftemp#1}\expandafter\NAT@UP\NAT@temp}\r
+\newcommand\NAT@deftemp[1]{\xdef\NAT@temp{#1}}\r
+\newcommand\NAT@UP[1]{\let\@tempa\NAT@UP\ifcat a#1\MakeUppercase{#1}%\r
+  \let\@tempa\relax\else#1\fi\@tempa}\r
+\newcommand\shortcites[1]{%\r
+  \@bsphack\@for\@citeb:=#1\do\r
+  {\edef\@citeb{\expandafter\@firstofone\@citeb}%\r
+   \global\@namedef{bv@\@citeb\@extra@b@citeb}{}}\@esphack}\r
+\newcommand\NAT@biblabel[1]{\hfill}\r
+\newcommand\NAT@biblabelnum[1]{\bibnumfmt{#1}}\r
+\newcommand\bibnumfmt[1]{[#1]}\r
+\def\@tempa#1{[#1]}\r
+\ifx\@tempa\@biblabel\let\@biblabel\@empty\fi\r
+\newcommand\NAT@bibsetnum[1]{\settowidth\labelwidth{\@biblabel{#1}}%\r
+   \setlength{\leftmargin}{\labelwidth}\addtolength{\leftmargin}{\labelsep}%\r
+   \setlength{\itemsep}{\bibsep}\setlength{\parsep}{\z@}%\r
+   \ifNAT@openbib\r
+     \addtolength{\leftmargin}{4mm}%\r
+     \setlength{\itemindent}{-4mm}%\r
+     \setlength{\listparindent}{\itemindent}%\r
+     \setlength{\parsep}{0pt}%\r
+   \fi\r
+}\r
+\newlength{\bibhang}\r
+\setlength{\bibhang}{1em}\r
+\newlength{\bibsep}\r
+{\@listi \global\bibsep\itemsep \global\advance\bibsep by\parsep}\r
+\r
+\newcommand\NAT@bibsetup%\r
+   [1]{\setlength{\leftmargin}{\bibhang}\setlength{\itemindent}{-\leftmargin}%\r
+       \setlength{\itemsep}{\bibsep}\setlength{\parsep}{\z@}}\r
+\newcommand\NAT@set@cites{\ifNAT@numbers\r
+  \ifNAT@super \let\@cite\NAT@citesuper\r
+     \def\NAT@mbox##1{\unskip\nobreak\hspace{1\p@}\textsuperscript{##1}}%\r
+     \let\citeyearpar=\citeyear\r
+     \let\NAT@space\relax\else\r
+     \let\NAT@mbox=\mbox\r
+     \let\@cite\NAT@citenum \def\NAT@space{ }\fi\r
+  \let\@citex\NAT@citexnum\r
+  \ifx\@biblabel\@empty\let\@biblabel\NAT@biblabelnum\fi\r
+  \let\@bibsetup\NAT@bibsetnum\r
+  \def\natexlab##1{}%\r
+ \else\r
+  \let\@cite\NAT@cite\r
+  \let\@citex\NAT@citex\r
+  \let\@biblabel\NAT@biblabel\r
+  \let\@bibsetup\NAT@bibsetup\r
+  \def\natexlab##1{##1}%\r
+ \fi}\r
+\AtBeginDocument{\NAT@set@cites}\r
+\AtBeginDocument{\ifx\SK@def\@undefined\else\r
+\ifx\SK@cite\@empty\else\r
+  \SK@def\@citex[#1][#2]#3{\SK@\SK@@ref{#3}\SK@@citex[#1][#2]{#3}}\fi\r
+\ifx\SK@citeauthor\@undefined\def\HAR@checkdef{}\else\r
+  \let\citeauthor\SK@citeauthor\r
+  \let\citefullauthor\SK@citefullauthor\r
+  \let\citeyear\SK@citeyear\fi\r
+\fi}\r
+\AtBeginDocument{\@ifpackageloaded{hyperref}{%\r
+  \ifnum\NAT@sort=2\def\NAT@sort{1}\fi}{}}\r
+\newif\ifNAT@full\NAT@fullfalse\r
+\newif\ifNAT@swa\r
+\DeclareRobustCommand\citet\r
+   {\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@partrue\r
+     \@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}\r
+\newcommand\NAT@citetp{\@ifnextchar[{\NAT@@citetp}{\NAT@@citetp[]}}\r
+\newcommand\NAT@@citetp{}\r
+\def\NAT@@citetp[#1]{\@ifnextchar[{\@citex[#1]}{\@citex[][#1]}}\r
+\DeclareRobustCommand\citep\r
+   {\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@partrue\r
+         \@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}\r
+\DeclareRobustCommand\cite\r
+    {\begingroup\def\NAT@ctype{0}\NAT@partrue\NAT@swatrue\r
+      \@ifstar{\NAT@fulltrue\NAT@cites}{\NAT@fullfalse\NAT@cites}}\r
+\newcommand\NAT@cites{\@ifnextchar [{\NAT@@citetp}{%\r
+     \ifNAT@numbers\else\r
+     \NAT@swafalse\r
+     \fi\r
+    \NAT@@citetp[]}}\r
+\DeclareRobustCommand\citealt\r
+   {\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@parfalse\r
+         \@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}\r
+\DeclareRobustCommand\citealp\r
+   {\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@parfalse\r
+         \@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}\r
+\DeclareRobustCommand\citeauthor\r
+   {\begingroup\NAT@swafalse\def\NAT@ctype{1}\NAT@parfalse\r
+    \@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}\r
+\DeclareRobustCommand\Citet\r
+   {\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@partrue\r
+     \let\NAT@up\NAT@Up\r
+     \@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}\r
+\DeclareRobustCommand\Citep\r
+   {\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@partrue\r
+     \let\NAT@up\NAT@Up\r
+         \@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}\r
+\DeclareRobustCommand\Citealt\r
+   {\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@parfalse\r
+     \let\NAT@up\NAT@Up\r
+         \@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}\r
+\DeclareRobustCommand\Citealp\r
+   {\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@parfalse\r
+     \let\NAT@up\NAT@Up\r
+         \@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}\r
+\DeclareRobustCommand\Citeauthor\r
+   {\begingroup\NAT@swafalse\def\NAT@ctype{1}\NAT@parfalse\r
+     \let\NAT@up\NAT@Up\r
+    \@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}\r
+\DeclareRobustCommand\citeyear\r
+   {\begingroup\NAT@swafalse\def\NAT@ctype{2}\NAT@parfalse\NAT@citetp}\r
+\DeclareRobustCommand\citeyearpar\r
+   {\begingroup\NAT@swatrue\def\NAT@ctype{2}\NAT@partrue\NAT@citetp}\r
+\newcommand\citetext[1]{\NAT@open#1\NAT@close}\r
+\DeclareRobustCommand\citefullauthor\r
+   {\citeauthor*}\r
+\newcommand\defcitealias[2]{%\r
+   \@ifundefined{al@#1\@extra@b@citeb}{}\r
+   {\PackageWarning{natbib}{Overwriting existing alias for citation #1}}\r
+   \@namedef{al@#1\@extra@b@citeb}{#2}}\r
+\DeclareRobustCommand\citetalias{\begingroup\r
+   \NAT@swafalse\def\NAT@ctype{3}\NAT@parfalse\NAT@citetp}\r
+\DeclareRobustCommand\citepalias{\begingroup\r
+   \NAT@swatrue\def\NAT@ctype{3}\NAT@partrue\NAT@citetp}\r
+\renewcommand\nocite[1]{\@bsphack\r
+  \@for\@citeb:=#1\do{%\r
+    \edef\@citeb{\expandafter\@firstofone\@citeb}%\r
+    \if@filesw\immediate\write\@auxout{\string\citation{\@citeb}}\fi\r
+    \if*\@citeb\else\r
+    \@ifundefined{b@\@citeb\@extra@b@citeb}{%\r
+       \NAT@citeundefined \PackageWarning{natbib}%\r
+       {Citation `\@citeb' undefined}}{}\fi}%\r
+  \@esphack}\r
+\newcommand\NAT@parse[1]{{%\r
+     \let\protect=\@unexpandable@protect\let~\relax\r
+     \let\active@prefix=\@gobble\r
+     \xdef\NAT@temp{\csname b@#1\@extra@b@citeb\endcsname}}%\r
+     \expandafter\NAT@split\NAT@temp\r
+     \expandafter\NAT@parse@date\NAT@date??????@@%\r
+     \ifciteindex\NAT@index\fi\r
+}\r
+\newcommand\NAT@split[4]{%\r
+  \gdef\NAT@num{#1}\gdef\NAT@name{#3}\gdef\NAT@date{#2}%\r
+  \gdef\NAT@all@names{#4}%\r
+  \ifx\NAT@noname\NAT@all@names \gdef\NAT@all@names{#3}\fi}\r
+\newcommand\NAT@parse@date{}\r
+\def\NAT@parse@date#1#2#3#4#5#6@@{%\r
+  \ifnum\the\catcode`#1=11\def\NAT@year{}\def\NAT@exlab{#1}\else\r
+  \ifnum\the\catcode`#2=11\def\NAT@year{#1}\def\NAT@exlab{#2}\else\r
+  \ifnum\the\catcode`#3=11\def\NAT@year{#1#2}\def\NAT@exlab{#3}\else\r
+  \ifnum\the\catcode`#4=11\def\NAT@year{#1#2#3}\def\NAT@exlab{#4}\else\r
+    \def\NAT@year{#1#2#3#4}\def\NAT@exlab{{#5}}\fi\fi\fi\fi}\r
+\newcommand\NAT@index{}\r
+\let\NAT@makeindex=\makeindex\r
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+\fi\r
+}\r
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+\if@filesw\r
+      {\let\protect\noexpand\let~\relax\r
+       \immediate\r
+       \write\@auxout{\string\bibcite{#5}{{#1}{#2}{{#3}}{{#4}}}}}\fi\r
+\ignorespaces}\r
+\def\NAT@noname{{}}\r
+\renewcommand\bibitem{%\r
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+    \stepcounter{NAT@ctr}\@lbibitem[\arabic{NAT@ctr}]}}\r
+\def\@lbibitem[#1]#2{%\r
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+    \@ifundefined{br@#2\@extra@b@citeb}{}{%\r
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+  {\ifNAT@stdbst\if@filesw\immediate\write\@auxout{\string\r
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+  \def\NAT@temp{#2}\expandafter \ifx \csname b@#1\@extra@binfo\endcsname\r
+    \NAT@temp \else \ifNAT@swa \NAT@swafalse\r
+       \PackageWarningNoLine{natbib}{Citation(s) may have\r
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+          Rerun to get citations correct}\fi\fi}\r
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+\def\NAT@apalk#1, #2, #3\@nil#4{\if\relax#2\relax\r
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+  \NAT@wrout{#1}{}{}{}{#4}\else\r
+  \stepcounter{NAT@ctr}%\r
+  \NAT@wrout{\arabic {NAT@ctr}}{#2}{#1}{}{#4}\fi}\r
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+   \NAT@wrout{\arabic {NAT@ctr}}{#2}{#1}{}{#4}\else\r
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+{NAT@ctr}}{#2}{#1}{}{#3}}\r
+\newcommand\citename{}\r
+\def\citename#1#2(@)(@)\@nil#3{\expandafter\NAT@apalk#1#2, \@nil{#3}}\r
+\newcommand\harvarditem[4][]%\r
+    {\if\relax#1\relax\bibitem[#2(#3)]{#4}\else\r
+        \bibitem[#1(#3)#2]{#4}\fi }\r
+\newcommand\harvardleft{\NAT@open}\r
+\newcommand\harvardright{\NAT@close}\r
+\newcommand\harvardyearleft{\NAT@open}\r
+\newcommand\harvardyearright{\NAT@close}\r
+\AtBeginDocument{\providecommand{\harvardand}{and}}\r
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+ \bibsection\r
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+    \sloppy\clubpenalty4000\widowpenalty4000\r
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+ }{\def\@noitemerr{%\r
+  \PackageWarning{natbib}\r
+     {Empty `thebibliography' environment}}%\r
+  \endlist\vskip-\lastskip}\r
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+    \PackageWarningNoLine{natbib}{There were undefined citations}}}\r
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+}\r
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+        \@celt{\number\@tempcnta}\@celt{#2}%\r
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diff --git a/synmut.aux b/synmut.aux
new file mode 100644 (file)
index 0000000..eb90501
--- /dev/null
@@ -0,0 +1,35 @@
+\relax 
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
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+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax 
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\citation{watts_architecture_2009}
+\citation{watts_architecture_2009}
+\bibstyle{natbib}
+\bibdata{bib}
+\bibcite{watts_architecture_2009}{{1}{2009}{{Watts {\em  et~al.}}}{{Watts, Dang, Gorelick, Leonard, Jr, Swanstrom, Burch, and Weeks}}}
+\select@language{english}
+\@writefile{toc}{\select@language{english}}
+\@writefile{lof}{\select@language{english}}
+\@writefile{lot}{\select@language{english}}
+\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Allele frequency trajectories of typical patient, C3-V5, nonsynonymous (solid) and synonymous mutations (dashed lines). Most synonymous mutations are not fixed.\relax }}{2}{figure.caption.1}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Fixation probability of derived synonymous alleles is strongly suppressed in C3-V5 versus other parts of the {\it  env} gene (left panel). Especially hard is fixation of new alleles in conserved regions flanking the V loops (right panel). The black dashed line is the prediction from neutral theory, for comparison purposes.\relax }}{2}{figure.caption.2}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Simulations show that the suppression of fixation probability can be generated by linkage to sweeping nonsynonymous alleles nearby. Two possible scenarios are competition between escape mutants (left panel) and time-dependent selection due to immune sytem recognition (right panel).\relax }}{3}{figure.caption.3}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces Watts et al. have measured the reactivity of HIV nucleotides to {\it  in vitro} chemical attack and shown that some nucleotides are more likely to be involved in RNA secondary folds. C1-C5 regions, in particular, show conserved stem-loop structures~\citep  {watts_architecture_2009}. We show that among all derived alleles in those regions reaching frequencies of order one, there is a negative correlation between fixation and involvement in a base pairing in a RNA stem (left panel). The rest of the genome does not show any correlation (right panel). There might be too few silent polymorphisms in the first place, or the signal might be masked by a lot of non-functional RNA structures.\relax }}{3}{figure.caption.4}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces The total density of polymorphisms (mostly nonsynonymous ones) is highest in the V regions (left panel). The density of synonymous mutations only, however, is not enriched there (right panel). This could be due to a more deleterious effect of synonymous mutations.\relax }}{4}{figure.caption.5}}
+\@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces Simulations on the escape competition scenario show that the density of selective sweeps and the size of the deleterious effects of synonymous mutations are the main driving forces of the phenomenon. A convex fixation probability is recovered, as seen in the data, along the diagonal (left panel): more dense sweeps can support more deleterious linked mutations. The density of sweeps is limited, however, by the nonsynonymous fixation probability, which is quite close to neutrality (right panel). Moreover, strong competition between escape mutants is required, so that several escape mutants are ``found'' by HIV within a few months of antibody production.\relax }}{4}{figure.caption.6}}
+\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{5}{section.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {2}Results}{5}{section.2}}
+\@writefile{toc}{\contentsline {section}{\numberline {3}Discussion}{5}{section.3}}
+\@writefile{toc}{\contentsline {section}{\numberline {4}Methods}{5}{section.4}}
diff --git a/synmut.bbl b/synmut.bbl
new file mode 100644 (file)
index 0000000..1e62ba8
--- /dev/null
@@ -0,0 +1,11 @@
+\begin{thebibliography}{}
+
+\bibitem[Watts {\em et~al.}(2009)Watts, Dang, Gorelick, Leonard, Jr, Swanstrom,
+  Burch, and Weeks]{watts_architecture_2009}
+Watts, J.~M., Dang, K.~K., Gorelick, R.~J., Leonard, C.~W., Jr, J. W.~B.,
+  Swanstrom, R., Burch, C.~L., and Weeks, K.~M. (2009).
+\newblock Architecture and secondary structure of an entire {HIV-1} {RNA}
+  genome.
+\newblock {\em Nature\/}, {\bf 460}(7256), 711--716.
+
+\end{thebibliography}
diff --git a/synmut.blg b/synmut.blg
new file mode 100644 (file)
index 0000000..176a9ff
--- /dev/null
@@ -0,0 +1,46 @@
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+The style file: natbib.bst
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diff --git a/synmut.fdb_latexmk b/synmut.fdb_latexmk
new file mode 100644 (file)
index 0000000..13bd9e6
--- /dev/null
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+# Fdb version 3
+["bibtex synmut"] 1354068796 "synmut.aux" "synmut.bbl" "synmut" 1354069057
+  "./natbib.bst" 1354038822 26224 f3907cf5bef1f44c8c15558e94274a18 ""
+  "bib.bib" 1354052674 2967 9d783f909037ab5869b80902be1ec150 ""
+  "synmut.aux" 1354069057 4290 7995a498c2af77089e2e7c2253a60cd2 ""
+  "synmut.bcf" 0 -1 0 ""
+  (generated)
+  "synmut.blg"
+  "synmut.bbl"
+["pdflatex"] 1354069055 "synmut.tex" "synmut.pdf" "synmut" 1354069057
+  "./figures/Bunnik2008_fixmid_syn_ShankanonShanka.pdf" 1354052151 46925 cb77fd4d3c620a7f88d5746364a9637b ""
+  "./figures/Henn_density_polymorphisms.pdf" 1354059763 41801 a33cfc74da7b1d05ef58534ca11849a0 ""
+  "./figures/Henn_density_polymorphisms_syn_over_chances.pdf" 1354059894 42601 31930041b127f9c59e408dd9521177ed ""
+  "./figures/Shankarappa_allele_freqs_trajectories_syn_nonsynp8.png" 1354051829 609794 c75e87d7bceb9d4b7191cac1e986e252 ""
+  "./figures/Shankarappa_fixmid_syn_V_regions.pdf" 1354052181 44554 3804bf7b3b4035a0b016ec470814af9e ""
+  "./figures/fixation_loss_shortgenome_area_ada_frac_del_eff_coi_0_01_nescepi_6_heat.pdf" 1354061909 180089 a8b64eeb397ba1703384c3ce4a5e4105 ""
+  "./figures/fixation_loss_shortgenome_area_ada_frac_del_eff_coi_0_01_nescepi_6_nonsyn_heat.pdf" 1354061959 180847 799c88edb7c9667d188edf0ccd430087 ""
+  "./figures/fixation_probability_N_1e4_3ingredients_3rddel_envnonenv_stopall.pdf" 1354053241 40809 4b8487f0b28c9f00da582b973529f5e7 ""
+  "./figures/fixation_probability_shortgenome_N_1e4_epitopes_example_longer.pdf" 1354053122 48732 f0b6d5bf2b86bc7f3fd8baf7ca4fdbda ""
+  "./figures/mixed_Shankarappa_Bunnik2008_Liu_fixation_reactivity_Vandflanking_fromSHAPE.pdf" 1354052621 28455 12b9e43eb3c5c8d2d4ff56b02ee13705 ""
+  "./figures/mixed_Shankarappa_Bunnik2008_Liu_fixation_reactivity_nonVandflanking.pdf" 1354060219 25778 a6e328f0f59a50c5a54ccab5d7401d34 ""
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+\BOOKMARK [1][-]{section.1}{Introduction}{}% 1
+\BOOKMARK [1][-]{section.2}{Results}{}% 2
+\BOOKMARK [1][-]{section.3}{Discussion}{}% 3
+\BOOKMARK [1][-]{section.4}{Methods}{}% 4
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+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% ARTICLE ABOUT FATE OF SYNONYMOUS MUTATIONS IN HIV
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\documentclass[12pt,a4paper,notitlepage,onecolumn]{article}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\newcommand{\Author}{Fabio~Zanini and Richard~A.~Neher}
+\newcommand{\Title}{(Rise and fall of synonymous mutations)}
+\newcommand{\Keywords}{{HIV}, {synonymous}, {population genetics}}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\usepackage[english]{babel}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amsfonts,amssymb,eucal,eurosym}
+\usepackage{color}
+\usepackage{subfig}
+\usepackage{graphicx}
+\usepackage[font=small, format=hang, labelfont={sf,bf}, figurename=Fig.]{caption}
+\usepackage{natbib}
+\usepackage{pslatex}
+\usepackage[colorlinks,linkcolor=red,citecolor=red]{hyperref}
+\hypersetup{pdfauthor={\Author}, pdftitle={\Title}, pdfkeywords={\Keywords}}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\graphicspath{{./figures/}}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\DeclareMathOperator\de{d\!}
+\newcommand{\comment}[1]{\textit{\textcolor{red}{#1}}}
+\newcommand{\mut}{u}
+\newcommand{\mfit}{\langle F\rangle}
+\newcommand{\mexpfit}{\langle e^{F}\rangle}
+\newcommand{\ox}{r}
+\newcommand{\co}{\rho}
+\newcommand{\gt}{g}
+\newcommand{\locus}{s}
+\newcommand{\locuspm}{t}
+\newcommand{\OO}{\mathcal{O}}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\title{\Title}
+\author{\Author}
+\date{\today}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{document}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\maketitle
+
+\begin{abstract}
+\noindent
+Intrapatient HIV evolution is goverened by selection on the protein level in the
+arms race with the immune system (killer T-cells and antibodies). Synonymous
+mutations do not have an immunity-related phenotype and are often assumed to be
+neutral. In this paper, we show that synonymous changes in epitope-rich regions
+are often deleterious but still reach frequencies of order one.  We analyze time
+series of viral sequences from the V1-C5 part of {\it env} within individual
+hosts and observe that synonymous derived alleles rarely fix in the
+viral population. Simulations suggest that such synonymous mutations
+have a (Malthisuan) selection coefficient of the order of $-0.001$, and that
+they are brought up to high frequency by linkage to neighbouring beneficial
+nonsynonymous alleles (genetic draft). As far as the biological causes are
+concerned, we detect a negative correlation between fixation of an allele and
+its involvement in evolutionarily conserved RNA stem-loop structures.
+This phenonenon is not observed in other parts of the HIV genome, in which
+selective sweeps are less dense and the genetic architecture less constrained.
+\end{abstract}
+
+\section{Introduction}
+\section{Results}
+
+\begin{figure}
+\begin{center}
+\includegraphics[width=\linewidth]{Shankarappa_allele_freqs_trajectories_syn_nonsynp8}
+\caption{Allele frequency trajectories of typical patient, C3-V5, nonsynonymous
+(solid) and synonymous mutations (dashed lines). Most synonymous mutations are
+not fixed.}
+\end{center}
+\end{figure}
+
+\begin{figure}
+\begin{center}
+\subfloat{\includegraphics[width=0.49\linewidth]{Bunnik2008_fixmid_syn_ShankanonShanka}}
+\subfloat{\includegraphics[width=0.49\linewidth]{Shankarappa_fixmid_syn_V_regions}}
+\caption{Fixation probability of derived synonymous alleles is strongly
+suppressed in C3-V5 versus other parts of the {\it env} gene (left panel).
+Especially hard is fixation of new alleles in conserved regions flanking the V
+loops (right panel). The black dashed line is the prediction from neutral
+theory, for comparison purposes.}
+\end{center}
+\end{figure}
+
+\begin{figure}
+\begin{center}
+\subfloat{\includegraphics[width=0.49\linewidth]{fixation_probability_shortgenome_N_1e4_epitopes_example_longer}}
+\subfloat{\includegraphics[width=0.49\linewidth]{fixation_probability_N_1e4_3ingredients_3rddel_envnonenv_stopall}}
+\caption{Simulations show that the suppression of fixation probability can be
+generated by linkage to sweeping nonsynonymous alleles nearby. Two possible
+scenarios are competition between escape mutants (left panel) and time-dependent
+selection due to immune sytem recognition (right panel).}
+\end{center}
+\end{figure}
+
+\begin{figure}
+\begin{center}
+\subfloat{\includegraphics[width=0.49\linewidth]{mixed_Shankarappa_Bunnik2008_Liu_fixation_reactivity_Vandflanking_fromSHAPE}}
+\subfloat{\includegraphics[width=0.49\linewidth]{mixed_Shankarappa_Bunnik2008_Liu_fixation_reactivity_nonVandflanking}}
+\caption{Watts et al. have measured the reactivity of HIV nucleotides to {\it in
+vitro} chemical attack and shown that some nucleotides are more likely to be
+involved in RNA secondary folds. C1-C5 regions, in particular, show conserved
+stem-loop structures~\citep{watts_architecture_2009}. We show that among all
+derived alleles in those regions reaching frequencies of order one, there is a negative
+correlation between fixation and involvement in a base pairing in a RNA stem
+(left panel). The rest of the genome does not show any correlation (right
+panel). There might be too few silent polymorphisms in the first place, or the
+signal might be masked by a lot of non-functional RNA structures.}
+\end{center}
+\end{figure}
+
+\begin{figure}
+\begin{center}
+\subfloat{\includegraphics[width=0.49\linewidth]{Henn_density_polymorphisms}}
+\subfloat{\includegraphics[width=0.49\linewidth]{Henn_density_polymorphisms_syn_over_chances}}
+\caption{The total density of polymorphisms (mostly nonsynonymous ones) is
+highest in the V regions (left panel). The density of synonymous mutations only,
+however, is not enriched there (right panel). This could be due to a more
+deleterious effect of synonymous mutations.}
+\end{center}
+\end{figure}
+
+
+\begin{figure}
+\begin{center}
+\subfloat{\includegraphics[width=0.49\linewidth]{fixation_loss_shortgenome_area_ada_frac_del_eff_coi_0_01_nescepi_6_heat.pdf}}
+\subfloat{\includegraphics[width=0.49\linewidth]{fixation_loss_shortgenome_area_ada_frac_del_eff_coi_0_01_nescepi_6_nonsyn_heat.pdf}}
+
+\caption{Simulations on the escape competition scenario show that the density of
+ selective sweeps and the size of the deleterious effects of synonymous
+ mutations are the main driving forces of the phenomenon. A convex fixation
+ probability is recovered, as seen in the data, along the diagonal (left panel):
+ more dense sweeps can support more deleterious linked mutations. The density of
+ sweeps is limited, however, by the nonsynonymous fixation probability, which is
+ quite close to neutrality (right panel). Moreover, strong competition between
+ escape mutants is required, so that several escape mutants are ``found'' by HIV
+within a few months of antibody production.}
+
+\end{center}
+\end{figure}
+
+\section{Discussion}
+\section{Methods}
+\section*{Acknowledgements}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\bibliographystyle{natbib}
+\bibliography{bib}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\end{document}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+