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Subject: Glioblastoma Subclasses Can Be Defined by Activity among Signal Transduction Pathways and Associated Genomic Alterations
Date: Tue, 1 Dec 2009 16:26:41 +0100
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            <DIV><SPAN class=3Dcitation-version></SPAN><SPAN=20
            class=3Dcitation-abbreviation>PLoS One. </SPAN><SPAN=20
            class=3Dcitation-publication-date>2009; </SPAN><SPAN=20
            class=3Dcitation-volume>4</SPAN><SPAN=20
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            e7752. </SPAN></DIV>
            <DIV><SPAN class=3Dfm-vol-iss-date>Published online 2009 =
November 13.=20
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            class=3Dfm-vol-iss-date>doi:=20
            10.1371/journal.pone.0007752.</SPAN></DIV></DIV></TD>
          <TD class=3Dfm-citation-ids>
            <DIV class=3Dfm-citation-pmcid><SPAN=20
            class=3Dfm-citation-ids-label>PMCID:=20
            =
</SPAN><SPAN>PMC2771920</SPAN></DIV></TD></TR></TBODY></TABLE>
      <DIV class=3Dfm-copyright><A class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/about/copyright.html">Copyright</=
A>=20
      Brennan et al. This is an open-access article distributed under =
the terms=20
      of the Creative Commons Attribution License, which permits =
unrestricted=20
      use, distribution, and reproduction in any medium, provided the =
original=20
      author and source are credited.</DIV>
      <DIV class=3Dfm-title>Glioblastoma Subclasses Can Be Defined by =
Activity=20
      among Signal Transduction Pathways and Associated Genomic=20
Alterations</DIV>
      <DIV class=3D"contrib-group fm-author">Cameron=20
      Brennan,<SUP>#</SUP><SUP>1,</SUP><SUP>2</SUP><SUP>*</SUP> Hiroyuki =

      Momota,<SUP>#</SUP><SUP>3</SUP> Dolores=20
      Hambardzumyan,<SUP>1,</SUP><SUP>2</SUP> Tatsuya Ozawa,<SUP>3</SUP> =
Adesh=20
      Tandon,<SUP>1</SUP> Alicia Pedraza,<SUP>1</SUP> and Eric=20
      =
Holland<SUP>1,</SUP><SUP>2,</SUP><SUP>3,</SUP><SUP>4,</SUP><SUP>5</SUP><S=
UP>*</SUP></DIV>
      <DIV class=3Dfm-affl><SUP>1</SUP>Department of Neurosurgery, =
Memorial Sloan=20
      Kettering Cancer Center, New York, New York, United States of=20
America</DIV>
      <DIV class=3Dfm-affl><SUP>2</SUP>Brain Tumor Center, Memorial =
Sloan=20
      Kettering Cancer Center, New York, New York, United States of=20
America</DIV>
      <DIV class=3Dfm-affl><SUP>3</SUP>Department of Cancer Biology and =
Genetics,=20
      Memorial Sloan Kettering Cancer Center, New York, New York, United =
States=20
      of America</DIV>
      <DIV class=3Dfm-affl><SUP>4</SUP>Department of Neurology, Memorial =
Sloan=20
      Kettering Cancer Center, New York, New York, United States of=20
America</DIV>
      <DIV class=3Dfm-affl><SUP>5</SUP>Department of Surgery, Memorial =
Sloan=20
      Kettering Cancer Center, New York, New York, United States of=20
America</DIV>
      <DIV class=3D"contrib-group fm-editor">Chad Creighton, <SPAN=20
      class=3Dfm-role>Editor</SPAN><SUP></SUP></DIV>
      <DIV class=3Dfm-affl>Baylor College of Medicine, United States of=20
      America</DIV>
      <DIV class=3Dfm-footnote><SUP>#</SUP>Contributed equally.</DIV>
      <DIV class=3Dfm-footnote id=3Dcor1>* E-mail: <SPAN=20
      class=3De_id607901>hollande/at/mskcc.org</SPAN>
      <SCRIPT language=3DJavaScript type=3Dtext/javascript><!--=0A=
                                    try{initUnObscureEmail =
("e_id607901", '<a class=3D"ext-reflink" href=3D"' + =
reverseAndReplaceString('gro.ccksm/ta/ednalloh:otliam', '/at/', '@') + =
'">' + reverseAndReplaceString('gro.ccksm/ta/ednalloh', '/at/','@') + =
'</a>')}catch(e){}=0A=
                                //--></SCRIPT>
       (EH); Email: <SPAN =
class=3De_id607905>cbrennan/at/mskcc.org</SPAN>
      <SCRIPT language=3DJavaScript type=3Dtext/javascript><!--=0A=
                                    try{initUnObscureEmail =
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'">' + reverseAndReplaceString('gro.ccksm/ta/nannerbc', '/at/','@') + =
'</a>')}catch(e){}=0A=
                                //--></SCRIPT>
       (CB)</DIV>
      <DIV class=3Dfm-footnote>
      <DIV class=3D"p p-first-last" id=3D__pid607912>Conceived and =
designed the=20
      experiments: CB HM EH. Performed the experiments: CB HM DH TO AT =
AP.=20
      Analyzed the data: CB DH. Contributed reagents/materials/analysis =
tools:=20
      CB HM EH. Wrote the paper: CB EH.</DIV></DIV>
      <DIV class=3Dfm-pubdate>Received July 22, 2009; Accepted October =
15,=20
      2009.</DIV></DIV>
      <DIV class=3Dsec id=3D__abstractid607974>
      <DIV class=3D"head1 section-title" =
id=3D__abstractid607974titletitle=20
      style=3D"TEXT-TRANSFORM: none">
      <DIV class=3Dother-sections>
      <UL class=3D"noext-menu noext-menu-hidden">
        <LI><A class=3Dfirst-link=20
        =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">&nbsp;Othe=
r=20
        Sections=E2=96=BC</A>
        <UL class=3D"submenu head1">
          <LI class=3D"submenu-item current-item"><A class=3D""=20
          style=3D"TEXT-TRANSFORM: none" onclick=3Dreturn(false)=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">Abstract</=
A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s1">Introduc=
tion</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s2">Results<=
/A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s3">Discussi=
on</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s4">Methods<=
/A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s5">Supporti=
ng=20
          Information</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__ref-listid=
665409">References</A></LI></UL></LI></UL></DIV>
      <DIV>Abstract</DIV></DIV>
      <DIV class=3Dsection-content =
id=3D__abstractid607974content><!--article-meta-->
      <DIV class=3D"sec sec-first" id=3D__secid607976>
      <DIV class=3D"abs-head2 head-separate">Background</DIV>
      <DIV class=3D"p p-first-last" id=3D__pid607980>Glioblastoma =
multiforme (GBM)=20
      is an umbrella designation that includes a heterogeneous group of =
primary=20
      brain tumors. Several classification strategies of GBM have been =
reported,=20
      some by clinical course and others by resemblance to cell types =
either in=20
      the adult or during development. From a practical and therapeutic=20
      standpoint, classifying GBMs by signal transduction pathway =
activation and=20
      by mutation in pathway member genes may be particularly valuable =
for the=20
      development of targeted therapies.</DIV></DIV>
      <DIV class=3Dsec id=3D__secid607986>
      <DIV class=3D"abs-head2 head-separate">Methodology/Principal =
Findings</DIV>
      <DIV class=3D"p p-first-last" id=3D__pid607990>We performed =
targeted proteomic=20
      analysis of 27 surgical glioma samples to identify patterns of =
coordinate=20
      activation among glioma-relevant signal transduction pathways, =
then=20
      compared these results with integrated analysis of genomic and =
expression=20
      data of 243 GBM samples from The Cancer Genome Atlas (TCGA). In =
the=20
      pattern of signaling, three subclasses of GBM emerge which appear =
to be=20
      associated with predominance of EGFR activation, PDGFR activation, =
or loss=20
      of the RAS regulator NF1. The EGFR signaling class has prominent =
Notch=20
      pathway activation measured by elevated expression of Notch =
ligands,=20
      cleaved Notch receptor, and downstream target Hes1. The PDGF class =
showed=20
      high levels of PDGFB ligand and phosphorylation of PDGFR=CE=B2 and =
NFKB.=20
      NF1-loss was associated with lower overall MAPK and PI3K =
activation and=20
      relative overexpression of the mesenchymal marker YKL40. These =
three=20
      signaling classes appear to correspond with distinct =
transcriptomal=20
      subclasses of primary GBM samples from TCGA for which copy number=20
      aberration and mutation of EGFR, PDGFRA, and NF1 are signature=20
      events.</DIV></DIV>
      <DIV class=3D"sec sec-last" id=3D__secid608002>
      <DIV class=3D"abs-head2 =
head-separate">Conclusions/Significance</DIV>
      <DIV class=3D"p p-first-last" id=3D__pid608006>Proteomic analysis =
of GBM=20
      samples revealed three patterns of expression and activation of =
proteins=20
      in glioma-relevant signaling pathways. These three classes are =
comprised=20
      of roughly equal numbers showing either EGFR activation associated =
with=20
      amplification and mutation of the receptor, PDGF-pathway =
activation that=20
      is primarily ligand-driven, or loss of NF1 expression. The =
associated=20
      signaling activities correlating with these sentinel alterations =
provide=20
      insight into glioma biology and therapeutic=20
      strategies.</DIV></DIV></DIV></DIV>
      <DIV class=3Dsec id=3Ds1><SPAN></SPAN>
      <DIV class=3D"head1 section-title" id=3Ds1titletitle=20
      style=3D"TEXT-TRANSFORM: none">
      <DIV class=3Dother-sections>
      <UL class=3D"noext-menu noext-menu-hidden">
        <LI><A class=3Dfirst-link=20
        =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">&nbsp;Othe=
r=20
        Sections=E2=96=BC</A>
        <UL class=3D"submenu head1">
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__abstractid=
607974">Abstract</A>
          <LI class=3D"submenu-item current-item"><A class=3D""=20
          style=3D"TEXT-TRANSFORM: none" onclick=3Dreturn(false)=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">Introducti=
on</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s2">Results<=
/A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s3">Discussi=
on</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s4">Methods<=
/A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s5">Supporti=
ng=20
          Information</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__ref-listid=
665409">References</A></LI></UL></LI></UL></DIV>
      <DIV>Introduction</DIV></DIV>
      <DIV class=3Dsection-content id=3Ds1content>
      <DIV class=3D"p p-first" id=3D__pid608027>Glioblastoma (GBM) is =
the most=20
      common malignant brain tumor and is characterized by intratumoral=20
      heterogeneity, invasive growth pattern and poor response to =
treatment.<A=20
      class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17974913"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Furnari1">[1]</A>=E2=80=93<A =
class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/11390353"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Maher1">[4]</A> While GBM comprises =
approximately 25% of=20
      all brain tumors in adults, in absolute numbers it is still an =
uncommon=20
      cancer. This low absolute incidence combined with high morbidity, =
poor=20
      response rates and short survival times pose practical problems =
for=20
      clinical trial execution, particularly if therapy is anticipated =
to target=20
      a molecularly-defined subset of tumors. The current first-line =
treatment=20
      for GBM is radiation with alkylating chemotherapy (Temozolomide) =
given=20
      concurrently and then continued after radiation. This uniform =
first-line=20
      treatment approach contrasts with the wealth of molecular data on=20
      mutations, genomic aberrations and transcriptomal features in GBM =
which=20
      indicate potential therapeutic targets and resolve apparently =
distinct=20
      subclasses of these tumors.<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18669428"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Wen1">[3]</A> We designed this investigation =
of signal=20
      transduction pathway activation in GBM with the expectation that =
tumor=20
      subclasses based on differential activation of glioma-relevant =
pathways=20
      would be of paramount utility for interpreting responses to =
therapies=20
      targeting these pathways, and potentially applicable for =
stratifying=20
      patients in clinical trials.</DIV>
      <DIV class=3Dp id=3D__pid608073>Historically, two subtypes of GBM =
were=20
      distinguished based on histologic grade at clinical presentation. =
Primary=20
      GBMs present initially as grade 4 tumors while secondary GBMs =
present as=20
      lower grade gliomas and progress to GBMs over time.<A=20
      class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17618441"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Louis1">[5]</A> Although primary and secondary =
GBM=20
      differ in the frequency of molecular abnormalities seen, they draw =
largely=20
      from a common palette of events: amplification and activating =
mutations in=20
      EGFR, over-expression of PDGF and its receptors and loss of the =
tumor=20
      suppressors INK4a/ARF, p53 and PTEN are well-documented, recurrent =

      mutations in these tumors.<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17974913"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Furnari1">[1]</A> Recent large-scale efforts =
to=20
      characterize the glioblastoma genome have identified additional =
recurrent=20
      alterations in genes not previously implicated in glioma, such as=20
      <EM>ERBB2</EM> and <EM>IDH1</EM> mutation in primary and secondary =
GBM=20
      respectively, and a significant incidence of mutation and genomic =
loss of=20
      <EM>NF1</EM>.<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/19228619"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Yan1">[6]</A>=E2=80=93<A class=3D"cite-reflink =
bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18772890"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Network1">[8]</A> While there is hope that =
further=20
      sequencing will yield new therapeutic targets, it should be noted =
that=20
      single-agent therapy trials of inhibitors directed to the two most =

      commonly altered receptors have not been successful in unselected=20
      populations.<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18356283"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Lamborn1">[9]</A>, <A class=3D"cite-reflink =
bibr popnode"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
-1"=20
      rid=3D"pone.0007752-1">[10]</A> At least in some cases this may be =
due to=20
      failure of RTK inhibition to impact downstream or parallel signal=20
      transduction pathway activation.<A class=3D"cite-reflink bibr =
popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/16278407"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Lassman1">[11]</A></DIV>
      <DIV class=3Dp id=3D__pid608171>The importance of signal =
transduction activity=20
      downstream of tyrosine kinase receptors in glioma biology is =
emphasized by=20
      the fact that these pathways are abnormally active in these tumors =
and=20
      causal in their formation in mice.<A class=3D"cite-reflink bibr =
popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/19076778"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Huse1">[12]</A>, <A class=3D"cite-reflink bibr =
popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17000661"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Fomchenko1">[13]</A> Therefore, there is =
significant=20
      interest in whether molecular subclasses of GBM might be =
identified based=20
      on distinct signaling characteristics, and whether such subclasses =
could=20
      be used to refine patient stratification in clinical trials or =
help=20
      interpret treatment responses. Several studies have subdivided =
GBMs by=20
      expression array analysis measuring total cellular mRNA levels.<A=20
      class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/12670911"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Nutt1">[14]</A>=E2=80=93<A =
class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/16530701"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Phillips1">[19]</A> However, because of =
differential=20
      translational efficiencies, total mRNA levels do not always =
correlate with=20
      protein levels. Moreover, most signaling activity is achieved by=20
      post-translational modifications of existing proteins such as =
Notch=20
      cleavage, phosphorylation of kinases, or stabilization of proteins =
such as=20
      beta catenin. To further complicate matters, signal transduction =
activity=20
      may affect, through feedback mechanisms, the translational =
efficiencies of=20
      mRNAs encoding proteins with effects on the oncogenic phenotype.<A =

      class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/14580340"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Rajasekhar1">[20]</A>, <A=20
      class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/15094774"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Rajasekhar2">[21]</A> Therefore, direct =
measurements of=20
      active signaling components at the protein level are critical to =
fully=20
      characterize the signal transduction state of the cell. Such =
measurements=20
      have been made on glioma samples and have shown correlation =
between the=20
      levels of active pathway components.<A class=3D"cite-reflink bibr =
popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/14580340"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Rajasekhar1">[20]</A>, <A=20
      class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/12782577"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Choe1">[22]</A></DIV>
      <DIV class=3D"p p-last" id=3D__pid608271>In this study, we have =
measured the=20
      relative protein levels of signaling molecules within pathways =
thought to=20
      be crucial to glioma biology among a panel of gliomas. This =
represents a=20
      more extensive proteomic analysis of signaling pathway members =
than has=20
      previously been done, and reveals three patterns of signaling =
pathway=20
      activation. Distinct patterns were each associated with EGFR and =
PDGF=20
      pathway activity while a third was associated with low levels of =
NF1=20
      protein. We present an analysis of genomic features among tumors =
in each=20
      group, and show how these proteomically-defined subclasses of GBM =
compare=20
      with genomic subclasses arising from integrated analysis of =
primary GBM in=20
      data from The Cancer Genome Atlas.</DIV></DIV></DIV>
      <DIV class=3Dsec id=3Ds2><SPAN></SPAN>
      <DIV class=3D"head1 section-title" id=3Ds2titletitle=20
      style=3D"TEXT-TRANSFORM: none">
      <DIV class=3Dother-sections>
      <UL class=3D"noext-menu noext-menu-hidden">
        <LI><A class=3Dfirst-link=20
        =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">&nbsp;Othe=
r=20
        Sections=E2=96=BC</A>
        <UL class=3D"submenu head1">
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__abstractid=
607974">Abstract</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s1">Introduc=
tion</A>
          <LI class=3D"submenu-item current-item"><A class=3D""=20
          style=3D"TEXT-TRANSFORM: none" onclick=3Dreturn(false)=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">Results</A=
>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s3">Discussi=
on</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s4">Methods<=
/A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s5">Supporti=
ng=20
          Information</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__ref-listid=
665409">References</A></LI></UL></LI></UL></DIV>
      <DIV>Results</DIV></DIV>
      <DIV class=3Dsection-content id=3Ds2content>
      <DIV class=3D"sec sec-first" id=3Ds2a><SPAN></SPAN>
      <DIV class=3D"head2 head-separate">Specimens and protein =
analysis</DIV>
      <DIV class=3D"p p-first" id=3D__pid608295>27 glioma surgical =
samples were=20
      identified from a database of patients operated on at MSKCC and =
consented=20
      to the IRB-approved protocol. Clinical and pathologic =
characteristics are=20
      summarized in <A class=3D"fig-table-link table"=20
      style=3D"TEXT-DECORATION: none"=20
      onclick=3D"startTarget(this, 'true', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/table/pone-00=
07752-t001/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Table 1</SPAN></A>. Pathology =
included=20
      20 GBM, 2 anaplastic astrocytomas, 4 oligodendrogliomas of which 2 =
were=20
      anaplastic tumors, and one tumor characterized as high grade =
glioma with=20
      glioneuronal elements. 11 GBM were recurrent after treatment (RT =
+/=E2=88=92=20
      temozolomide) and two of these were secondary GBM. The age range =
was from=20
      32 to 74 (median 53).</DIV>
      <DIV class=3Dcanvas-table-ref-outer>
      <DIV class=3Dcanvas-table-ref-inner><A id=3Dpone-0007752-t001=20
      name=3Dpone-0007752-t001></A>
      <TABLE class=3Dthumb-caption style=3D"CLEAR: both; WIDTH: 100%" =
cellSpacing=3D0=20
      cellPadding=3D0 border=3D0>
        <TBODY>
        <TR vAlign=3Dtop align=3Dleft>
          <TD class=3Dthumb-cell><A=20
            onclick=3D"startTarget(this, 'table', 1024, 800)"=20
            =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/table/pone-00=
07752-t001/">
            <DIV class=3Dthumb-ph><IMG class=3Dicon-reflink =
title=3D"Table 1"=20
            style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
            alt=3D"Table 1"=20
            =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/table-icon.gif"><=
/DIV></A></TD>
          <TD class=3Dcaption-cell>
            <DIV class=3Dcaption-ph><A class=3Dside-caption=20
            onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
            =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/table/pone-00=
07752-t001/"><STRONG>Table=20
            1</STRONG></A>
            <DIV class=3Dfigure-table-caption-in-article><SPAN>Patient =
and tumor=20
            characteristics.</SPAN></DIV>
            <DIV=20
      =
class=3Dfigure-table-caption-in-article></DIV></DIV></TD></TR></TBODY></T=
ABLE></DIV></DIV>
      <DIV style=3D"CLEAR: both"></DIV>
      <DIV class=3D"p p-last" id=3D__pid663381>Protein extracts from =
these tumors=20
      were analyzed by western blot for the activity of various =
signaling=20
      pathways related to glioma formation or stem cell character, =
totaling 55=20
      antibodies for proteins in total and active forms (<A=20
      class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s008"=20
      rid=3D"pone.0007752.s008">Table S1</A>). Antibodies were selected =
based on=20
      known performance. Briefly, PDGF pathway activity was measured by =
PDGF=20
      ligand (PDGFB), PDGFR=CE=B1, PDGFR=CE=B2 and phospho-PDGFR=CE=B2. =
EGFR activity was=20
      assessed by antibodies specific for EGFR and phospho-EGFR. The =
downstream=20
      pathways interrogated included Ras, Akt, Notch, Wnt and SHH. The =
Akt=20
      pathway was interrogated by PTEN, total AKT, phospho-AKT and RHEB. =

      Activation of mTOR was measured by phospho-S6 ribosomal protein =
(p-S6RP).=20
      The Ras pathway was interrogated by BRAF and total/phospho-MEK and =
ERK.=20
      Notch pathway activity was measured by the Notch ligands Delta =
(DLL1) and=20
      Jagged (JAG1), full length Notch receptors 1 and 2, cleaved Notch =
1 and 2=20
      and downstream Notch target HES1. The Wnt pathway was assessed by =
beta=20
      catenin levels and the SHH pathway by SHH levels. NF1 was assayed =
in=20
      preserved lysates at a later date, after mutations were reported =
for this=20
      gene in GBM.<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18772396"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Parsons1">[7]</A>, <A class=3D"cite-reflink =
bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18772890"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Network1">[8]</A> Quantified bands for 55 =
antibodies=20
      were normalized against actin or tubulin. HEB, Notch1 and Notch2=20
      antibodies each generated two bands which were independently =
quantified.=20
      Therefore a total of 58 protein forms were quantified and =
normalized.=20
      Relevant western bands selected by size are summarized in <A=20
      class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s001"=20
      rid=3D"pone.0007752.s001">Figure S1A, S1B, S1C, S1D</A>, and =
quantified=20
      values normalized against actin are given in <A=20
      class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s009"=20
      rid=3D"pone.0007752.s009">Table S2A, S2B, S2C</A>.</DIV></DIV>
      <DIV class=3Dsec id=3Ds2b><SPAN></SPAN>
      <DIV class=3D"head2 head-separate">Principal Component Analysis =
and=20
      unsupervised clustering identify three patterns of signaling in =
GBM</DIV>
      <DIV class=3D"p p-first" id=3D__pid663458>As expected, overall =
activation of=20
      signal transduction pathways differed markedly between the glioma =
samples=20
      and the normal brain reference. While some pathways such as PI3K =
and MAPK=20
      were active nearly uniformly among gliomas, we sought to =
investigate=20
      whether relative differences might distinguish subclasses among =
the=20
      samples with GBM pathology. The overall pattern of protein =
expression and=20
      activation was first assessed by Principal Component Analysis =
(PCA).=20
      Quantified western data for 57 protein forms were standardized =
across the=20
      set of GBM samples for analysis (n<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>20). We excluded p53 from analysis because common =
inactivating=20
      mutations can be associated with increased or decreased protein =
levels.=20
      For clarity in the figure, NF1 was represented as =E2=80=9CNF1 =
loss=E2=80=9D (zero minus=20
      standardized expression), reflecting the role of NF1 as an =
inhibitor of=20
      RAS signaling. The first two PCA components together accounted for =
the=20
      majority of variation in protein levels (<A=20
      class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s002"=20
      rid=3D"pone.0007752.s002">Figure S2</A>). A cloud plot showing the =
first two=20
      principal components is shown in <A class=3D"fig-table-link fig =
figpopup"=20
      style=3D"TEXT-DECORATION: none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g001/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 1A</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 1"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 1"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g001.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g001.jpg"></SPAN></SPA=
N></A>=20
      and revealed three patterns of total and activated protein levels. =
One=20
      component (PC2) distinguished proteins which were correlated with =
EGFR=20
      total protein versus those correlated with PDGFB levels. The other =

      component (PC1) distinguished a third group of proteins =
anti-correlated=20
      with EGFR and PDGFB. Elevated levels of these proteins were =
associated=20
      with low levels of Neurofibromin 1 protein (=E2=80=9CNF1 =
loss=E2=80=9D in <A=20
      class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g001/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 1A</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 1"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 1"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g001.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g001.jpg"></SPAN></SPA=
N></A>).</DIV>
      <DIV class=3Dcanvas-figure-ref-outer>
      <DIV class=3Dcanvas-figure-ref-inner><A id=3Dpone-0007752-g001=20
      name=3Dpone-0007752-g001></A>
      <TABLE class=3Dthumb-caption style=3D"CLEAR: both; WIDTH: 100%" =
cellSpacing=3D0=20
      cellPadding=3D0 border=3D0>
        <TBODY>
        <TR vAlign=3Dtop align=3Dleft>
          <TD class=3Dthumb-cell><A class=3D"icon-reflink figpopup"=20
            onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
            =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g001/">
            <DIV class=3Dthumb-ph><SPAN class=3Dlarge-thumb-canvas><SPAN =

            class=3Dlarge-thumb-canvas-1><IMG class=3D"icon-reflink =
large-thumb"=20
            title=3D"Figure 1"=20
            style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
            alt=3D"Figure 1"=20
            =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g001.gif"=20
            =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g001.jpg"></SPAN></SPA=
N>
            <DIV class=3Dsmall-thumb-canvas>
            <DIV class=3Dsmall-thumb-canvas-1><IMG=20
            class=3D"icon-reflink small-thumb" title=3D"Figure 1" =
alt=3D"Figure 1"=20
            =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g001.gif"></DIV></DIV></DIV></A></TD>
          <TD class=3Dcaption-cell>
            <DIV class=3Dcaption-ph><A class=3Dside-caption=20
            onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
            =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g001/"><STRONG>Figure=20
            1</STRONG></A>
            <DIV class=3Dfigure-table-caption-in-article><SPAN>Analysis =
of=20
            quantified western data in 20 GBM identifies three signaling =
axes=20
            associated with EGFR overexpression, PDGFB overexpression, =
and loss=20
            of NF1.</SPAN></DIV>
            <DIV=20
      =
class=3Dfigure-table-caption-in-article></DIV></DIV></TD></TR></TBODY></T=
ABLE>
      <DIV class=3Dfigure-table-caption-in-article></DIV></DIV></DIV>
      <DIV style=3D"CLEAR: both"></DIV>
      <DIV class=3D"p p-last" id=3D__pid663566>In order to evaluate the =
significance=20
      of this three-way classification, we performed unsupervised =
k-means=20
      analysis on the same standardized data from the 20 GBM samples and =

      evaluated the fit and stability over a range of cluster sizes. =
K-means for=20
      cluster sizes from 2=E2=80=938 was run for 10,000 iterations, =
leaving out 15% of=20
      the data with each iteration (i.e. three randomly chosen samples =
left=20
      out). Consensus matrices were evaluated for cluster assignment =
stability=20
      both visually and by cophenetic correlation (see <A=20
      class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s003"=20
      rid=3D"pone.0007752.s003">Figure S3A</A>). As predicted from PCA, =
the=20
      correlation of protein levels was well-described by 3-way =
clustering (<A=20
      class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g001/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 1B</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 1"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 1"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g001.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g001.jpg"></SPAN></SPA=
N></A>).=20
      Considering only those proteins which co-cluster in &gt;95% of =
k-means=20
      iterations, three =E2=80=9Ccore=E2=80=9D protein groups were =
identified. These protein=20
      groups were named according to the strong separation by PCA of =
EGFR, PDGF=20
      and NF1 levels, with consideration that alterations in these three =
genes=20
      are common in glioblastoma and each is pathogenic in=20
      genetically-engineered mouse glioma models:</DIV>
      <DIV class=3Dsec id=3Ds2b1><SPAN></SPAN><SPAN class=3Dhead3>EGFR =
core </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid663605>This cluster of 15 =
proteins=20
      features high levels of total and phospho-EGFR. Prominent Notch =
activity=20
      is represented in this group by high levels of the active cleaved =
form of=20
      Notch 1 (Notch 1 ICD) as well as of ligands Jagged (JAG1) and =
Delta-like 1=20
      (DLL1) and of the downstream Notch transcriptional target HES1. =
Wnt=20
      signaling is suggested by increased (stabilized) B-catenin levels. =
Other=20
      proteins relatively increased in this core group are EIF4EBP1, =
EIF4E,=20
      RHEB, phospho-BAD, INI1, La/SSB, FGF2, and phospho-Rb1. There was =
a trend=20
      for higher phospho-Akt levels, though this did not reach =
significance=20
      (p<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>0.08).</DIV></DIV>
      <DIV class=3Dsec id=3Ds2b2><SPAN></SPAN><SPAN class=3Dhead3>PDGF =
core </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid663620>This cluster is =
comprised of 17=20
      proteins including PDGFB, phospho-PDGFR=CE=B2 and phospho-NFKB1. =
PTEN levels=20
      are higher in this group and relatively increased Ras activity is=20
      evidenced by elevated total and phosphorylated MEK and ERK. Levels =
of MTOR=20
      and downstream targets S6K and p-S6K were better-correlated with =
the PDGF=20
      core than the EGFR core, though levels were high in tumors of both =

      classes. Other PDGF-associated proteins were SHH, HEB 1/2 (TCF12,=20
      associated with oligodendrocyte development), BRAF, p-FOXO1 and=20
      TSC1.</DIV></DIV>
      <DIV class=3D"sec sec-last" id=3Ds2b3><SPAN></SPAN><SPAN =
class=3Dhead3>NF1 Core=20
      </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid663635>This group is =
defined by higher=20
      levels of 5 proteins: IRS1, IGFBP5, YKL40 and VEGF. As suggested =
by PCA=20
      analysis, the group is also strongly associated with low levels of =
NF1=20
      (plotted as the inverse protein level, =E2=80=9CNF1 =
loss=E2=80=9D). Sporadic elevation of=20
      MYC, NMYC, and KRAS-GTP was also seen in this group. Compared to =
the other=20
      classes, GBM samples showing NF1-core expression pattern showed =
relatively=20
      suppressed levels of total- and phospho-proteins in the PI3K and =
MAPK=20
      pathways. These differences were relative, however, and evaluation =
of the=20
      Western bands shows that high levels of phosphorylation were =
common in=20
      nearly all tumors (see <A class=3D"side-supplink =
supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s001"=20
      rid=3D"pone.0007752.s001">Figure S1</A>).</DIV></DIV></DIV>
      <DIV class=3Dsec id=3Ds2c><SPAN></SPAN>
      <DIV class=3D"head2 head-separate">Identification of proteomic =
tumor classes=20
      by signaling pattern</DIV>
      <DIV class=3D"p p-first" id=3D__pid663661>The 44 core proteins =
identified in=20
      the previous analysis were then used to cluster the larger set of =
27=20
      glioma samples. K-means clustering of samples was performed as =
before,=20
      leaving out 15% of proteins (7 out of 44) with each of 10,000 =
iterations.=20
      As expected in this supervised approach, three-way clustering was =
the best=20
      fit and all but three glioma samples showed stable clustering into =

      signaling classes associated with EGFR, PDGF and NF1-loss (<A=20
      class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s003"=20
      rid=3D"pone.0007752.s003">Figure S3B</A>). <A=20
      class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g002/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 2</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 2"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 2"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g002.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g002.jpg"></SPAN></SPA=
N></A>=20
      summarizes how tumors are clustered by core signature proteins, =
and how=20
      these groups relate to tumor histopathology and genotype derived =
from aCGH=20
      profiling and resequencing of EGFR.</DIV>
      <DIV class=3Dcanvas-figure-ref-outer>
      <DIV class=3Dcanvas-figure-ref-inner><A id=3Dpone-0007752-g002=20
      name=3Dpone-0007752-g002></A>
      <TABLE class=3Dthumb-caption style=3D"CLEAR: both; WIDTH: 100%" =
cellSpacing=3D0=20
      cellPadding=3D0 border=3D0>
        <TBODY>
        <TR vAlign=3Dtop align=3Dleft>
          <TD class=3Dthumb-cell><A class=3D"icon-reflink figpopup"=20
            onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
            =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g002/">
            <DIV class=3Dthumb-ph><SPAN class=3Dlarge-thumb-canvas><SPAN =

            class=3Dlarge-thumb-canvas-1><IMG class=3D"icon-reflink =
large-thumb"=20
            title=3D"Figure 2"=20
            style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
            alt=3D"Figure 2"=20
            =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g002.gif"=20
            =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g002.jpg"></SPAN></SPA=
N>
            <DIV class=3Dsmall-thumb-canvas>
            <DIV class=3Dsmall-thumb-canvas-1><IMG=20
            class=3D"icon-reflink small-thumb" title=3D"Figure 2" =
alt=3D"Figure 2"=20
            =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g002.gif"></DIV></DIV></DIV></A></TD>
          <TD class=3Dcaption-cell>
            <DIV class=3Dcaption-ph><A class=3Dside-caption=20
            onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
            =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g002/"><STRONG>Figure=20
            2</STRONG></A>
            <DIV class=3Dfigure-table-caption-in-article><SPAN>K-means =
clustering=20
            of gliomas by signature-defining proteins.</SPAN></DIV>
            <DIV=20
      =
class=3Dfigure-table-caption-in-article></DIV></DIV></TD></TR></TBODY></T=
ABLE>
      <DIV class=3Dfigure-table-caption-in-article></DIV></DIV></DIV>
      <DIV style=3D"CLEAR: both"></DIV>
      <DIV class=3Dp id=3D__pid663752>Tumors with GBM histopathology =
were evenly=20
      distributed among the three core groups, six in each group. The =
only known=20
      secondary GBM clustered with the NF1-loss group. Two anaplastic=20
      astrocytomas (AA23 and AA.26) were found to cluster disparately =
with the=20
      PDGF and NF1 groups, respectively. Two of the four =
oligodendrogliomas=20
      clustered with the PDGF group: one low-grade (ODG.25) and one =
anaplastic=20
      (AO.24). Interestingly, one of the two low-grade =
oligodendrogliomas=20
      clustered with the EGFR group (ODG.22) and did in fact harbor =
high-level=20
      EGFR amplification. One anaplastic oligodendroglioma (AO.21) =
showed no=20
      distinct proteomic pattern and remained unclassified. There was a =
trend=20
      for untreated tumors in the EGFR tumor group (6 untreated vs. 1 =
treated)=20
      and for treated tumors in the PDGF group (3 untreated, 6 treated) =
but this=20
      was neither significant for GBM (p<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>0.11) nor for all tumors (p<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>0.09). Testing protein levels individually between =
treated and=20
      untreated GBM, PDGFB was the most significantly different and was =
higher=20
      in treated GBM (p<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>0.009) and in treated tumors overall (p<IMG title=3D"" =
alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>0.028) although neither was significant after =
correction for=20
      multiple testing.</DIV>
      <DIV class=3D"p p-last" id=3D__pid663765>24 of the 27 tumors for =
which=20
      sufficient tissue was available were analyzed by array-CGH =
(Agilent Whole=20
      Genome 244K) and resequencing of EGFR, PTEN and TP53. Array-CGH =
profiles=20
      were analyzed for copy number aberrations commonly described in =
GBM: focal=20
      amplification of <EM>EGFR</EM>, <EM>MET</EM> and <EM>PDGFRA</EM>; =
gain of=20
      chr7 without focal amplification; loss of chr10 or 10q23 region =
spanning=20
      <EM>PTEN</EM>; loss and/or homozygous deletion of 9p21 including=20
      Ink4a/ARF.<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17974913"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Furnari1">[1]</A>, <A class=3D"cite-reflink =
bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18077431"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Beroukhim1">[23]</A>, <A=20
      class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17114236"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Maher2">[24]</A> <A class=3D"fig-table-link =
fig figpopup"=20
      style=3D"TEXT-DECORATION: none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g002/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 2</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 2"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 2"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g002.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g002.jpg"></SPAN></SPA=
N></A>=20
      summarizes the finding of focal amplification of <EM>MET</EM> and=20
      <EM>EGFR</EM>, gain of chromosome 7, homozygous deletion spanning =
the=20
      <EM>Ink4a/ARF</EM> locus, and loss at PTEN locus. Complete ACGH =
profiles=20
      are depicted in <A class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s004"=20
      rid=3D"pone.0007752.s004">Figure S4</A>.</DIV>
      <DIV class=3Dsec id=3Ds2c1><SPAN></SPAN><SPAN class=3Dhead3>EGFR =
proteomic tumor=20
      class </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid663859>Six of the seven =
tumors in this=20
      class showed <EM>EGFR</EM>-region amplification and four showed =
point=20
      mutations in the extracellular domain (ECD) previously described =
in GBM as=20
      activating mutations: A289V (GBM.10 and GBM.6), T263P (GBM.8), =
G598V=20
      (GBM.1) and R108K (GBM.6).<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17177598"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Lee1">[25]</A> The only tumor in the EGFR =
signaling=20
      cluster that did not show focal <EM>EGFR</EM> amplification was =
found to=20
      harbor amplification of a narrow region including <EM>MET</EM>. =
Neither=20
      overexpression nor significant phosphorylation of EGFR protein was =
seen in=20
      this case. All tumors in the EGFR proteomic tumor class had =
deletion of=20
      the <EM>Ink4a/ARF</EM> locus compared with only 3/17 (18%) in the =
other=20
      groups. All had loss of ch10 and mutation of PTEN in the remaining =
allele=20
      was observed in one case.</DIV></DIV>
      <DIV class=3Dsec id=3Ds2c2><SPAN></SPAN><SPAN class=3Dhead3>PDGF =
proteomic tumor=20
      class </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid663902>Although this group =
of tumors=20
      is defined by evidence of PDGF signaling at the protein level, =
none of the=20
      9 tumors in this class showed gene amplification of either PDGF =
receptors=20
      or ligands. One tumor had both <EM>Ink4a/ARF</EM> region deletion =
and=20
      <EM>EGFR</EM> amplification, however total and phosphorylated EGFR =
levels=20
      in this tumor were low and PDGFB was present. Of note, a second =
tumor with=20
      focal <EM>MET</EM> amplification, GBM.18, was classified here and =
showed=20
      extremely high levels of PDGFB and associated =
signaling.</DIV></DIV>
      <DIV class=3D"sec sec-last" id=3Ds2c3><SPAN></SPAN><SPAN =
class=3Dhead3>NF1=20
      proteomic tumor class </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid663928>Tumors in this =
class included=20
      six GBM, one of which was a secondary GBM, one anaplastic =
astrocytoma, and=20
      one tumor with histopathologic features of GBM and synaptophysin=20
      positivity (=E2=80=9Cglioneuronal tumor=E2=80=9D, GNT.15). The =
NF1-associated class is=20
      distinguished by chr7 gain without focal amplification of either=20
      <EM>EGFR</EM> or the <EM>MET</EM> receptor which is significantly =
more=20
      frequent in this class (5/7, 71%) compared to the others (2/14, =
14%, p<IMG=20
      title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>0.017, Fisher's Exact test).</DIV></DIV></DIV>
      <DIV class=3Dsec id=3Ds2d><SPAN></SPAN>
      <DIV class=3D"head2 head-separate">Integrated analysis of =
molecularly=20
      defined subclasses of GBM from The Cancer Genome Atlas identifies =
distinct=20
      tumor subclasses enriched for mutations in <EM>EGFR</EM>, =
<EM>PDGFRA</EM>,=20
      and <EM>NF1</EM></DIV>
      <DIV class=3D"p p-first" id=3D__pid663962>Glioblastoma datasets =
from The=20
      Cancer Genome Atlas were analyzed for alterations in =
<EM>EGFR</EM>,=20
      <EM>PDGFRA</EM> and <EM>NF1</EM> and the possible association of =
mutations=20
      in these genes with transcriptomally-defined subclasses. Of 278 =
tumors for=20
      which chromosomal copy number and/or mutation data were available, =

      amplification and/or somatic non-synonymous mutation of =
<EM>EGFR</EM> was=20
      found in 40% (n<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>111) and of <EM>PDGFRA</EM> in 7% (n<IMG title=3D"" =
alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>19), while chromosomal loss and/or mutation of =
<EM>NF1</EM> was=20
      found in 16% (n<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>45). As shown in <A class=3D"fig-table-link fig =
figpopup"=20
      style=3D"TEXT-DECORATION: none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g003/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 3</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 3"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 3"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g003.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g003.jpg"></SPAN></SPA=
N></A>,=20
      genomic alterations in these three genes are largely mutually =
exclusive,=20
      suggesting distinct tumor subclasses among this portion of GBM =
samples for=20
      which clear genomic alterations could be detected.</DIV>
      <DIV class=3Dcanvas-figure-ref-outer>
      <DIV class=3Dcanvas-figure-ref-inner><A id=3Dpone-0007752-g003=20
      name=3Dpone-0007752-g003></A>
      <TABLE class=3Dthumb-caption style=3D"CLEAR: both; WIDTH: 100%" =
cellSpacing=3D0=20
      cellPadding=3D0 border=3D0>
        <TBODY>
        <TR vAlign=3Dtop align=3Dleft>
          <TD class=3Dthumb-cell><A class=3D"icon-reflink figpopup"=20
            onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
            =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g003/">
            <DIV class=3Dthumb-ph><SPAN class=3Dlarge-thumb-canvas><SPAN =

            class=3Dlarge-thumb-canvas-1><IMG class=3D"icon-reflink =
large-thumb"=20
            title=3D"Figure 3"=20
            style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
            alt=3D"Figure 3"=20
            =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g003.gif"=20
            =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g003.jpg"></SPAN></SPA=
N>
            <DIV class=3Dsmall-thumb-canvas>
            <DIV class=3Dsmall-thumb-canvas-1><IMG=20
            class=3D"icon-reflink small-thumb" title=3D"Figure 3" =
alt=3D"Figure 3"=20
            =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g003.gif"></DIV></DIV></DIV></A></TD>
          <TD class=3Dcaption-cell>
            <DIV class=3Dcaption-ph><A class=3Dside-caption=20
            onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
            =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g003/"><STRONG>Figure=20
            3</STRONG></A>
            <DIV =
class=3Dfigure-table-caption-in-article><SPAN>Integration of=20
            mutation and chromosomal copy number data from TCGA reveals=20
            aberrations of EGFR to be mutually exclusive of aberrations =
in=20
            PDGFRA and NF1.</SPAN></DIV>
            <DIV=20
      =
class=3Dfigure-table-caption-in-article></DIV></DIV></TD></TR></TBODY></T=
ABLE>
      <DIV class=3Dfigure-table-caption-in-article></DIV></DIV></DIV>
      <DIV style=3D"CLEAR: both"></DIV>
      <DIV class=3Dp id=3D__pid664038>We next sought to determine if =
these=20
      subclasses might be associated with distinct transcriptomal =
signatures.=20
      Using normalized gene expression profiles on 243 tumors downloaded =
from=20
      The Cancer Genome Atlas public portal, we applied unsupervised=20
      hierarchical clustering which identified 4 main cluster branches =
(<A=20
      class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g004/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 4</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 4"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 4"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g004.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g004.jpg"></SPAN></SPA=
N></A>).=20
      This grouping was concordant with comparable 4-way cluster =
structure=20
      recently reported by the TCGA.<A class=3D"cite-reflink bibr =
popnode"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
-Verhaak1"=20
      rid=3D"pone.0007752-Verhaak1">[26]</A> Integration of copy number=20
      aberration, mutation and expression of <EM>EGFR</EM>, =
<EM>PDGFRA</EM> and=20
      <EM>NF1</EM> revealed that three of the transcriptomal classes =
were=20
      enriched for alterations in each gene, respectively, although the=20
      segregation was imperfect. We named these three subclasses =
=E2=80=9CEGFR=20
      cocluster=E2=80=9D, =E2=80=9CPDGFRA cocluster=E2=80=9D and =
=E2=80=9CNF1 cocluster=E2=80=9D based on the=20
      predominant signal transduction pathway member enriched for =
mutation in=20
      each group. A fourth transcriptomal class had neither significant=20
      enrichment for mutations in either of <EM>EGFR</EM>, =
<EM>PDGFRA</EM> or=20
      <EM>NF1</EM>, nor enrichment for mutations in any other sequenced =
gene in=20
      the TCGA dataset. As shown in <A class=3D"fig-table-link fig =
figpopup"=20
      style=3D"TEXT-DECORATION: none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g004/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 4</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 4"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 4"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g004.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g004.jpg"></SPAN></SPA=
N></A>=20
      as described below, <EM>PDGFRA</EM> amplification was only present =
in the=20
      minority of PDGFRA-cocluster tumors and this transcriptomal class =
included=20
      a subset of tumors with EGFR or Met amplifications. The =
PDGFRA-cocluster=20
      showed high expression of <EM>GRIA2</EM>, <EM>OLIG2</EM>, and=20
      <EM>NCAM1/2</EM> as well as other genes which are signatures of =
the=20
      =E2=80=9CProneural=E2=80=9D transcriptomal class of GBM previously =
described.<A=20
      class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/16530701"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Phillips1">[19]</A> Conversely, signature =
genes of the=20
      =E2=80=9CMesenchymal=E2=80=9D GBM class such as =
<EM>YKL40/CHI3L1</EM>, <EM>IGFBP2</EM> and=20
      <EM>VEGFA</EM> were most highly expressed in the NF1-cocluster=20
      transcriptomal group (<A class=3D"side-supplink =
supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s005"=20
      rid=3D"pone.0007752.s005">Figure S5</A>). The EGFR-cocluster class =
showed=20
      intermediate expression levels of Proneural and Mesenchymal =
signature=20
      genes.</DIV>
      <DIV class=3Dcanvas-figure-ref-outer>
      <DIV class=3Dcanvas-figure-ref-inner><A id=3Dpone-0007752-g004=20
      name=3Dpone-0007752-g004></A>
      <TABLE class=3Dthumb-caption style=3D"CLEAR: both; WIDTH: 100%" =
cellSpacing=3D0=20
      cellPadding=3D0 border=3D0>
        <TBODY>
        <TR vAlign=3Dtop align=3Dleft>
          <TD class=3Dthumb-cell><A class=3D"icon-reflink figpopup"=20
            onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
            =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g004/">
            <DIV class=3Dthumb-ph><SPAN class=3Dlarge-thumb-canvas><SPAN =

            class=3Dlarge-thumb-canvas-1><IMG class=3D"icon-reflink =
large-thumb"=20
            title=3D"Figure 4"=20
            style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
            alt=3D"Figure 4"=20
            =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g004.gif"=20
            =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g004.jpg"></SPAN></SPA=
N>
            <DIV class=3Dsmall-thumb-canvas>
            <DIV class=3Dsmall-thumb-canvas-1><IMG=20
            class=3D"icon-reflink small-thumb" title=3D"Figure 4" =
alt=3D"Figure 4"=20
            =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g004.gif"></DIV></DIV></DIV></A></TD>
          <TD class=3Dcaption-cell>
            <DIV class=3Dcaption-ph><A class=3Dside-caption=20
            onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
            =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g004/"><STRONG>Figure=20
            4</STRONG></A>
            <DIV =
class=3Dfigure-table-caption-in-article><SPAN>Unsupervised=20
            transcriptomal clustering of GBM from the TCGA =
dataset.</SPAN></DIV>
            <DIV=20
      =
class=3Dfigure-table-caption-in-article></DIV></DIV></TD></TR></TBODY></T=
ABLE>
      <DIV class=3Dfigure-table-caption-in-article></DIV></DIV></DIV>
      <DIV style=3D"CLEAR: both"></DIV>
      <DIV class=3D"p p-last" id=3D__pid664202>Unsupervised clustering =
reflects the=20
      combined effect of multiple confounding influences on the =
transcriptome,=20
      including presence of necrosis, inflammatory cells, inclusion of =
brain=20
      parenchyma, etc. In order to clarify the specific relationship of=20
      <EM>EGFR</EM>, <EM>PDGFRA</EM> and <EM>NF1</EM> mutations to the=20
      transcriptome in GBM, we derived distinct expression signatures =
associated=20
      with mutation/aberration of these genes among the set of 147 =
tumors for=20
      which mutation/aberration was found in one and only one of the =
three.=20
      Together, 1,943 genes were identified which distinguished the =
three=20
      mutation classes (see <A class=3D"cite-reflink sec"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s4"=20
      rid=3D"s4">Methods</A>). Hierarchical clustering performed with =
this gene=20
      set on the full set of 243 GBM profiles resulted in clear division =
of GBM=20
      into just 3 subclasses, each enriched for the associated =
alteration of=20
      <EM>EGFR</EM>, <EM>PDGFRA</EM> and <EM>NF1</EM> (<A=20
      class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s006"=20
      rid=3D"pone.0007752.s006">Figure S6</A>).</DIV></DIV>
      <DIV class=3D"sec sec-last" id=3Ds2e><SPAN></SPAN>
      <DIV class=3D"head2 head-separate">Comparison of proteomic and=20
      transcriptomal subclasses</DIV>
      <DIV class=3D"p p-first" id=3D__pid664262>We investigated possible =

      correspondence between the proteomic EGFR, PDGF and NF1 classes =
and the=20
      transcriptomal EGFR-, PDGFRA-, and NF1-coclusters derived from =
TCGA data=20
      by comparing signature genomic aberrations. As shown in <A=20
      class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g004/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 4</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 4"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 4"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g004.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g004.jpg"></SPAN></SPA=
N></A>,=20
      integration of mutation and copy number data confirmed the strong=20
      association of <EM>EGFR</EM> amplification and mutation in tumors =
from the=20
      EGFR-cocluster (59/79, 75%) significantly more than in the other =
two=20
      classes (21/99, 21.2%, p<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>7.8e=E2=88=9213). This subset of samples also harbored =
frequent=20
      homozygous deletion of 9p21 spanning the <EM>Ink4a/ARF</EM> locus =
(75% vs=20
      35%, p<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>2.0e=E2=88=927). These findings were concordant with =
genomic profiling of=20
      tumors the EGFR signaling class. Conversely, chr7 gain without =
focal=20
      amplification of either <EM>EGFR</EM> or <EM>MET</EM> was most =
common in=20
      the NF1 transcriptomal cocluster (60.7% vs 23%, p<IMG title=3D"" =
alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>1.6e=E2=88=926), and this was concordant with aCGH =
profiling of tumors in=20
      the NF1 signaling class.</DIV>
      <DIV class=3Dp id=3D__pid664299>Among TCGA samples, amplifications =
of=20
      <EM>PDGFRA</EM> were more commonly seen in the PDGFRA =
transcriptomal=20
      cocluster (25.6% vs 1.5% in other classes; p<IMG title=3D"" =
alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>2.9e=E2=88=926) as were <EM>PDGFRA</EM> mutations =
(3/29<IMG title=3D""=20
      alt=3D" " =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>10.3% vs 0/79, p<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>0.049). However 4 out of 5 <EM>MET</EM>-amplified =
tumors were in=20
      this class and 7 tumors showed focal amplification of =
<EM>EGFR</EM>.=20
      Therefore there was no single copy number aberration =
distinguishing this=20
      class. There were no cases of <EM>PDGFRA</EM> amplification among =
the 24=20
      tumors in our study for which aCGH was performed. Among the 9 =
tumors in=20
      our PDGF signaling class, one had <EM>MET</EM> amplification and =
one had=20
      <EM>EGFR</EM> amplification. Despite the absence of=20
      <EM>PDGFRA</EM>-amplified cases in our sample set, the overall=20
      distribution of <EM>EGFR</EM>, <EM>PDGFRA</EM> and <EM>MET</EM>=20
      amplifications was found to be within the normal sampling error if =
one=20
      derives expectation frequencies from the TCGA data.</DIV>
      <DIV class=3Dp id=3D__pid664352>Comparison of genomic aberrations =
suggested a=20
      correspondence between proteomic classes of EGFR, NF1 and PDGF and =
the=20
      corresponding TCGA transcriptomal classes, therefore expression =
levels for=20
      genes encoding the core proteins (total forms) were next assessed =
in each=20
      of the four transcriptomal clusters. Among genes encoding =
EGFR-core=20
      proteins, the corresponding EGFR transcriptomal cocluster subclass =
showed=20
      significant overexpression of <EM>EGFR</EM>, <EM>JAG1</EM>, and=20
      <EM>HES1</EM> compared to the other subclasses (p&lt;1e=E2=88=925 =
for each gene).=20
      However other EGFR core proteins and Notch pathway members showed =
no=20
      elevation of mRNA expression in the corresponding transcriptomal =
class and=20
      therefore direct correlation could not be established.</DIV>
      <DIV class=3Dp id=3D__pid664372>Within the transcriptomal =
NF1-cocluster, the=20
      only overexpressed genes encoding NF1 core proteins were =
<EM>IRS1</EM> and=20
      <EM>YKL40/CHI3L1</EM>. As seen in <A class=3D"fig-table-link fig =
figpopup"=20
      style=3D"TEXT-DECORATION: none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g004/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 4</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 4"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 4"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g004.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g004.jpg"></SPAN></SPA=
N></A>,=20
      NF1 mRNA was strongly underexpressed in the NF1-cocluster class =
compared=20
      to other classes (p<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>4.4e=E2=88=9215), making <EM>NF1</EM> mRNA =
underexpression among the=20
      strongest signatures of the transcriptomal class.</DIV>
      <DIV class=3D"p p-last" id=3D__pid664399>Within the PDGFRA =
transcriptomal=20
      cocluster, <EM>TSC2</EM> and <EM>HEB/TCF12</EM> were the only =
genes among=20
      the PDGF core protein group significantly overexpressed =
(p&lt;1e=E2=88=924). The=20
      <EM>PDGFRB</EM> gene was significantly <EM>underexpressed</EM> in =
this=20
      group, concordant with our observation that total protein levels =
were=20
      higher in the EGFR class even while the phosphorylated receptor =
was=20
      correlated with the PDGF class. Overexpression of <EM>PDGFRA</EM> =
was a=20
      prominent feature of the PDGFRA-cocluster tumors =
(p&lt;1e=E2=88=9212), nearly=20
      always associated with gene amplification. Messenger RNA levels of =
genes=20
      encoding PDGF ligands were not elevated in the PDGFRA cocluster =
even among=20
      the subset of tumors showing <EM>PDGFRA</EM> amplification. We =
further=20
      investigated the relationship of PDGFB mRNA and protein levels in =
a=20
      validation set of 40 gliomas and found no correlation between mRNA =

      expression and levels of protein even though the latter were =
highly=20
      variable (<A class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s007"=20
      rid=3D"pone.0007752.s007">Figure S7</A>). This reflects the strong =

      regulation of PDGF at the level of translation rather than=20
      transcription.<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/2651898"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Pech1">[27]</A>, <A class=3D"cite-reflink bibr =
popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/3275870"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Rao1">[28]</A> It is likely that some =
signaling proteins=20
      in our study are closely coupled to mRNA levels while many others =
are=20
      regulated independently (or in negative feedback) with =
corresponding=20
      mRNA.</DIV></DIV></DIV></DIV>
      <DIV class=3Dsec id=3Ds3><SPAN></SPAN>
      <DIV class=3D"head1 section-title" id=3Ds3titletitle=20
      style=3D"TEXT-TRANSFORM: none">
      <DIV class=3Dother-sections>
      <UL class=3D"noext-menu noext-menu-hidden">
        <LI><A class=3Dfirst-link=20
        =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">&nbsp;Othe=
r=20
        Sections=E2=96=BC</A>
        <UL class=3D"submenu head1">
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__abstractid=
607974">Abstract</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s1">Introduc=
tion</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s2">Results<=
/A>
          <LI class=3D"submenu-item current-item"><A class=3D""=20
          style=3D"TEXT-TRANSFORM: none" onclick=3Dreturn(false)=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">Discussion=
</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s4">Methods<=
/A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s5">Supporti=
ng=20
          Information</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__ref-listid=
665409">References</A></LI></UL></LI></UL></DIV>
      <DIV>Discussion</DIV></DIV>
      <DIV class=3Dsection-content id=3Ds3content>
      <DIV class=3D"p p-first" id=3D__pid664474>Given the importance of =
signaling in=20
      the biology of gliomas, dividing these tumors into subsets by the =
pattern=20
      of coordinate signaling pathway activation may have practical =
implications=20
      for choice of therapies and for interpretation of patient =
responses in=20
      existing clinical trials. In order to clarify the net activation =
of=20
      signaling pathways we used a targeted proteomic analysis to =
determine not=20
      only the levels but the posttranslational modifications associated =
with=20
      signaling activity. The intrinsic cellular heterogeneity of =
gliomas is=20
      masked by the methods used in this study since both the proteomic =
and TCGA=20
      genomic analyses are performed on homogenized tissue, blending the =

      characteristics of the cells together. Additionally, the small =
sample size=20
      and selection of proteins in this study limits the statistical =
power to=20
      define protein correlations and sample assignments. Nonetheless, =
we find=20
      common features defining three basic groups by both genomic and =
protein=20
      analysis, illustrating the high complementarity between protein =
signaling=20
      activity, transcriptomal signature and genomic alteration in GBM. =
The=20
      observed enrichment of <EM>EGFR</EM>, <EM>PDGFRA</EM> and =
<EM>NF</EM>=20
      genomic alterations with transcriptome pattern could mean that =
signaling=20
      activity directly influences the transcriptome and/or that both =
signaling=20
      and the transcriptome patterns are part of a common underlying =
phenotype.=20
      Comparing unsupervised and supervised clustering results, it is =
likely=20
      that only a portion of the transcriptomal features distinguishing=20
      unsupervised clusters are associated with signaling, either =
directly or=20
      indirectly. In fact, unsupervised clustering identifies four =
clusters and=20
      broader phenotypic and genetic differences distinguishing these =
four=20
      transcriptomal groups have been reported.<A=20
      class=3D"cite-reflink bibr popnode"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
-Verhaak1"=20
      rid=3D"pone.0007752-Verhaak1">[26]</A></DIV>
      <DIV class=3Dp id=3D__pid664512>Analysis of the downstream =
signaling=20
      components of the PDGF proteomic group revealed generally lower =
PI3K/Akt=20
      activity than in the EGFR glioma group although S6 phosphorylation =
was=20
      paradoxically high. Histologic analysis of the tumors provided an=20
      explanation by demonstrating that strong pS6 immunopositivity was=20
      localized in reactive astrocytes rather than tumor cells per se =
(data not=20
      shown), concordant with recent observations of mTOR activation in =
reactive=20
      astrocytes under experimental conditions of injury.<A=20
      class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/19176818"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Codeluppi1">[29]</A> These cells were more =
common in=20
      PDGF-class tumors. We found a trend for treated tumors to be in =
the PDGF=20
      proteomic class and PDGFB levels were significantly higher in =
treated=20
      compared to untreated tumors. It is possible that some of the =
features of=20
      the PDGF signaling pattern are influenced by prior treatment =
though it is=20
      unlikely that this accounts for the genotypic differences in this=20
      proteomic tumor class, such as the paucity of EGFR amplification, =
chr7=20
      gain and Ink4a/ARF locus deletion. Comparison with treated samples =
in TCGA=20
      is complicated by the fact that the current dataset contains few =
treated=20
      cases and of these, many are secondary GBM which would arguably be =

      assigned to the PDGFRA co-cluster by their common Proneural=20
      signature.</DIV>
      <DIV class=3Dp id=3D__pid664536>The histology of the TCGA samples =
was=20
      uniformly GBM, but this is a histologically heterogeneous tumor =
type. A=20
      priori, it is possible that the transcriptomal classes identified =
in this=20
      analysis could be related to tumor sampling or microenvironment. =
However,=20
      this does not appear to be the case since well-defined genetic =
lesions are=20
      enriched in specific tumor classes and there is no evidence for =
regional=20
      localization of mutations in glioma as a general phenomenon. =
Although=20
      clinical and pathologic data are limited and a more detailed =
review of=20
      this information is underway, there appeared little clinical or=20
      histological differences between the three groups identified in =
this=20
      analysis. PDGFRA-cocluster tumors in TCGA occurred in younger =
patients,=20
      and there were small but significant differences in the amount of=20
      associated necrosis and inflammatory cells (data not shown).</DIV>
      <DIV class=3Dp id=3D__pid664546>It remains to be established =
whether=20
      ligand-driven PDGF signaling is common among tumors in the =
transcriptomal=20
      PDGFRA-cocluster and whether this is functionally important. We =
have shown=20
      that PDGFB ligand levels are highly variable in GBM, are =
associated with=20
      receptor activation, and are not correlated with mRNA expression. =
The=20
      PDGFRA-cocluster transcriptomal class shares features with the =
Proneural=20
      group of gliomas identified by Phillips et al using transcription=20
      analysis, and is characterized by genes expressed during normal =
cortical=20
      oligodendrocyte development such as olig2, Sox2 and doublecortin =
and=20
      signaling pathways involved in that process as well, such as PDGF =
and SHH.=20
      While the PDGFRA-cocluster group is enriched for Proneural =
signature=20
      genes, it is important to note that the original signature was =
derived=20
      from a dataset of mixed histologies and the analysis designed =
specifically=20
      to resolve a prognostic signature. Therefore the exact =
relationship=20
      between our PDGF proteomic class, the PDGFRA co-cluster, and =
gliomas=20
      harboring Proneural signature is unclear and will need to be =
further=20
      investigated.</DIV>
      <DIV class=3Dp id=3D__pid664558>Although <EM>PDGFRA</EM> =
amplification=20
      predominated in the PDGFRA-cocluster transcriptomal group, a full =
15%=20
      showed amplified <EM>EGFR</EM> and another 15% showed amplified=20
      <EM>MET</EM>. From the prevalence of PDGF signaling we found at =
the=20
      protein level one might hypothesize the existence of concurrent =
PDGF=20
      signaling in <EM>EGFR</EM>- and <EM>MET</EM>- amplified tumors in =
this=20
      class. In fact, we found two such tumors in our proteomic =
analysis: one=20
      <EM>EGFR</EM>- and one <EM>MET</EM>-amplified, both with high =
levels of=20
      PDGFB, phosphorylation of PDGFR=CE=B2 and an overall signaling =
pattern matching=20
      the PDGF proteomic class. It is unclear in these cases whether the =
level=20
      of PDGF pathway activation is functionally important, perhaps in a =

      subpopulation of cells. It is notable that 6 tumors in TCGA show =
focal=20
      amplification of both <EM>PDGFRA</EM> and another RTK: four cases =
sharing=20
      focal co-amplification of <EM>EGFR</EM>, and two cases sharing =
focal=20
      co-amplifications of <EM>PDGFRA</EM> and <EM>MET</EM>.</DIV>
      <DIV class=3D"p p-last" id=3D__pid664610>In conclusion, our =
findings support a=20
      division of GBMs into three classes according to patterns of =
signal=20
      transduction pathway activation. These patterns reflect, in part, =
mutually=20
      exclusive signaling involving EGFR, PDGF RTK activation or NF1 =
silencing.=20
      Both the transcriptomal and proteomic classes were imperfectly =
related to=20
      genotype, suggesting that molecular assays used in patient =
stratification=20
      and clinical trial analysis should include measures of PDGF ligand =
and=20
      receptor phosphorylation as well as NF1 expression. Notch =
signaling was=20
      prominently associated with the EGFR class at the protein level, =
an=20
      observation which was not predicted by mRNA expression levels of =
Notch=20
      pathway members in EGFR-altered tumors from TCGA. Whether one or =
more=20
      non-EGF/PDGF RTKs are contributing to NF1 tumors is uncertain, but =
the=20
      finding that NF1-silenced tumors show elevated MET, HGF and IRS1 =
at the=20
      transcriptomal level and validation of IRS1 at the protein level =
suggest=20
      IGF and or MET signaling may be contributory. Further refinement =
of GBM=20
      subclasses will likely come from direct investigations of these =
and other=20
      signaling proteins, as well as investigation of newly described =
recurrent=20
      mutations in GBM such as ERBB2 and IDH1. The current study =
provides an=20
      initial architecture for such subclasses and suggests the =
potential for=20
      class-directed therapies.</DIV></DIV></DIV>
      <DIV class=3Dsec id=3Ds4><SPAN></SPAN>
      <DIV class=3D"head1 section-title" id=3Ds4titletitle=20
      style=3D"TEXT-TRANSFORM: none">
      <DIV class=3Dother-sections>
      <UL class=3D"noext-menu noext-menu-hidden">
        <LI><A class=3Dfirst-link=20
        =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">&nbsp;Othe=
r=20
        Sections=E2=96=BC</A>
        <UL class=3D"submenu head1">
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__abstractid=
607974">Abstract</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s1">Introduc=
tion</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s2">Results<=
/A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s3">Discussi=
on</A>
          <LI class=3D"submenu-item current-item"><A class=3D""=20
          style=3D"TEXT-TRANSFORM: none" onclick=3Dreturn(false)=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">Methods</A=
>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s5">Supporti=
ng=20
          Information</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__ref-listid=
665409">References</A></LI></UL></LI></UL></DIV>
      <DIV>Methods</DIV></DIV>
      <DIV class=3Dsection-content id=3Ds4content>
      <DIV class=3D"sec sec-first" id=3Ds4a><SPAN></SPAN>
      <DIV class=3D"head2 head-separate">Ethics statement</DIV>
      <DIV class=3D"p p-first-last" id=3D__pid664642>The collection and =
use of the=20
      human tissues in this study were performed after obtaining written =
consent=20
      from all participants, in accordance with a study protocol =
approved by the=20
      Institutional Review Board of Memorial Sloan-Kettering Cancer =
Center. Data=20
      from The Cancer Genome Atlas public portal were obtained under an =
approved=20
      Data Access Request.</DIV></DIV>
      <DIV class=3Dsec id=3Ds4b><SPAN></SPAN>
      <DIV class=3D"head2 head-separate">Surgical glioma sample =
analysis</DIV>
      <DIV class=3D"sec sec-first" id=3Ds4b1><SPAN></SPAN><SPAN =
class=3Dhead3>Tumor=20
      samples </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid664663>Tumors were =
snap-frozen in the=20
      operating room, and stored at =E2=88=9280=C2=B0C. Samples in =
liquid nitrogen were=20
      ground to powder and protein was extracted through lysis with =
T-per tissue=20
      extract solution (Pierce) supplemented with 30 mM sodium fluoride, =
1 mM=20
      sodium vanadate, and protease inhibitor cocktail tablets (Roche). =
Protein=20
      concentrations were determined by bicinchoninic acid assay (BCA) =
method=20
      (Bio-Rad).</DIV></DIV>
      <DIV class=3Dsec id=3Ds4b2><SPAN></SPAN><SPAN =
class=3Dhead3>Western blot=20
      analysis </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid664676>Samples (100 =
=C2=B5g) were separated=20
      by 6, 8, 10, or 12% SDS-PAGE gel, and transferred onto =
polyvinylidene=20
      difluoride membrane (Millipore). For qualitative comparison, =
analysis=20
      included normal brain cortex lysate as previously described =
(Analytical=20
      Biological Services Inc).<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18472967"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Lyustikman1">[30]</A> Membranes were blocked =
with 5%=20
      nonfat milk in PBS-0.1% Tween 20. Primary and secondary antibodies =
were=20
      diluted in the blocking solution. Signal was visualized using =
enhanced=20
      chemiluminescence (Amersham Biosciences). Primary antibodies used =
in this=20
      study are listed in <A class=3D"side-supplink =
supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s008"=20
      rid=3D"pone.0007752.s008">Table S1</A>. Secondary =
peroxidase-conjugated=20
      anti-rabbit antibody (Amersham Biosciences), anti-mouse and =
anti-goat=20
      antibodies (Roche) were used at 1<IMG title=3D"" alt=3D[ratio]=20
      src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/x2236.gif" =

      border=3D0>1,000 dilution. For NF1, 50 ug of lysate was run on 6% =
gel and=20
      secondary antibody was 1<IMG title=3D"" alt=3D[ratio]=20
      src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/x2236.gif" =

      border=3D0>10,000 dilution. PDGFR=CE=B1 total protein was assayed =
at a later date=20
      by western blot of frozen banked lysate aliquots (Santa Cruz, =
#sc-338,=20
      1<IMG title=3D"" alt=3D[ratio]=20
      src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/x2236.gif" =

      border=3D0>500, secondary 1<IMG title=3D"" alt=3D[ratio]=20
      src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/x2236.gif" =

      border=3D0>10,000). Because of low band intensity a second =
PDGFR=CE=B1 antibody=20
      was tested as well and gave concordant results (Cell Signaling =
#3174,=20
      1<IMG title=3D"" alt=3D[ratio]=20
      src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/x2236.gif" =

      border=3D0>1000, secondary 1<IMG title=3D"" alt=3D[ratio]=20
      src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/x2236.gif" =

      border=3D0>2,000). The density of each band was read and =
quantified using=20
      Adobe Photoshop and NIH Image 1.63 software and normalized by =
actin=20
      control. PDGFR=CE=B1 western was normalized to =
tubulin.</DIV></DIV>
      <DIV class=3Dsec id=3Ds4b3><SPAN></SPAN><SPAN =
class=3Dhead3>Activated ras=20
      pull-down assay </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid664719>Activated K-ras =
(K-ras-GTP) was=20
      tested by using 500 =C2=B5g samples for activated Ras pull-down =
with 10 =C2=B5g of=20
      glutathione-conjugated Raf-1 GST-RBD beads (Upstate Biotechnology) =
as=20
      previously described.<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/15967117"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Dai1">[31]</A></DIV></DIV>
      <DIV class=3Dsec id=3Ds4b4><SPAN></SPAN><SPAN =
class=3Dhead3>Unsupervised=20
      clustering of protein data </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid664741>Quantified western =
data were=20
      standardized for each protein by mean and standard deviation =
across the=20
      sample cohorts. Standardization was done first on the glioblastoma =
samples=20
      (n<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>20) for unsupervised clustering analysis of protein =
level, then=20
      again separately on the whole sample set (n<IMG title=3D"" alt=3D" =
"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>27) for cluster analysis of samples. For the purpose of =
display,=20
      NF1 is represented as =E2=80=9CNF1-loss=E2=80=9D, or zero minus =
standardized NF1 quantity=20
      on western. All statistical analyses and plotting were done in R =
(<SPAN=20
      class=3Dext-reflink><A class=3Dext-reflink =
onclick=3D"focuswin('pmc_ext')"=20
      href=3D"http://www.cran.org/" target=3Dpmc_ext=20
      =
ref=3D"reftype=3Dextlink&amp;article-id=3D2771920&amp;issue-id=3D182378&a=
mp;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DExternal%7CLink%7C=
URI&amp;rendering-type=3Dnormal">http://www.cran.org/</A></SPAN>).=20
      Principal component analysis was performed on standardized data. =
K-means=20
      clustering of quantified protein levels for 20 GBM samples was =
performed=20
      in R, and stability of cluster assignment assessed over 10,000 =
iterations=20
      leaving out 15% of tumors with each iteration (kmeans, stats =
package,=20
      <SPAN class=3Dext-reflink><A class=3Dext-reflink =
onclick=3D"focuswin('pmc_ext')"=20
      href=3D"http://www.cran.org/" target=3Dpmc_ext=20
      =
ref=3D"reftype=3Dextlink&amp;article-id=3D2771920&amp;issue-id=3D182378&a=
mp;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DExternal%7CLink%7C=
URI&amp;rendering-type=3Dnormal">http://www.cran.org/</A></SPAN>).=20
      Consensus matrices were generated for each k-clustering over all=20
      iterations and assessed visually as well as by cophenetic =
correlation.=20
      Core correlated protein clusters are defined for 3-way clustering =
as=20
      &gt;95% consensus. Proteins in these core clusters were selected =
for=20
      k-means analysis of 27 gliomas using, as before, an 85% resampling =
of=20
      proteins and consensus matrix analysis over 10,000 =
iterations.</DIV></DIV>
      <DIV class=3D"sec sec-last" id=3Ds4b5><SPAN></SPAN><SPAN =
class=3Dhead3>ACGH and=20
      resequencing </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid664779>Genomic DNA was =
extracted from=20
      primary tumors using standard techniques. DNA was then digested =
and=20
      labeled and hybridized to 244K CGH arrays according to =
manufacturer=20
      guidelines (Genomic DNA labeling kit PLUS, Agilent). This array =
consists=20
      of &gt;238,000 coding and non-coding sequences allotted to =
assembly map=20
      positions (NCBI, Build 35). Normal male genomic DNA (Promega, =
Madison, WI)=20
      was used as a reference. After washing, the slides were scanned =
with an=20
      Agilent scanner and images quantified using Feature Extraction =
9.5.3.1=20
      (Agilent). Fluorescence ratios of the scanned images were =
calculated and=20
      the raw aCGH profiles were processed to identify statistically =
significant=20
      transitions in copy number using the Circular Binary Segmentation=20
      algorithm.<A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/15475419"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Olshen1">[32]</A> Each profile was centered so =
that log2=20
      ratio of zero is assigned to the predominant copy number, =
determined by=20
      the mode of the distribution of the mean log2 ratio for each =
segment,=20
      weighted by the number of probes per segment . After =
mode-centering, gains=20
      and losses for a subset of analyses were defined as segment mean =
log2=20
      ratios of &gt;0.2 or &lt;=E2=88=920.2 and amplification and =
deletions as &gt;2 or=20
      &lt;=E2=88=921, respectively. Additionally, sample-specific =
thresholds for=20
      alterations were computed for all other analyses. The annotated =
microarray=20
      data for the sample set is available on GEO (<SPAN =
class=3Dext-reflink><A=20
      class=3Dext-reflink onclick=3D"focuswin('pmc_ext')"=20
      href=3D"http://www.ncbi.nlm.nih.gov/geo" target=3Dpmc_ext=20
      =
ref=3D"reftype=3Dextlink&amp;article-id=3D2771920&amp;issue-id=3D182378&a=
mp;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DExternal%7CLink%7C=
URI&amp;rendering-type=3Dnormal">www.ncbi.nlm.nih.gov/geo</A></SPAN>,=20
      <SPAN class=3Dext-reflink><A class=3Dext-reflink =
onclick=3D"focuswin('pmc_ext')"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=3DGSE17381"=20
      target=3Dpmc_ext=20
      =
ref=3D"reftype=3Dextlink-entrez-geo&amp;article-id=3D2771920&amp;issue-id=
=3D182378&amp;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%=
7CTerm%7CGEO%20DataSets&amp;rendering-type=3Dnormal">GSE17381</A></SPAN>)=
.</DIV></DIV></DIV>
      <DIV class=3D"sec sec-last" id=3Ds4c><SPAN></SPAN>
      <DIV class=3D"head2 head-separate">Integrated analysis of genomic =
data from=20
      The Cancer Genome Atlas</DIV>
      <DIV class=3D"sec sec-first" id=3Ds4c1><SPAN></SPAN><SPAN =
class=3Dhead3>Dataset=20
      compilation and analysis </SPAN>
      <DIV class=3D"p p-first" id=3D__pid664839>A description of TCGA =
data types,=20
      platforms and analyses are as previously described.<A=20
      class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18772890"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Network1">[8]</A> Processed genomic datasets =
were=20
      downloaded from The Cancer Genome Atlas public data portal (<SPAN=20
      class=3Dext-reflink><A class=3Dext-reflink =
onclick=3D"focuswin('pmc_ext')"=20
      href=3D"http://cancergenome.nih.gov/dataportal/" target=3Dpmc_ext=20
      =
ref=3D"reftype=3Dextlink&amp;article-id=3D2771920&amp;issue-id=3D182378&a=
mp;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DExternal%7CLink%7C=
URI&amp;rendering-type=3Dnormal">http://cancergenome.nih.gov/dataportal/<=
/A></SPAN>)=20
      as available on May, 2009. Specific data sources were as follows: =
For mRNA=20
      expression, =E2=80=9CLevel 3=E2=80=9D normalized gene expression =
derived from the Cancer=20
      Genome Characterization Center (CGCC) at the Broad Institute, MIT=20
      (Affymetrix Human Genome HTS U133A 2.0). For chromosomal copy =
number,=20
      =E2=80=9CLevel 3=E2=80=9D normalized and segmented copy number =
data from the CGCC at=20
      Memorial Sloan-Kettering Cancer Center (Agilent 244K CGH Array). =
From this=20
      array-CGH dataset one unique profile was selected for each tumor =
based on=20
      the highest signal-to-noise estimate. For sequencing data, we =
combined all=20
      available sequencing data summaries in =E2=80=9Cmultiple alignment =
format=E2=80=9D (MAF)=20
      files as of May 2009: broad.mit.edu GBM.ABI.1, genome.wustl.edu=20
      GBM.ABI.53, hgsc.bcm.edu GBM.ABI.1.maf and GBM.ABI.2. Mutations =
were=20
      further filtered by excluding events which were classified as =
=E2=80=9Csomatic,=E2=80=9D=20
      =E2=80=9Csynonymous=E2=80=9D or =E2=80=9Csilent,=E2=80=9D or =
=E2=80=9Cunvalidated,=E2=80=9D</DIV>
      <DIV class=3D"p p-last" id=3D__pid664871>A list of the sample IDs =
and the=20
      summary of genomic data are given in <A=20
      class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s010"=20
      rid=3D"pone.0007752.s010">Table S3</A>. 243 samples had gene =
expression from=20
      Affymetrix U133A platform. Of these, 237 also had aCGH data and =
159 had=20
      mutation data available. Level 3 array-CGH data was used for local =
copy=20
      number estimation. Amplification was defined by regional log2 =
ratio=20
      &gt;2.0. Gene loss was classified by minimal log2 ratio (log2R) =
across the=20
      gene as follows: =E2=80=9Csingle copy loss=E2=80=9D<IMG title=3D"" =
alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=E2=88=921.0&lt;log2R&lt;=E2=88=920.2; =
=E2=80=9Chomozygous deletion=E2=80=9D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>log2R&lt;=E2=88=921.0.</DIV></DIV>
      <DIV class=3D"sec sec-last" id=3Ds4c2><SPAN></SPAN><SPAN=20
      class=3Dhead3>Clustering of TCGA expression dataset </SPAN>
      <DIV class=3D"p p-first-last" id=3D__pid664896>Unsupervised =
clustering of TCGA=20
      Level 3 expression data was performed on 1,807 genes representing =
the top=20
      15%ile of variance (hierarchical clustering, correlation metric, =
complete=20
      linkage; hclust, R package:stats,). Supervised cluster analysis =
was=20
      performed as follows: 147 samples were identified harboring only =
one of=20
      either EGFR mutation/amplification (n<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>103), PDGFRA mutation/amplification (n<IMG title=3D"" =
alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>14) or NF1 mutation/loss (n<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>30). Kruskal-Wallis (kruskal.test, R package:stats) =
test was used=20
      to identify genes which discriminate between EGFR-, PDGFRA- and=20
      NF1-altered samples. Because only 14 samples in TCGA set harbor =
solitary=20
      PDGFRA alteration, the numbers of profiles in each class are =
balanced by=20
      sampling 14 of the 103 EGFR-altered and 14 of the 30 NF1-altered =
samples=20
      and the KW test is run iteratively 1000 times with resampling. =
1,953 genes=20
      were found to show KW p-values &lt;0.05 in &gt;95% of iterations =
and these=20
      were used to perform supervised hierarchical clustering. =
Calculation of=20
      significance for differences between cluster was by Fisher's Exact =
Test (R=20
      package:stats) using cluster assignments for PDGFRA, NF1 and=20
      EGFR-coclusters derived from unsupervised clustering, and =
excluding=20
      samples belonging to the =E2=80=9CIndeterminate Genotype=E2=80=9D=20
      cluster.</DIV></DIV></DIV></DIV></DIV>
      <DIV class=3Dsec id=3Ds5><SPAN></SPAN>
      <DIV class=3D"head1 section-title" id=3Ds5titletitle=20
      style=3D"TEXT-TRANSFORM: none">
      <DIV class=3Dother-sections>
      <UL class=3D"noext-menu noext-menu-hidden">
        <LI><A class=3Dfirst-link=20
        =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">&nbsp;Othe=
r=20
        Sections=E2=96=BC</A>
        <UL class=3D"submenu head1">
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__abstractid=
607974">Abstract</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s1">Introduc=
tion</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s2">Results<=
/A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s3">Discussi=
on</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s4">Methods<=
/A>
          <LI class=3D"submenu-item current-item"><A class=3D""=20
          style=3D"TEXT-TRANSFORM: none" onclick=3Dreturn(false)=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">Supporting=
=20
          Information</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__ref-listid=
665409">References</A></LI></UL></LI></UL></DIV>
      <DIV><A id=3Dsupplementary-material-sec></A>Supporting=20
      Information</DIV></DIV>
      <DIV class=3Dsection-content id=3Ds5content><!--body-->
      <DIV class=3Dp id=3Dpone.0007752.s001>Figure S1
      <DIV class=3Dp id=3D__pid664933>Selected bands from western blots =
which were=20
      quantified in this study. Signaling class assignments are shown =
for those=20
      samples with stable clustering: =E2=80=9CP=E2=80=9D<IMG title=3D"" =
alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0> PDGF class, =E2=80=9CN=E2=80=9D<IMG title=3D"" alt=3D" =
"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>NF1 class, and =E2=80=9CE=E2=80=9D<IMG title=3D"" =
alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>EGFR class.</DIV>
      <DIV class=3Dp id=3D__pid664938>(6.30 MB TIF)</DIV>
      <DIV class=3Dsupplementary-material-media-label-caption><A =
class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.0007=
752.s001.tif">Click=20
      here for additional data file.</A><SUP>(6.0M, =
tif)</SUP></DIV></DIV>
      <DIV class=3Dp id=3Dpone.0007752.s002>Figure S2
      <DIV class=3Dp id=3D__pid664968>Principal Componenet Analysis of =
Quantified=20
      Protein Levels: Fractional variance for principal components from =
the=20
      analysis of quantified protein levels in 20 GBM samples. The first =
two=20
      components together account for 51% of total variance and are =
plotted in=20
      <A class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g001/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 1A</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 1"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 1"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g001.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g001.jpg"></SPAN></SPA=
N></A>.</DIV>
      <DIV class=3Dp id=3D__pid664983>(0.34 MB TIF)</DIV>
      <DIV class=3Dsupplementary-material-media-label-caption><A =
class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.0007=
752.s002.tif">Click=20
      here for additional data file.</A><SUP>(334K, =
tif)</SUP></DIV></DIV>
      <DIV class=3Dp id=3Dpone.0007752.s003>Figure S3
      <DIV class=3Dp id=3D__pid665013>Analysis of stable cluster =
assignment by=20
      k-means for varying cluster count: K-means clustering of =
quantified and=20
      standardized protein levels in GBM; classification of gliomas by =
core=20
      protein expression patterns. For each analysis, K-means was run =
for 10,000=20
      iterations leaving out 15% of data with each iteration. Shown are=20
      consensus matrices for division into 2=E2=80=934 clusters, and =
cophenetic=20
      correlations for division into 2=E2=80=938 clusters. (A) =
Clustering of 55 proteins=20
      in 20 GBM samples shows stable two-way and three-way clustering =
with peak=20
      cophenetic correlations ~0.98. Details for 3-way clustering are =
shown in=20
      <A class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g001/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 1B</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 1"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 1"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g001.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g001.jpg"></SPAN></SPA=
N></A>=20
      in the main text. Three sets of =E2=80=9Ccore=E2=80=9D proteins =
(n<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>46 total) are defined by their stable cluster =
membership in=20
      &gt;95% of iterations. (B) 27 glioma samples clustered by 44 core =
proteins=20
      identified in the preceding analysis and highlighted in <A=20
      class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g001/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 1B</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 1"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 1"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g001.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g001.jpg"></SPAN></SPA=
N></A>.=20
      Gliomas are classified into 3 types based on the levels of 44 =
total and=20
      activated protein forms.</DIV>
      <DIV class=3Dp id=3D__pid665044>(1.04 MB TIF)</DIV>
      <DIV class=3Dsupplementary-material-media-label-caption><A =
class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.0007=
752.s003.tif">Click=20
      here for additional data file.</A><SUP>(1012K, =
tif)</SUP></DIV></DIV>
      <DIV class=3Dp id=3Dpone.0007752.s004>Figure S4
      <DIV class=3Dp id=3D__pid665073>Genomic profiling of gliomas =
clustered by=20
      signaling class: Array-CGH shows high concordance between EGFR =
signaling=20
      class and amplification of EGFR locus and deletion of the =
Ink4a/ARF locus.=20
      Tumors in the NF1 class show frequent gain of chr7 without focal=20
      amplification of either EGFR or MET. Of the two tumors which do =
have focal=20
      MET amplification, one clusters with EGFR-class and the other with =

      PDGF-class. No amplification of PDGFRA was found in any of the=20
      samples.</DIV>
      <DIV class=3Dp id=3D__pid665080>(0.96 MB TIF)</DIV>
      <DIV class=3Dsupplementary-material-media-label-caption><A =
class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.0007=
752.s004.tif">Click=20
      here for additional data file.</A><SUP>(934K, =
tif)</SUP></DIV></DIV>
      <DIV class=3Dp id=3Dpone.0007752.s005>Figure S5
      <DIV class=3Dp id=3D__pid665110>Expression of Proneural and =
Mesenchymal=20
      signature genes in transcriptomal subclasses: Expression analysis =
of=20
      Proneural and Mesenchymal signature genes across transcriptomal =
subclasses=20
      derived from The Cancer Genome Atlas. Unsupervised clustering of =
TCGA=20
      samples and subclass assignments are as shown in <A=20
      class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g004/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 4</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 4"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 4"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g004.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g004.jpg"></SPAN></SPA=
N></A>.=20
      Tumor profiles in each subclass are assessed for enrichment of =
signature=20
      genes defining the Proneural and Mesenchymal transcriptomal =
classes of GBM=20
      previously described <A class=3D"cite-reflink bibr popnode"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pubmed/16530701"=20
      =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DEntrez%7CPubMed%7CR=
ecord&amp;rendering-type=3Dnormal"=20
      rid=3D"pone.0007752-Phillips1">[19]</A>. Box plots show the =
distribution of=20
      mean percentile rank for expression of Proneural and Mesenchymal =
signature=20
      gene sets courtesy of Kenneth Aldape, MD: Proneural<IMG title=3D"" =
alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0> BMP2, GRIA2, OMG, NCAM1&amp;2, OLIG2, BCAN, RTN1, =
SNAP91,=20
      GABBR1&amp;2, and KCNB1; Mesenchymal<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0>=3D<IMG title=3D"" alt=3D" "=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcents/thinsp.gif"=20
      border=3D0> YKL40/CHI3L1, IGF2BP3, VEGFA, COL1A1, COL5A2, =
COL3A1.</DIV>
      <DIV class=3Dp id=3D__pid665139>(0.35 MB TIF)</DIV>
      <DIV class=3Dsupplementary-material-media-label-caption><A =
class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.0007=
752.s005.tif">Click=20
      here for additional data file.</A><SUP>(345K, =
tif)</SUP></DIV></DIV>
      <DIV class=3Dp id=3Dpone.0007752.s006>Figure S6
      <DIV class=3Dp id=3D__pid665169>Supervised transcriptomal =
clustering of GBM=20
      tumors in The Cancer Genome Atlas: Clustering of 243 GBM samples =
form TCGA=20
      using ~1,900 genes selected for their ability to discriminate =
three=20
      genotypes: EGFR mutation/amplification, PDGFRA =
mutation/amplification or=20
      NF1 mutation/deletion (see <A class=3D"cite-reflink sec"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s4"=20
      rid=3D"s4">Methods</A>). Sample set and figure legend are as shown =
in <A=20
      class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g004/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 4</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 4"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 4"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g004.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g004.jpg"></SPAN></SPA=
N></A>=20
      and clustering methods differ only in the subset of genes used. =
Samples=20
      are clustered into three divisions each enriched for one of the =
three=20
      genotypes.</DIV>
      <DIV class=3Dp id=3D__pid665195>(0.91 MB TIF)</DIV>
      <DIV class=3Dsupplementary-material-media-label-caption><A =
class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.0007=
752.s006.tif">Click=20
      here for additional data file.</A><SUP>(891K, =
tif)</SUP></DIV></DIV>
      <DIV class=3Dp id=3Dpone.0007752.s007>Figure S7
      <DIV class=3Dp id=3D__pid665225>PDGFB protein levels are not =
correlated with=20
      mRNA expression: PDGFB protein levels were assessed in a =
validation panel=20
      of 40 gliomas by western blot and compared with mRNA expression =
levels.=20
      Although the ligand is expressed at highly variable amounts there =
is no=20
      correlation with mRNA, concordant with post-transcriptional =
regulation of=20
      PDGF.</DIV>
      <DIV class=3Dp id=3D__pid665230>(0.77 MB TIF)</DIV>
      <DIV class=3Dsupplementary-material-media-label-caption><A =
class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.0007=
752.s007.tif">Click=20
      here for additional data file.</A><SUP>(750K, =
tif)</SUP></DIV></DIV>
      <DIV class=3Dp id=3Dpone.0007752.s008>Table S1
      <DIV class=3Dp id=3D__pid665260>Antibodies and conditions used for =
western=20
      blot panel. Antibody sources and conditions as shown. *Hes1 =
antibody=20
      kindly provided by Dr. Tetsuo Sudo (Toray Scientific, =
Japan).</DIV>
      <DIV class=3Dp id=3D__pid665264>(0.03 MB XLS)</DIV>
      <DIV class=3Dsupplementary-material-media-label-caption><A =
class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.0007=
752.s008.xls">Click=20
      here for additional data file.</A><SUP>(27K, =
xls)</SUP></DIV></DIV>
      <DIV class=3Dp id=3Dpone.0007752.s009>Table S2
      <DIV class=3Dp id=3D__pid665294>Quantified western results. =
Western bands=20
      quantified by densitometry and normalized to actin (see <A=20
      class=3D"cite-reflink sec"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s4"=20
      rid=3D"s4">Methods</A>). Images of selected bands are shown in <A=20
      class=3D"side-supplink supplementary-material"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#pone.0007752=
.s001"=20
      rid=3D"pone.0007752.s001">Figure S1</A>.</DIV>
      <DIV class=3Dp id=3D__pid665318>(0.05 MB XLS)</DIV>
      <DIV class=3Dsupplementary-material-media-label-caption><A =
class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.0007=
752.s009.xls">Click=20
      here for additional data file.</A><SUP>(53K, =
xls)</SUP></DIV></DIV>
      <DIV class=3Dp id=3Dpone.0007752.s010>Table S3
      <DIV class=3Dp id=3D__pid665347>Summary of integrated analysis of =
genomic data=20
      from 278 samples in The Cancer Genome Atlas. In this table, =
mutations are=20
      denoted in blue and designated =E2=80=9Cvalidated=E2=80=9D and =
=E2=80=9Cunvalidated=E2=80=9D according to=20
      whether TCGA reports that the mutation was verified by second =
sequencing=20
      method or whether such verification is pending. Focal =
amplifications in=20
      red and single-copy loss or homozygous deletion (light and dark =
green,=20
      respectively) are inferred from array-CGH log2 ratios (see <A=20
      class=3D"cite-reflink sec"=20
      href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s4"=20
      rid=3D"s4">Methods</A>). Cluster assignments are derived from <A=20
      class=3D"fig-table-link fig figpopup" style=3D"TEXT-DECORATION: =
none"=20
      onclick=3D"startTarget(this, 'figure', 1024, 800)"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/figure/pone-0=
007752-g004/"><SPAN=20
      style=3D"TEXT-DECORATION: underline">Figure 4</SPAN><SPAN=20
      class=3Dlarge-thumb-canvas><SPAN class=3Dlarge-thumb-canvas-1><IMG =

      class=3D"icon-reflink large-thumb" title=3D"Figure 4"=20
      style=3D"BORDER-RIGHT: 1px solid; BORDER-TOP: 1px solid; =
BORDER-LEFT: 1px solid; BORDER-BOTTOM: 1px solid"=20
      alt=3D"Figure 4"=20
      =
src=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.00077=
52.g004.gif"=20
      =
hires=3D"/pmc/articles/PMC2771920/bin/pone.0007752.g004.jpg"></SPAN></SPA=
N></A>.</DIV>
      <DIV class=3Dp id=3D__pid665374>(0.08 MB XLS)</DIV>
      <DIV class=3Dsupplementary-material-media-label-caption><A =
class=3Dint-reflink=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/bin/pone.0007=
752.s010.xls">Click=20
      here for additional data file.</A><SUP>(76K,=20
      xls)</SUP></DIV></DIV></DIV></DIV>
      <DIV class=3Dsec id=3D__ackid665392>
      <DIV class=3D"head1 section-title" id=3D__ackid665392titletitle=20
      style=3D"TEXT-TRANSFORM: none">
      <DIV>Acknowledgments</DIV></DIV>
      <DIV class=3Dsection-content id=3D__ackid665392content>
      <DIV class=3Dsec>
      <DIV class=3Dp id=3D__pid665394>The authors would like to thank =
David Gutmann,=20
      MD, PhD, and Ken Aldape, MD, for helpful discussions. The results=20
      published here are in part based upon data generated by The Cancer =
Genome=20
      Atlas pilot project established by the NCI and NHGRI. Information =
about=20
      TCGA and the investigators and institutions who constitute the =
TCGA=20
      research network can be found at <SPAN class=3Dext-reflink><A=20
      class=3Dext-reflink onclick=3D"focuswin('pmc_ext')"=20
      href=3D"http://cancergenome.nih.gov/" target=3Dpmc_ext=20
      =
ref=3D"reftype=3Dextlink&amp;article-id=3D2771920&amp;issue-id=3D182378&a=
mp;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3DExternal%7CLink%7C=
URI&amp;rendering-type=3Dnormal">http://cancergenome.nih.gov/</A></SPAN>.=
</DIV></DIV></DIV></DIV>
      <DIV class=3Dsec id=3D__articleid626723footnotes>
      <DIV class=3D"head1 section-title" =
id=3D__articleid626723footnotestitletitle=20
      style=3D"TEXT-TRANSFORM: none">
      <DIV>Footnotes</DIV></DIV>
      <DIV class=3Dsection-content =
id=3D__articleid626723footnotescontent>
      <DIV class=3Dfm-footnote id=3D__fnid667517>
      <DIV class=3D"p p-first-last" id=3D__pid667521><STRONG>Competing =
Interests:=20
      </STRONG>The authors have declared that no competing interests=20
      exist.</DIV></DIV>
      <DIV class=3Dfm-footnote id=3D__fnid667526>
      <DIV class=3D"p p-first-last" id=3D__pid667530><STRONG>Funding: =
</STRONG>This=20
      work was supported by NIH U24 CA126543-01, <SPAN =
class=3Dext-reflink><A=20
      class=3Dext-reflink onclick=3D"focuswin('pmc_ext')"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=3DRetrieve&amp;db=3D=
nucleotide&amp;dopt=3DGenBank&amp;list_uids=3D34953995"=20
      target=3Dpmc_ext=20
      =
ref=3D"reftype=3Dextlink-entrez-nucleotide&amp;article-id=3D2771920&amp;i=
ssue-id=3D182378&amp;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3D=
Entrez%7CTerm%7CNucleotide&amp;rendering-type=3Dnormal">CA100688</A></SPA=
N>,=20
      <SPAN class=3Dext-reflink><A class=3Dext-reflink =
onclick=3D"focuswin('pmc_ext')"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=3DRetrieve&amp;db=3D=
nucleotide&amp;dopt=3DGenBank&amp;list_uids=3D35005487"=20
      target=3Dpmc_ext=20
      =
ref=3D"reftype=3Dextlink-entrez-nucleotide&amp;article-id=3D2771920&amp;i=
ssue-id=3D182378&amp;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3D=
Entrez%7CTerm%7CNucleotide&amp;rendering-type=3Dnormal">CA126518</A></SPA=
N>,=20
      <SPAN class=3Dext-reflink><A class=3Dext-reflink =
onclick=3D"focuswin('pmc_ext')"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=3DRetrieve&amp;db=3D=
nucleotide&amp;dopt=3DGenBank&amp;list_uids=3D35035555"=20
      target=3Dpmc_ext=20
      =
ref=3D"reftype=3Dextlink-entrez-nucleotide&amp;article-id=3D2771920&amp;i=
ssue-id=3D182378&amp;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3D=
Entrez%7CTerm%7CNucleotide&amp;rendering-type=3Dnormal">CA141502</A></SPA=
N>,=20
      and <SPAN class=3Dext-reflink><A class=3Dext-reflink=20
      onclick=3D"focuswin('pmc_ext')"=20
      =
href=3D"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=3DRetrieve&amp;db=3D=
nucleotide&amp;dopt=3DGenBank&amp;list_uids=3D35040139"=20
      target=3Dpmc_ext=20
      =
ref=3D"reftype=3Dextlink-entrez-nucleotide&amp;article-id=3D2771920&amp;i=
ssue-id=3D182378&amp;journal-id=3D440&amp;FROM=3DArticle%7CBody&amp;TO=3D=
Entrez%7CTerm%7CNucleotide&amp;rendering-type=3Dnormal">CA143798</A></SPA=
N>=20
      and by the Geoffrey Beene Cancer Research Center at Memorial=20
      Sloan-Kettering Cancer Center, which had no role in study design, =
data=20
      collection and analysis, decision to publish, or preparation of =
the=20
      manuscript.</DIV></DIV></DIV></DIV>
      <DIV class=3Dsec id=3D__ref-listid665409>
      <DIV class=3D"head1 section-title" =
id=3D__ref-listid665409titletitle=20
      style=3D"TEXT-TRANSFORM: none">
      <DIV class=3Dother-sections>
      <UL class=3D"noext-menu noext-menu-hidden">
        <LI><A class=3Dfirst-link=20
        =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">&nbsp;Othe=
r=20
        Sections=E2=96=BC</A>
        <UL class=3D"submenu head1">
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#__abstractid=
607974">Abstract</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s1">Introduc=
tion</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s2">Results<=
/A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s3">Discussi=
on</A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s4">Methods<=
/A>
          <LI class=3Dsubmenu-item><A class=3D"" =
style=3D"TEXT-TRANSFORM: none"=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#s5">Supporti=
ng=20
          Information</A>
          <LI class=3D"submenu-item current-item"><A class=3D""=20
          style=3D"TEXT-TRANSFORM: none" onclick=3Dreturn(false)=20
          =
href=3D"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771920/#">References=
</A></LI></UL></LI></UL></DIV>
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p;journal-id=3D440&amp;FROM=3DArticle|RelatedArticles&amp;TO=3DEntrez|Pub=
med|Record"><SPAN=20
        class=3Dreviewflag>Review</SPAN>Targeted molecular therapy of =
GBM.</A>=20
        <P class=3Ddesc><EM class=3Dcit>Brain Pathol. 2003 Jan; =
13(1):52-61.=20
        </EM></P>
        <P class=3Dnote>[Brain Pathol. 2003]</P></LI>
        <LI class=3D"item popnode note"><A=20
        =
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/9440022?ordinalpos=3D1&amp;ito=
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p;journal-id=3D440&amp;FROM=3DArticle|RelatedArticles&amp;TO=3DEntrez|Pub=
med|Record"><SPAN=20
        class=3Dreviewflag>Review</SPAN>Signal transduction pathways and =
their=20
        relevance in human astrocytomas.</A>=20
        <P class=3Ddesc><EM class=3Dcit>J Neurooncol. 1997 Dec; =
35(3):223-48.=20
        </EM></P>
        <P class=3Dnote>[J Neurooncol. 1997]</P>
        <LI class=3Dmore>=C2=BB <A=20
        =
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Histology.</A></DIV></LI>
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ahead of print]"=20
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activity&amp;recordid=3D1259680176355180">Human=20
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<DIV class=3DArticleRefDocsums id=3DArticleRefDocsums>
<DIV class=3Dcited-ref id=3Dcite-__pid608027 rid=3D"__pid608027"=20
pmids=3D"17974913 11390353 18669428">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17974913"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record"><SPAN=20
  class=3Dflag>Review</SPAN>Malignant astrocytic glioma: genetics, =
biology, and=20
  paths to treatment.</A>
  <P class=3Ddesc><EM class=3Dcit>Genes Dev. 2007 Nov 1;=20
  21(21):2683-710.</EM></P><SPAN class=3Dpub>[Genes Dev. =
2007]</SPAN></LI>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/11390353"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record"><SPAN=20
  class=3Dflag>Review</SPAN>Malignant glioma: genetics and biology of a =
grave=20
  matter.</A>
  <P class=3Ddesc><EM class=3Dcit>Genes Dev. 2001 Jun 1;=20
  15(11):1311-33.</EM></P><SPAN class=3Dpub>[Genes Dev. =
2001]</SPAN></LI>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18669428"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record"><SPAN=20
  class=3Dflag>Review</SPAN>Malignant gliomas in adults.</A>
  <P class=3Ddesc><EM class=3Dcit>N Engl J Med. 2008 Jul 31;=20
  359(5):492-507.</EM></P><SPAN class=3Dpub>[N Engl J Med. =
2008]</SPAN></LI></UL><A=20
class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17974913,11390353,18669428/?re=
port=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid608073 rid=3D"__pid608073"=20
pmids=3D"17618441 17974913 19228619 18772890 18356283 16278407">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17618441"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record"><SPAN=20
  class=3Dflag>Review</SPAN>The 2007 WHO classification of tumours of =
the central=20
  nervous system.</A>
  <P class=3Ddesc><EM class=3Dcit>Acta Neuropathol. 2007 Aug;=20
  114(2):97-109.</EM></P><SPAN class=3Dpub>[Acta Neuropathol. =
2007]</SPAN></LI>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17974913"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record"><SPAN=20
  class=3Dflag>Review</SPAN>Malignant astrocytic glioma: genetics, =
biology, and=20
  paths to treatment.</A>
  <P class=3Ddesc><EM class=3Dcit>Genes Dev. 2007 Nov 1;=20
  21(21):2683-710.</EM></P><SPAN class=3Dpub>[Genes Dev. =
2007]</SPAN></LI>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/19228619"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">IDH1=20
  and IDH2 mutations in gliomas.</A>
  <P class=3Ddesc><EM class=3Dcit>N Engl J Med. 2009 Feb 19;=20
  360(8):765-73.</EM></P><SPAN class=3Dpub>[N Engl J Med. =
2009]</SPAN></LI>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18772890"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Comprehensive=20
  genomic characterization defines human glioblastoma genes and core=20
  pathways.</A>
  <P class=3Ddesc><EM class=3Dcit>Nature. 2008 Oct 23;=20
  455(7216):1061-8.</EM></P><SPAN class=3Dpub>[Nature. 2008]</SPAN></LI>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18356283"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Progression-free=20
  survival: an important end point in evaluating therapy for recurrent=20
  high-grade gliomas.</A>
  <P class=3Ddesc><EM class=3Dcit>Neuro Oncol. 2008 Apr; =
10(2):162-70.</EM></P><SPAN=20
  class=3Dpub>[Neuro Oncol. 2008]</SPAN></LI></UL><A =
class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17618441,17974913,19228619,187=
72890,18356283,16278407/?report=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid608171 rid=3D"__pid608171"=20
pmids=3D"19076778 17000661 12670911 16530701 14580340 15094774 =
12782577">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/19076778"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record"><SPAN=20
  class=3Dflag>Review</SPAN>Genetically engineered mouse models of brain =
cancer=20
  and the promise of preclinical testing.</A>
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  19(1):132-43.</EM></P><SPAN class=3Dpub>[Brain Pathol. =
2009]</SPAN></LI>
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  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17000661"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record"><SPAN=20
  class=3Dflag>Review</SPAN>Mouse models of brain tumors and their =
applications in=20
  preclinical trials.</A>
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  12(18):5288-97.</EM></P><SPAN class=3Dpub>[Clin Cancer Res. =
2006]</SPAN></LI>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/12670911"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Gene=20
  expression-based classification of malignant gliomas correlates better =
with=20
  survival than histological classification.</A>
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  63(7):1602-7.</EM></P><SPAN class=3Dpub>[Cancer Res. 2003]</SPAN></LI>
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  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/16530701"=20
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ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Molecular=20
  subclasses of high-grade glioma predict prognosis, delineate a pattern =
of=20
  disease progression, and resemble stages in neurogenesis.</A>
  <P class=3Ddesc><EM class=3Dcit>Cancer Cell. 2006 Mar; =
9(3):157-73.</EM></P><SPAN=20
  class=3Dpub>[Cancer Cell. 2006]</SPAN></LI>
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  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/14580340"=20
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ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Oncogenic=20
  Ras and Akt signaling contribute to glioblastoma formation by =
differential=20
  recruitment of existing mRNAs to polysomes.</A>
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12(4):889-901.</EM></P><SPAN=20
  class=3Dpub>[Mol Cell. 2003]</SPAN></LI></UL><A class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/19076778,17000661,12670911,165=
30701,14580340,15094774,12782577/?report=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid663381 rid=3D"__pid663381"=20
pmids=3D"18772396 18772890">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
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ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">An=20
  integrated genomic analysis of human glioblastoma multiforme.</A>
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  321(5897):1807-12.</EM></P><SPAN class=3Dpub>[Science. =
2008]</SPAN></LI>
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  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18772890"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Comprehensive=20
  genomic characterization defines human glioblastoma genes and core=20
  pathways.</A>
  <P class=3Ddesc><EM class=3Dcit>Nature. 2008 Oct 23;=20
  455(7216):1061-8.</EM></P><SPAN class=3Dpub>[Nature. =
2008]</SPAN></LI></UL><A=20
class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18772396,18772890/?report=3Dsu=
mmary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid663765 rid=3D"__pid663765"=20
pmids=3D"17974913 18077431 17114236">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17974913"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record"><SPAN=20
  class=3Dflag>Review</SPAN>Malignant astrocytic glioma: genetics, =
biology, and=20
  paths to treatment.</A>
  <P class=3Ddesc><EM class=3Dcit>Genes Dev. 2007 Nov 1;=20
  21(21):2683-710.</EM></P><SPAN class=3Dpub>[Genes Dev. =
2007]</SPAN></LI>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18077431"=20
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ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Assessing=20
  the significance of chromosomal aberrations in cancer: methodology and =

  application to glioma.</A>
  <P class=3Ddesc><EM class=3Dcit>Proc Natl Acad Sci U S A. 2007 Dec 11; =

  104(50):20007-12.</EM></P><SPAN class=3Dpub>[Proc Natl Acad Sci U S A. =

  2007]</SPAN></LI>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17114236"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Marked=20
  genomic differences characterize primary and secondary glioblastoma =
subtypes=20
  and identify two distinct molecular and clinical secondary =
glioblastoma=20
  entities.</A>
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  66(23):11502-13.</EM></P><SPAN class=3Dpub>[Cancer Res. =
2006]</SPAN></LI></UL><A=20
class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17974913,18077431,17114236/?re=
port=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid663859 rid=3D"__pid663859" =
pmids=3D"17177598">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17177598"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Epidermal=20
  growth factor receptor activation in glioblastoma through novel =
missense=20
  mutations in the extracellular domain.</A>
  <P class=3Ddesc><EM class=3Dcit>PLoS Med. 2006 Dec; =
3(12):e485.</EM></P><SPAN=20
  class=3Dpub>[PLoS Med. 2006]</SPAN></LI></UL><A class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17177598/?report=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid664038 rid=3D"__pid664038" =
pmids=3D"16530701">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/16530701"=20
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ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Molecular=20
  subclasses of high-grade glioma predict prognosis, delineate a pattern =
of=20
  disease progression, and resemble stages in neurogenesis.</A>
  <P class=3Ddesc><EM class=3Dcit>Cancer Cell. 2006 Mar; =
9(3):157-73.</EM></P><SPAN=20
  class=3Dpub>[Cancer Cell. 2006]</SPAN></LI></UL><A =
class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/16530701/?report=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid664399 rid=3D"__pid664399"=20
pmids=3D"2651898 3275870">
<UL>
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ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Functional=20
  identification of regulatory elements within the promoter region of=20
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1989]</SPAN></LI>
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ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">The=20
  5' untranslated sequence of the c-sis/platelet-derived growth factor 2 =

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1988]</SPAN></LI></UL><A=20
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href=3D"http://www.ncbi.nlm.nih.gov/pubmed/2651898,3275870/?report=3Dsumm=
ary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid664512 rid=3D"__pid664512" =
pmids=3D"19176818">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/19176818"=20
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ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">The=20
  Rheb-mTOR pathway is upregulated in reactive astrocytes of the injured =
spinal=20
  cord.</A>
  <P class=3Ddesc><EM class=3Dcit>J Neurosci. 2009 Jan 28;=20
  29(4):1093-104.</EM></P><SPAN class=3Dpub>[J Neurosci. =
2009]</SPAN></LI></UL><A=20
class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/19176818/?report=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid664676 rid=3D"__pid664676" =
pmids=3D"18472967">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18472967"=20
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ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Constitutive=20
  activation of Raf-1 induces glioma formation in mice.</A>
  <P class=3Ddesc><EM class=3Dcit>Neoplasia. 2008 May; =
10(5):501-10.</EM></P><SPAN=20
  class=3Dpub>[Neoplasia. 2008]</SPAN></LI></UL><A class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18472967/?report=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid664719 rid=3D"__pid664719" =
pmids=3D"15967117">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/15967117"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">The=20
  characteristics of astrocytomas and oligodendrogliomas are caused by =
two=20
  distinct and interchangeable signaling formats.</A>
  <P class=3Ddesc><EM class=3Dcit>Neoplasia. 2005 Apr; =
7(4):397-406.</EM></P><SPAN=20
  class=3Dpub>[Neoplasia. 2005]</SPAN></LI></UL><A class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/15967117/?report=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">See=20
more articles cited in this paragraph</A></DIV>
<DIV class=3Dcited-ref id=3Dcite-__pid664779 rid=3D"__pid664779" =
pmids=3D"15475419">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/15475419"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Circular=20
  binary segmentation for the analysis of array-based DNA copy number =
data.</A>
  <P class=3Ddesc><EM class=3Dcit>Biostatistics. 2004 Oct;=20
  5(4):557-72.</EM></P><SPAN class=3Dpub>[Biostatistics. =
2004]</SPAN></LI></UL><A=20
class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/15475419/?report=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
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<DIV class=3Dcited-ref id=3Dcite-__pid664839 rid=3D"__pid664839" =
pmids=3D"18772890">
<UL>
  <LI class=3Dovfl><A class=3D"pl popnode"=20
  href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18772890"=20
  =
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Comprehensive=20
  genomic characterization defines human glioblastoma genes and core=20
  pathways.</A>
  <P class=3Ddesc><EM class=3Dcit>Nature. 2008 Oct 23;=20
  455(7216):1061-8.</EM></P><SPAN class=3Dpub>[Nature. =
2008]</SPAN></LI></UL><A=20
class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/18772890/?report=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
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pmids=3D"16530701">
<UL>
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ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
p;journal-id=3D440&amp;FROM=3DArticle|CitedRefBlock&amp;TO=3DEntrez|Pubme=
d|Record">Molecular=20
  subclasses of high-grade glioma predict prognosis, delineate a pattern =
of=20
  disease progression, and resemble stages in neurogenesis.</A>
  <P class=3Ddesc><EM class=3Dcit>Cancer Cell. 2006 Mar; =
9(3):157-73.</EM></P><SPAN=20
  class=3Dpub>[Cancer Cell. 2006]</SPAN></LI></UL><A =
class=3Dall-articles=20
href=3D"http://www.ncbi.nlm.nih.gov/pubmed/16530701/?report=3Dsummary"=20
ref=3D"reftype=3Dpubmed&amp;article-id=3D2771920&amp;issue-id=3D182378&am=
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}
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}
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}
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}
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}
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------=_NextPart_000_0000_01CA72A3.109DE760
Content-Type: text/css;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Content-Location: http://www.ncbi.nlm.nih.gov/corehtml/pmc/css/noext-menu.css

DIV.sec DIV.other-sections {
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TEXT-ALIGN: left
}
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TEXT-ALIGN: left
}
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}
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=09
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}
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UL.noext-menu LI SPAN.delta {
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UL.noext-menu LI.submenu-item UL {
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UL.noext-menu LI.active-item UL {
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UL.noext-menu LI UL.opened {
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UL.noext-menu LI UL.opened LI.active-item {
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UL.opened LI.active-item A {
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UL.noext-menu LI UL A {
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------=_NextPart_000_0000_01CA72A3.109DE760
Content-Type: text/css;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Content-Location: http://www.ncbi.nlm.nih.gov/core/extjs/ext-2.2/resources/css/panel.css

.x-panel {
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PADDING-BOTTOM: 4px; FONT: bold 11px/15px =
tahoma,arial,verdana,sans-serif; OVERFLOW: hidden; BORDER-LEFT: #99bbe8 =
1px solid; COLOR: #15428b; PADDING-TOP: 5px; BORDER-BOTTOM: #99bbe8 1px =
solid; ZOOM: 1
}
.x-panel-body {
	BORDER-RIGHT: #99bbe8 1px solid; BORDER-TOP: #99bbe8 0px; BACKGROUND: =
white; OVERFLOW: hidden; BORDER-LEFT: #99bbe8 1px solid; BORDER-BOTTOM: =
#99bbe8 1px solid; POSITION: relative
}
.x-panel-bbar .x-toolbar {
	BORDER-RIGHT: #99bbe8 1px solid; PADDING-RIGHT: 2px; BORDER-TOP: =
#99bbe8 0px; PADDING-LEFT: 2px; PADDING-BOTTOM: 2px; OVERFLOW: hidden; =
BORDER-LEFT: #99bbe8 1px solid; PADDING-TOP: 2px; BORDER-BOTTOM: #99bbe8 =
1px solid
}
.x-panel-tbar .x-toolbar {
	BORDER-RIGHT: #99bbe8 1px solid; PADDING-RIGHT: 2px; BORDER-TOP: =
#99bbe8 0px; PADDING-LEFT: 2px; PADDING-BOTTOM: 2px; OVERFLOW: hidden; =
BORDER-LEFT: #99bbe8 1px solid; PADDING-TOP: 2px; BORDER-BOTTOM: #99bbe8 =
1px solid
}
.x-panel-tbar-noheader .x-toolbar {
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}
.x-panel-header {
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}
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0px; BACKGROUND: none transparent scroll repeat 0% 0%; PADDING-BOTTOM: =
4px; FONT: bold 11px tahoma,arial,verdana,sans-serif; BORDER-LEFT: 0px; =
COLOR: #15428b; PADDING-TOP: 5px; BORDER-BOTTOM: 0px
}
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}
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BACKGROUND-REPEAT: no-repeat; ZOOM: 1
}
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VERTICAL-ALIGN: middle; WIDTH: 16px; MARGIN-RIGHT: 4px; =
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}
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}
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}
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BORDER-BOTTOM: #99bbe8 1px solid; ZOOM: 1
}
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url(../images/default/panel/corners-sprite.gif) no-repeat right 0px; =
ZOOM: 1
}
.x-panel-bc {
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bottom; ZOOM: 1
}
.x-panel-bc .x-panel-footer {
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}
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url(../images/default/panel/corners-sprite.gif) no-repeat 0px bottom; =
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}
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url(../images/default/panel/corners-sprite.gif) no-repeat right bottom; =
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}
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0px; BACKGROUND: #dfe8f6; PADDING-BOTTOM: 0px; MARGIN: 0px; FONT: 11px =
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repeat 0% 0%; BORDER-LEFT: 0px; BORDER-BOTTOM: 0px
}
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url(../images/default/panel/left-right.gif) #fff repeat-y 0px 0px; ZOOM: =
1
}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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FLOAT: right; MARGIN-LEFT: 2px; OVERFLOW: hidden; WIDTH: 15px; CURSOR: =
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
.x-panel-ghost {
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}
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#99bbe8 0px; DISPLAY: block; PADDING-LEFT: 0px; FONT-SIZE: 0px; =
PADDING-BOTTOM: 0px; MARGIN: 0px; OVERFLOW: hidden; BORDER-LEFT: #99bbe8 =
1px solid; LINE-HEIGHT: 0; PADDING-TOP: 0px; BORDER-BOTTOM: #99bbe8 1px =
solid
}
.x-panel-ghost * {
	CURSOR: move! important
}
.x-panel-dd-spacer {
	BORDER-RIGHT: #99bbe8 2px dashed; BORDER-TOP: #99bbe8 2px dashed; =
BORDER-LEFT: #99bbe8 2px dashed; BORDER-BOTTOM: #99bbe8 2px dashed
}
.x-panel-btns-ct {
	PADDING-RIGHT: 5px; PADDING-LEFT: 5px; PADDING-BOTTOM: 5px; =
PADDING-TOP: 5px
}
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}
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BORDER-LEFT-WIDTH: 0px; BORDER-BOTTOM-WIDTH: 0px; PADDING-BOTTOM: 0px; =
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}
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}
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}
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	TEXT-ALIGN: center
}
.x-panel-btns-ct .x-panel-btns-center TABLE {
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}
.x-panel-btns-ct TABLE TD.x-panel-btn-td {
	PADDING-RIGHT: 3px; PADDING-LEFT: 3px; PADDING-BOTTOM: 3px; =
PADDING-TOP: 3px
}
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}
.x-panel-btns-ct .x-btn-focus .x-btn-right {
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}
.x-panel-btns-ct .x-btn-focus .x-btn-center {
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}
.x-panel-btns-ct .x-btn-over .x-btn-left {
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}
.x-panel-btns-ct .x-btn-over .x-btn-right {
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}
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}
.x-panel-btns-ct .x-btn-click .x-btn-center {
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}
.x-panel-btns-ct .x-btn-click .x-btn-right {
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}
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}

------=_NextPart_000_0000_01CA72A3.109DE760
Content-Type: text/css;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Content-Location: http://www.ncbi.nlm.nih.gov/core/ext.ncbi/1/css/themes/xtheme-oldentrez.css

.x-panel {
	BORDER-LEFT-COLOR: #d0d0d0; BORDER-BOTTOM-COLOR: #d0d0d0; =
BORDER-TOP-STYLE: solid; BORDER-TOP-COLOR: #d0d0d0; BORDER-RIGHT-STYLE: =
solid; BORDER-LEFT-STYLE: solid; BORDER-RIGHT-COLOR: #d0d0d0; =
BORDER-BOTTOM-STYLE: solid
}
.x-panel-header {
	BORDER-RIGHT: #d0d0d0 1px solid; BORDER-TOP: #d0d0d0 1px solid; =
BACKGROUND-IMAGE: url(../../img/oldentrez/panel/white-top-bottom.gif); =
BORDER-LEFT: #d0d0d0 1px solid; COLOR: #333; BORDER-BOTTOM: #d0d0d0 1px =
solid
}
.x-panel-body {
	BORDER-LEFT-COLOR: #d0d0d0; BORDER-BOTTOM-COLOR: #d0d0d0; =
BORDER-TOP-COLOR: #d0d0d0; BORDER-RIGHT-COLOR: #d0d0d0
}
.x-panel-bbar .x-toolbar {
	BORDER-LEFT-COLOR: #d0d0d0; BORDER-BOTTOM-COLOR: #d0d0d0; =
BORDER-TOP-COLOR: #d0d0d0; BORDER-RIGHT-COLOR: #d0d0d0
}
.x-panel-tbar .x-toolbar {
	BORDER-LEFT-COLOR: #d0d0d0; BORDER-BOTTOM-COLOR: #d0d0d0; =
BORDER-TOP-COLOR: #d0d0d0; BORDER-RIGHT-COLOR: #d0d0d0
}
.x-panel-tbar-noheader .x-toolbar {
	BORDER-LEFT-COLOR: #d0d0d0; BORDER-BOTTOM-COLOR: #d0d0d0; =
BORDER-TOP-COLOR: #d0d0d0; BORDER-RIGHT-COLOR: #d0d0d0
}
.x-panel-mc .x-panel-tbar .x-toolbar {
	BORDER-LEFT-COLOR: #d0d0d0; BORDER-BOTTOM-COLOR: #d0d0d0; =
BORDER-TOP-COLOR: #d0d0d0; BORDER-RIGHT-COLOR: #d0d0d0
}
.x-panel-body-noheader {
	BORDER-LEFT-COLOR: #d0d0d0; BORDER-BOTTOM-COLOR: #d0d0d0; =
BORDER-TOP-COLOR: #d0d0d0; BORDER-RIGHT-COLOR: #d0d0d0
}
.x-panel-mc .x-panel-body {
	BORDER-LEFT-COLOR: #d0d0d0; BORDER-BOTTOM-COLOR: #d0d0d0; =
BORDER-TOP-COLOR: #d0d0d0; BORDER-RIGHT-COLOR: #d0d0d0
}
.x-panel-tl .x-panel-header {
	COLOR: #333
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------=_NextPart_000_0000_01CA72A3.109DE760
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}

------=_NextPart_000_0000_01CA72A3.109DE760
Content-Type: text/css;
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Content-Transfer-Encoding: quoted-printable
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BODY {
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}
#pagewrap {
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}
#page {
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}
#footer {
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}
#pmc-home-hdr {
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#pmc-home-hdr #homelink {
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}
#pmc-home-hdr #homelink IMG {
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}
#pmc-home-hdr H1 {
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#pmc-home-hdr UL {
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}
#pmc-home-hdr H1 {
	PADDING-RIGHT: 2em; BORDER-TOP: transparent 2px solid; FONT-SIZE: 2em; =
COLOR: white; LINE-HEIGHT: 52px; TEXT-ALIGN: right
}
#pmc-home-hdr UL {
	BORDER-RIGHT: #3c78bc 1px solid; BORDER-BOTTOM: #3c78bc 3px solid; =
HEIGHT: 18px; BACKGROUND-COLOR: #a0c0e0
}
#pmc-home-hdr UL LI {
	PADDING-RIGHT: 40px; DISPLAY: inline; PADDING-LEFT: 40px; FONT-SIZE: =
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}
#pmc-home-hdr UL LI A {
	PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 2px; =
PADDING-TOP: 2px; TEXT-DECORATION: none
}
#pmc-home-hdr UL LI A:hover {
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}
A:visited {
	COLOR: #7119b4
}
#pmc-home-hdr UL LI.sel A {
	FONT-WEIGHT: bold; COLOR: white; BACKGROUND-COLOR: #3c78bc; =
TEXT-DECORATION: none
}
#pmc-home-hdr UL LI.sel A:visited {
	FONT-WEIGHT: bold; COLOR: white; BACKGROUND-COLOR: #3c78bc; =
TEXT-DECORATION: none
}
#pmc-home-hdr UL LI.sel A:hover {
	FONT-WEIGHT: bold; COLOR: white; BACKGROUND-COLOR: #3c78bc; =
TEXT-DECORATION: none
}
.footer-section {
	MARGIN: 0px 1em 1em; TEXT-ALIGN: center
}
BODY #cols {
	BORDER-RIGHT: transparent 1px solid; BORDER-TOP: transparent 1px solid; =
BORDER-LEFT: transparent 1px solid; BORDER-BOTTOM: transparent 1px solid
}

@media Print   =20
{
.footer {
	DISPLAY: none
}
TD.pmc-watermark {
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}
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.nopagesectioncontent {
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}
.port {
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}
.port {
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.port DIV {
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}
.port DL {
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}
.port DT {
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}
.port DD {
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.port UL {
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}
.port OL {
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}
.port LI {
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0px; PADDING-TOP: 0px
}
.port H1 {
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.port H2 {
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.port H3 {
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.port H4 {
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.port H5 {
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.port H6 {
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.port PRE {
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}
.port FORM {
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}
.port FIELDSET {
	PADDING-RIGHT: 0px; PADDING-LEFT: 0px; PADDING-BOTTOM: 0px; MARGIN: =
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}
.port INPUT {
	PADDING-RIGHT: 0px; PADDING-LEFT: 0px; PADDING-BOTTOM: 0px; MARGIN: =
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}
.port P {
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0px; PADDING-TOP: 0px
}
.port BLOCKQUOTE {
	PADDING-RIGHT: 0px; PADDING-LEFT: 0px; PADDING-BOTTOM: 0px; MARGIN: =
0px; PADDING-TOP: 0px
}
.port TH {
	PADDING-RIGHT: 0px; PADDING-LEFT: 0px; PADDING-BOTTOM: 0px; MARGIN: =
0px; PADDING-TOP: 0px
}
.port TD {
	PADDING-RIGHT: 0px; PADDING-LEFT: 0px; PADDING-BOTTOM: 0px; MARGIN: =
0px; PADDING-TOP: 0px
}
.port IMG {
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}
.port OL {
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}
.port UL {
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}
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}
.x-panel {
	BORDER-RIGHT: #99bbe8 0px solid; BORDER-TOP: #99bbe8 0px solid; =
BORDER-LEFT: #99bbe8 0px solid; BORDER-BOTTOM: #99bbe8 0px solid
}
.x-panel-header {
	BORDER-RIGHT: #99bbe8 1px solid; PADDING-RIGHT: 3px; BORDER-TOP: =
#99bbe8 1px solid; PADDING-LEFT: 5px; BACKGROUND: =
url(/core/extjs/ext-2.1/resources/images/default/panel/white-top-bottom.g=
if) repeat-x 0px -1px; PADDING-BOTTOM: 4px; FONT: bold 11px/15px =
tahoma,arial,verdana,sans-serif; OVERFLOW: hidden; BORDER-LEFT: #99bbe8 =
1px solid; COLOR: #15428b; PADDING-TOP: 5px; BORDER-BOTTOM: #99bbe8 1px =
solid; ZOOM: 1
}
.x-panel-body {
	BORDER-RIGHT: #99bbe8 1px solid; BORDER-TOP: #99bbe8 0px; BACKGROUND: =
white; OVERFLOW: hidden; BORDER-LEFT: #99bbe8 1px solid; BORDER-BOTTOM: =
#99bbe8 1px solid; POSITION: relative
}
.x-panel-bbar .x-toolbar {
	BORDER-RIGHT: #99bbe8 1px solid; PADDING-RIGHT: 2px; BORDER-TOP: =
#99bbe8 0px; PADDING-LEFT: 2px; PADDING-BOTTOM: 2px; OVERFLOW: hidden; =
BORDER-LEFT: #99bbe8 1px solid; PADDING-TOP: 2px; BORDER-BOTTOM: #99bbe8 =
1px solid
}
.x-panel-tbar .x-toolbar {
	BORDER-RIGHT: #99bbe8 1px solid; PADDING-RIGHT: 2px; BORDER-TOP: =
#99bbe8 0px; PADDING-LEFT: 2px; PADDING-BOTTOM: 2px; OVERFLOW: hidden; =
BORDER-LEFT: #99bbe8 1px solid; PADDING-TOP: 2px; BORDER-BOTTOM: #99bbe8 =
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}
.x-panel-tbar-noheader .x-toolbar {
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}
.x-panel-mc .x-panel-tbar .x-toolbar {
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}
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}
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}
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}
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0px; BACKGROUND: none transparent scroll repeat 0% 0%; PADDING-BOTTOM: =
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}
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}
.x-window-tl .x-panel-icon {
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}
.x-panel-inline-icon {
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VERTICAL-ALIGN: middle; WIDTH: 16px; MARGIN-RIGHT: 4px; =
BACKGROUND-REPEAT: no-repeat; HEIGHT: 16px
}
.x-panel-tc {
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url(/core/extjs/ext-2.1/resources/images/default/panel/top-bottom.gif) =
repeat-x 0px 0px; OVERFLOW: hidden
}
.ext-strict .ext-ie7 .x-panel-tc {
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}
.x-panel-tl {
	PADDING-LEFT: 6px; BACKGROUND: =
url(/core/extjs/ext-2.1/resources/images/default/panel/corners-sprite.gif=
) no-repeat 0px 0px; BORDER-BOTTOM: #99bbe8 1px solid; ZOOM: 1
}
.x-panel-tr {
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url(/core/extjs/ext-2.1/resources/images/default/panel/corners-sprite.gif=
) no-repeat right 0px; ZOOM: 1
}
.x-panel-bc {
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url(/core/extjs/ext-2.1/resources/images/default/panel/top-bottom.gif) =
repeat-x 0px bottom; ZOOM: 1
}
.x-panel-bc .x-panel-footer {
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}
.x-panel-bl {
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) no-repeat 0px bottom; ZOOM: 1
}
.x-panel-br {
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url(/core/extjs/ext-2.1/resources/images/default/panel/corners-sprite.gif=
) no-repeat right bottom; ZOOM: 1
}
.x-panel-mc {
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0px; BACKGROUND: #dfe8f6; PADDING-BOTTOM: 0px; MARGIN: 0px; FONT: 11px =
tahoma,arial,helvetica,sans-serif; BORDER-LEFT: 0px; PADDING-TOP: 6px; =
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}
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}
.x-panel-ml {
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url(/core/extjs/ext-2.1/resources/images/default/panel/left-right.gif) =
#fff repeat-y 0px 0px; ZOOM: 1
}
.x-panel-mr {
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url(/core/extjs/ext-2.1/resources/images/default/panel/left-right.gif) =
repeat-y right 0px; ZOOM: 1
}
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}
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}
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}
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}
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}
.x-panel-collapsed .x-resizable-handle {
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}
.ext-gecko .x-panel-animated DIV {
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}
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}
.x-plain-bbar .x-toolbar {
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}
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hidden; PADDING-TOP: 2px
}
.x-plain-bwrap {
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}
.x-plain {
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}
.x-tool {
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url(/core/extjs/ext-2.1/resources/images/default/panel/tool-sprites.gif) =
no-repeat; FLOAT: right; MARGIN-LEFT: 2px; OVERFLOW: hidden; WIDTH: =
15px; CURSOR: pointer; HEIGHT: 15px
}
.x-tool-toggle {
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}
.x-tool-toggle-over {
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}
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}
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}
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}
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}
.x-tool-minimize {
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}
.x-tool-minimize-over {
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}
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}
.x-tool-maximize-over {
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
.x-tool-right-over {
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}
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}
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}
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}
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}
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}
.x-tool-down-over {
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}
.x-tool-refresh {
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}
.x-tool-refresh-over {
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
.x-panel-ghost {
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}
.x-panel-ghost UL {
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PADDING-BOTTOM: 0px; MARGIN: 0px; OVERFLOW: hidden; BORDER-LEFT: #99bbe8 =
1px solid; LINE-HEIGHT: 0; PADDING-TOP: 0px; BORDER-BOTTOM: #99bbe8 1px =
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}
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}
.x-panel-dd-spacer {
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}
.x-panel-btns-ct {
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PADDING-TOP: 5px
}
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}
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BORDER-LEFT-WIDTH: 0px; BORDER-BOTTOM-WIDTH: 0px; PADDING-BOTTOM: 0px; =
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}
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}
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}
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}
.x-panel-btns-ct .x-panel-btns-center TABLE {
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}
.x-panel-btns-ct TABLE TD.x-panel-btn-td {
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PADDING-TOP: 3px
}
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}
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}
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}
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}
.x-panel-btns-ct .x-btn-over .x-btn-right {
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}
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}
.x-panel-btns-ct .x-btn-click .x-btn-center {
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}
.x-panel-btns-ct .x-btn-click .x-btn-right {
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}
.x-panel-btns-ct .x-btn-click .x-btn-left {
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}
.x-btn-menu-wrap {
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}
.x-menu {
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}
.x-menu-list-item IMG {
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}
.x-menu-list-item A.x-menu-item {
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}
.port H1.x-panel-header-text {
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0px; MARGIN: 0px; PADDING-TOP: 0px
}
.port H2.x-panel-header-text {
	PADDING-RIGHT: 0px; PADDING-LEFT: 0px; FONT-SIZE: 100%; PADDING-BOTTOM: =
0px; MARGIN: 0px; PADDING-TOP: 0px
}
.port H3.x-panel-header-text {
	PADDING-RIGHT: 0px; PADDING-LEFT: 0px; FONT-SIZE: 100%; PADDING-BOTTOM: =
0px; MARGIN: 0px; PADDING-TOP: 0px
}
.port H4.x-panel-header-text {
	PADDING-RIGHT: 0px; PADDING-LEFT: 0px; FONT-SIZE: 100%; PADDING-BOTTOM: =
0px; MARGIN: 0px; PADDING-TOP: 0px
}
.port H5.x-panel-header-text {
	PADDING-RIGHT: 0px; PADDING-LEFT: 0px; FONT-SIZE: 100%; PADDING-BOTTOM: =
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}
.port H6.x-panel-header-text {
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}
DIV.x-panel-body {
	PADDING-RIGHT: 5px; PADDING-LEFT: 5px; PADDING-BOTTOM: 5px; =
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}
.port .x-panel-header {
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PADDING-TOP: 5px
}
.x-panel {
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}
DIV#HTDisplay UL LI.query {
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DIV#HTDisplay UL LI.query DIV.textwrapper {
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DIV#HTDisplay UL LI.record {
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DIV#HTDisplay UL .count {
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DIV#HTDisplay DIV.action {
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DIV#HTDisplay DIV.action A {
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DIV#HTDisplay P {
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}
DIV#HTDisplay UL LI .thumb {
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white; _padding-right: 0.4em
}
DIV#HTDisplay P {
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}
DIV#HTDisplay .action A.HTOff {
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}
DIV.HTOff#HTDisplay .action A.HTOn {
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DIV.HTOff#HTDisplay P.HTOff {
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DIV.HTOn#HTDisplay P.HTOn {
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DIV.HTOff#HTDisplay .action A.HTOff {
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}
DIV.HTOn#HTDisplay .action A.HTOn {
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}
DIV#HTDisplay UL.hide {
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}
IMG.htbpoparrow {
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right top; LEFT: 22px; FLOAT: right; ZOOM: 1; POSITION: relative; TOP: =
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}
DIV#htbpopper {
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5; PADDING-BOTTOM: 0.5em; BORDER-LEFT: #369 1px solid; WIDTH: 32em; =
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FONT-FAMILY: Verdana; POSITION: absolute; BACKGROUND-COLOR: #f0f8ff; =
opacity: 100
}
DIV.popper P {
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}
P#htbpcit {
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P.pmid {
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DIV#HTDisplay UL LI SPAN.thumb {
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UNKNOWN {
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}
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DIV.popper EM.cit {
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italic
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DIV.popper EM.author {
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DIV.Pubmed_Discovery_RA SPAN.reviewflag {
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DIV.popper SPAN.reviewflag {
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DIV.PPMCPubmedRA SPAN.reviewflag {
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}
DIV.popper SPAN.reviewflag {
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}
BODY #col1 {
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#00c 1px solid; BORDER-BOTTOM: #00c 1px solid
}
BODY #col2 {
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#00c 1px solid; BORDER-BOTTOM: #00c 1px solid
}
BODY #subheader {
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#00c 1px solid; BORDER-BOTTOM: #00c 1px solid
}
BODY #subfooter {
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#00c 1px solid; BORDER-BOTTOM: #00c 1px solid
}
BODY #subfooter {
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}
#Table2 {
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}
#Table3 {
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TD.pmc-watermark {
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}
TD.format-menu {
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PADDING-BOTTOM: 0px; PADDING-TOP: 0px
}
TD.format-menu UL {
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PADDING-BOTTOM: 0px; MARGIN: 0px 0px 0px 0.2em; PADDING-TOP: 0px
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TD.format-menu H2 {
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TD.format-menu UL LI A {
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TD.format-menu UL LI.selected {
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}
TD.content-cell {
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TD.content-cell > DIV TD.content-cell > DIV > DIV {
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}
DIV.cited-ref {
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}
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DIV.sec {
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}
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DIV.ArticleRefDocsums {
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DIV.pmlinks UL.links LI.ovfl {
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DIV.cited-ref LI.ovfl {
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DIV.pmlinks UL.links LI.ovfl SPAN.flag {
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}
DIV.cited-ref LI.ovfl SPAN.flag {
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P.desc {
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DIV.brieflink DIV.PPMCPubmedRA UL LI.item P.note {
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DIV.cited-ref {
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DIV.cited-ref UL {
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DIV.cited-ref A.all-articles {
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}
DIV.cited-ref A.all-articles:hover {
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}
DIV.port {
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DIV.x-panel-body {
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}
DIV.sameauthor-seemore {
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}
DIV.x-panel-body SPAN.separator-bar {
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}
SPAN.review {
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}

@media Print   =20
{
HTML BODY.pmc-body {
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}
TD.sidebar-cell DIV.port {
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}
#ArticleRefDocsums {
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}
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}
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}
TD.content-cell {
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DIV.section-content > DIV.p {
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DIV.sec {
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}
#Table3 TD.sidebar-cell {
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}
TD.content-cell {
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}
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}
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}
.mb A {
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underline; outline: none
}
.mb LI {
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}
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}
UL.mb LI SPAN.delta {
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}
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}
.mb LI UL UL {
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}
UL.mb LI.submenu-item UL {
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BORDER-LEFT: red 1px solid; BORDER-BOTTOM: red 1px solid; POSITION: =
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}
UL.mb LI.active-item UL {
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}
UL.mb LI UL.opened {
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#ffffff 1px solid; MARGIN-TOP: 4px; PADDING-LEFT: 2px; LEFT: auto; =
PADDING-BOTTOM: 2px; BORDER-LEFT: #ffffff 1px solid; PADDING-TOP: 2px; =
BORDER-BOTTOM: #ffffff 1px solid; BACKGROUND-COLOR: #ffffff
}
UL.mb LI UL.opened LI {
	MARGIN-BOTTOM: 3px
}
UL.mb LI UL.opened LI.active-item {
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PADDING-BOTTOM: 0px; PADDING-TOP: 0px
}
UL.opened LI.active-item A {
	COLOR: #ffffff
}
UL.mb LI UL A {
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3px; COLOR: #222222; PADDING-TOP: 2px; TEXT-DECORATION: none
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------=_NextPart_000_0000_01CA72A3.109DE760
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------=_NextPart_000_0000_01CA72A3.109DE760
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'x0011c':'G',=0A=
'x0011d':'g',=0A=
'x0011e':'G',=0A=
'x0011f':'g',=0A=
'x00120':'G',=0A=
'x00121':'g',=0A=
'x00122':'G',=0A=
'x00124':'H',=0A=
'x00125':'h',=0A=
'x00126':'H',=0A=
'x00127':'h',=0A=
'x00128':'I',=0A=
'x00129':'ij',=0A=
'x0012a':'I',=0A=
'x0012b':'ij',=0A=
'x0012e':'I',=0A=
'x0012f':'ij',=0A=
'x00130':'I',=0A=
'x00131':'ij',=0A=
'x00132':'IJ',=0A=
'x00133':'ij',=0A=
'x00134':'J',=0A=
'x00135':'j',=0A=
'x00136':'K',=0A=
'x00137':'k',=0A=
'x00138':'k',=0A=
'x00139':'L',=0A=
'x0013a':'l',=0A=
'x0013b':'L',=0A=
'x0013c':'l',=0A=
'x0013d':'L',=0A=
'x0013e':'l',=0A=
'x0013f':'L',=0A=
'x00140':'l',=0A=
'x00141':'L',=0A=
'x00142':'l',=0A=
'x00143':'N',=0A=
'x00144':'n',=0A=
'x00145':'N',=0A=
'x00146':'n',=0A=
'x00147':'N',=0A=
'x00148':'n',=0A=
'x00149':'n',=0A=
'x0014c':'O',=0A=
'x0014d':'o',=0A=
'x00150':'O',=0A=
'x00151':'o',=0A=
'x00152':'OE',=0A=
'x00153':'oe',=0A=
'x00154':'R',=0A=
'x00155':'r',=0A=
'x00156':'R',=0A=
'x00157':'r',=0A=
'x00158':'R',=0A=
'x00159':'r',=0A=
'x0015a':'S',=0A=
'x0015b':'s',=0A=
'x0015c':'S',=0A=
'x0015d':'s',=0A=
'x0015e':'S',=0A=
'x0015f':'s',=0A=
'x00160':'S',=0A=
'x00161':'s',=0A=
'x00162':'T',=0A=
'x00163':'t',=0A=
'x00164':'T',=0A=
'x00165':'t',=0A=
'x00166':'T',=0A=
'x00167':'t',=0A=
'x00168':'U',=0A=
'x00169':'u',=0A=
'x0016a':'U',=0A=
'x0016b':'u',=0A=
'x0016c':'U',=0A=
'x0016d':'u',=0A=
'x0016e':'U',=0A=
'x0016f':'u',=0A=
'x00170':'U',=0A=
'x00171':'u',=0A=
'x00172':'U',=0A=
'x00173':'u',=0A=
'x00174':'W',=0A=
'x00175':'w',=0A=
'x00176':'Y',=0A=
'x00177':'y',=0A=
'x00178':'Y',=0A=
'x00179':'Z',=0A=
'x0017a':'z',=0A=
'x0017b':'Z',=0A=
'x0017c':'z',=0A=
'x0017d':'Z',=0A=
'x0017e':'z',=0A=
'x001f5':'g',=0A=
'x00405':'S',=0A=
'x00406':'I',=0A=
'x00408':'J',=0A=
'x00455':'s',=0A=
'x00456':'i',=0A=
'x00458':'j',=0A=
'x02102':'C',=0A=
'x0210b':'H',=0A=
'x0210c':'H',=0A=
'x02110':'I',=0A=
'x02111':'I',=0A=
'x02112':'L',=0A=
'x02115':'N',=0A=
'x02119':'P',=0A=
'x0211a':'Q',=0A=
'x0211c':'R',=0A=
'x0211d':'R',=0A=
'x0211e':'Rx',=0A=
'x02124':'Z',=0A=
'x0212b':'A',=0A=
'x0212c':'B',=0A=
'x0212f':'e',=0A=
'x02130':'E',=0A=
'x02131':'F',=0A=
'x02133':'M',=0A=
'x02134':'o',=0A=
'x0e05d':'h',=0A=
'x0e05f':'k',=0A=
'x0e3b2':'fj',=0A=
'x0e500':'A',=0A=
'x0e501':'B',=0A=
'x0e503':'D',=0A=
'x0e504':'E',=0A=
'x0e505':'F',=0A=
'x0e506':'G',=0A=
'x0e507':'H',=0A=
'x0e508':'I',=0A=
'x0e509':'J',=0A=
'x0e50a':'K',=0A=
'x0e50b':'L',=0A=
'x0e50c':'M',=0A=
'x0e50e':'O',=0A=
'x0e512':'S',=0A=
'x0e513':'T',=0A=
'x0e514':'U',=0A=
'x0e515':'V',=0A=
'x0e516':'W',=0A=
'x0e517':'X',=0A=
'x0e518':'Y',=0A=
'x0e520':'A',=0A=
'x0e522':'C',=0A=
'x0e523':'D',=0A=
'x0e526':'G',=0A=
'x0e529':'J',=0A=
'x0e52a':'K',=0A=
'x0e52d':'N',=0A=
'x0e52e':'O',=0A=
'x0e52f':'P',=0A=
'x0e530':'Q',=0A=
'x0e531':'R',=0A=
'x0e532':'S',=0A=
'x0e533':'T',=0A=
'x0e534':'U',=0A=
'x0e535':'V',=0A=
'x0e536':'W',=0A=
'x0e537':'X',=0A=
'x0e538':'Y',=0A=
'x0e539':'Z',=0A=
'x0e540':'a',=0A=
'x0e541':'b',=0A=
'x0e542':'c',=0A=
'x0e543':'d',=0A=
'x0e545':'f',=0A=
'x0e546':'g',=0A=
'x0e547':'h',=0A=
'x0e548':'i',=0A=
'x0e549':'j',=0A=
'x0e54a':'k',=0A=
'x0e54b':'l',=0A=
'x0e54c':'m',=0A=
'x0e54d':'n',=0A=
'x0e54f':'p',=0A=
'x0e550':'q',=0A=
'x0e551':'r',=0A=
'x0e552':'s',=0A=
'x0e553':'t',=0A=
'x0e554':'u',=0A=
'x0e555':'v',=0A=
'x0e556':'w',=0A=
'x0e557':'x',=0A=
'x0e558':'y',=0A=
'x0e559':'z',=0A=
'x0e560':'A',=0A=
'x0e561':'B',=0A=
'x0e562':'C',=0A=
'x0e563':'D',=0A=
'x0e564':'E',=0A=
'x0e565':'F',=0A=
'x0e566':'G',=0A=
'x0e569':'J',=0A=
'x0e56a':'K',=0A=
'x0e56b':'L',=0A=
'x0e56c':'M',=0A=
'x0e56d':'N',=0A=
'x0e56e':'O',=0A=
'x0e56f':'P',=0A=
'x0e570':'Q',=0A=
'x0e572':'S',=0A=
'x0e573':'T',=0A=
'x0e574':'U',=0A=
'x0e575':'V',=0A=
'x0e576':'W',=0A=
'x0e577':'X',=0A=
'x0e578':'Y',=0A=
'x0e579':'Z',=0A=
'x0e580':'a',=0A=
'x0e581':'b',=0A=
'x0e582':'c',=0A=
'x0e583':'d',=0A=
'x0e584':'e',=0A=
'x0e585':'f',=0A=
'x0e586':'g',=0A=
'x0e587':'h',=0A=
'x0e588':'i',=0A=
'x0e589':'j',=0A=
'x0e58a':'k',=0A=
'x0e58b':'l',=0A=
'x0e58c':'m',=0A=
'x0e58d':'n',=0A=
'x0e58e':'o',=0A=
'x0e58f':'p',=0A=
'x0e590':'q',=0A=
'x0e591':'r',=0A=
'x0e592':'s',=0A=
'x0e593':'t',=0A=
'x0e594':'u',=0A=
'x0e595':'v',=0A=
'x0e596':'w',=0A=
'x0e597':'x',=0A=
'x0e598':'y',=0A=
'x0e599':'z',=0A=
'x0ea00':'1',=0A=
'x0ea01':'1',=0A=
'x0ea02':'2',=0A=
'x0ea03':'2',=0A=
'x0ea04':'3',=0A=
'x0ea05':'3',=0A=
'x0ea06':'4',=0A=
'x0ea07':'a',=0A=
'x0ea08':'a',=0A=
'x0ea09':'A',=0A=
'x0ea0a':'a',=0A=
'x0ea0b':'A',=0A=
'x0ea0c':'AB',=0A=
'x0ea10':'b',=0A=
'x0ea11':'B',=0A=
'x0ea12':'b',=0A=
'x0ea13':'B',=0A=
'x0ea14':'B',=0A=
'x0ea15':'B',=0A=
'x0ea16':'BC',=0A=
'x0ea19':'c',=0A=
'x0ea1a':'c',=0A=
'x0ea1b':'c',=0A=
'x0ea1c':'C',=0A=
'x0ea1d':'c',=0A=
'x0ea1e':'c',=0A=
'x0ea1f':'c',=0A=
'x0ea20':'c',=0A=
'x0ea21':'c',=0A=
'x0ea25':'d',=0A=
'x0ea26':'D',=0A=
'x0ea27':'d',=0A=
'x0ea28':'D',=0A=
'x0ea29':'d',=0A=
'x0ea2a':'D',=0A=
'x0ea2b':'D',=0A=
'x0ea2f':'dl',=0A=
'x0ea30':'e',=0A=
'x0ea31':'e',=0A=
'x0ea32':'l',=0A=
'x0ea33':'l',=0A=
'x0ea34':'f',=0A=
'x0ea35':'f',=0A=
'x0ea36':'F',=0A=
'x0ea37':'f',=0A=
'x0ea38':'F',=0A=
'x0ea39':'f',=0A=
'x0ea3a':'F',=0A=
'x0ea3d':'g',=0A=
'x0ea3e':'g',=0A=
'x0ea3f':'G',=0A=
'x0ea40':'g',=0A=
'x0ea41':'G',=0A=
'x0ea46':'H',=0A=
'x0ea47':'h',=0A=
'x0ea48':'h',=0A=
'x0ea49':'i',=0A=
'x0ea4a':'I',=0A=
'x0ea4b':'j',=0A=
'x0ea4c':'J',=0A=
'x0ea4d':'J',=0A=
'x0ea4e':'J',=0A=
'x0ea4f':'k',=0A=
'x0ea50':'k',=0A=
'x0ea51':'k',=0A=
'x0ea52':'K',=0A=
'x0ea53':'K',=0A=
'x0ea54':'k',=0A=
'x0ea55':'l',=0A=
'x0ea56':'L',=0A=
'x0ea57':'l',=0A=
'x0ea5b':'lnV',=0A=
'x0ea5c':'m',=0A=
'x0ea5d':'M',=0A=
'x0ea5e':'m',=0A=
'x0ea5f':'m',=0A=
'x0ea63':'n',=0A=
'x0ea64':'n',=0A=
'x0ea65':'N',=0A=
'x0ea66':'n',=0A=
'x0ea67':'N',=0A=
'x0ea68':'n',=0A=
'x0ea69':'n',=0A=
'x0ea6a':'N',=0A=
'x0ea6d':'nv',=0A=
'x0ea6e':'O',=0A=
'x0ea6f':'O',=0A=
'x0ea70':'O',=0A=
'x0ea72':'F',=0A=
'x0ea73':'p',=0A=
'x0ea74':'P',=0A=
'x0ea75':'p',=0A=
'x0ea76':'P',=0A=
'x0ea77':'p',=0A=
'x0ea78':'P',=0A=
'x0ea79':'p',=0A=
'x0ea7a':'P',=0A=
'x0ea8d':'q',=0A=
'x0ea8e':'Q',=0A=
'x0ea8f':'q',=0A=
'x0ea90':'q',=0A=
'x0ea91':'Q',=0A=
'x0ea92':'q',=0A=
'x0ea93':'Q',=0A=
'x0ea94':'q',=0A=
'x0ea95':'q',=0A=
'x0ea96':'q',=0A=
'x0ea97':'Q',=0A=
'x0ea98':'r',=0A=
'x0ea99':'R',=0A=
'x0ea9a':'R',=0A=
'x0ea9b':'r',=0A=
'x0ea9c':'R',=0A=
'x0ea9d':'R',=0A=
'x0ea9e':'r',=0A=
'x0ea9f':'R',=0A=
'x0eaa0':'r',=0A=
'x0eaa1':'ri',=0A=
'x0eaa2':'R',=0A=
'x0eaa3':'r',=0A=
'x0eaa4':'r1',=0A=
'x0eaa5':'RE',=0A=
'x0eaa9':'ri',=0A=
'x0eaaa':'rj',=0A=
'x0eaab':'rN',=0A=
'x0eaac':'s',=0A=
'x0eaad':'S',=0A=
'x0eaae':'S',=0A=
'x0eaaf':'s',=0A=
'x0eab0':'S',=0A=
'x0eab1':'s',=0A=
'x0eab2':'S',=0A=
'x0eab3':'S',=0A=
'x0eab4':'B',=0A=
'x0eab5':'E',=0A=
'x0eab6':'G',=0A=
'x0eab7':'P',=0A=
'x0eab8':'Q',=0A=
'x0eab9':'t',=0A=
'x0eaba':'T',=0A=
'x0eabb':'T',=0A=
'x0eabc':'t',=0A=
'x0eabd':'T',=0A=
'x0eabe':'t',=0A=
'x0eabf':'T',=0A=
'x0eac5':'TT',=0A=
'x0eac6':'u',=0A=
'x0eac7':'u',=0A=
'x0eac8':'U',=0A=
'x0eac9':'u',=0A=
'x0eaca':'u',=0A=
'x0eacc':'V',=0A=
'x0eacd':'v',=0A=
'x0eace':'v',=0A=
'x0eacf':'V',=0A=
'x0ead0':'v',=0A=
'x0ead1':'V',=0A=
'x0ead2':'v',=0A=
'x0ead3':'v',=0A=
'x0ead4':'V',=0A=
'x0ead5':'v',=0A=
'x0eadc':'w',=0A=
'x0eadd':'w',=0A=
'x0eade':'w',=0A=
'x0eadf':'x',=0A=
'x0eae0':'X',=0A=
'x0eae1':'x',=0A=
'x0eae2':'X',=0A=
'x0eae3':'x',=0A=
'x0eae4':'x',=0A=
'x0eae5':'X',=0A=
'x0eae6':'x',=0A=
'x0eae8':'y',=0A=
'x0eae9':'Y',=0A=
'x0eaea':'y',=0A=
'x0eaeb':'Y',=0A=
'x0eaec':'y',=0A=
'x0eaed':'y',=0A=
'x0eaee':'z',=0A=
'x0eaef':'Z',=0A=
'x0eaf0':'z',=0A=
'x0eaf1':'z',=0A=
'x0eaf2':'Z',=0A=
'x0eaf3':'z',=0A=
'x0eaf4':'z',=0A=
'x0eafc':'B',=0A=
'x0eaff':'A',=0A=
'x0eb04':'w',=0A=
'x0eb05':'m',=0A=
'x0eb06':'M',=0A=
'x0eb07':'E',=0A=
'x0eb08':'W',=0A=
'x0eb0a':'h',=0A=
'x0eb0b':'n',=0A=
'x0eb0d':'H',=0A=
'x0eb0f':'M',=0A=
'x0eb10':'m',=0A=
'x0eb11':'Z',=0A=
'x0eb12':'g',=0A=
'x0eb14':'C',=0A=
'x0eb15':'E',=0A=
'x0eb19':'W',=0A=
'x0eb1a':'a',=0A=
'x0eb1b':'b',=0A=
'x0eb1c':'S',=0A=
'x0eb1e':'J',=0A=
'x0eb1f':'b',=0A=
'x0eb20':'Z',=0A=
'x0eb21':'L',=0A=
'x0eb22':'g',=0A=
'x0fb00':'ffi',=0A=
'x0fb01':'fi',=0A=
'x0fb02':'fl',=0A=
'x0fb03':'ffi',=0A=
'x0fb04':'ffl'=0A=
    }=0A=
=0A=
// Called from many places to handle links.=0A=
// Params:=0A=
//     link:         URL. 'this' to reuse same window, else ""=0A=
//     windowname:   Reference name for window=0A=
//     additional:   Attributes for window.open, from:=0A=
//        width, height, resizable, scrollbars, toolbar, location, =
directories,=0A=
//        status, menubar, copyhistory.=0A=
// Notes: Book version always provides menubar, toolbar, etc.=0A=
//=0A=
function startTargetBook(link,windowname,width,height,additional)=0A=
{=0A=
    startTarget(link,windowname,width,height,additional)=0A=
}=0A=
=0A=
=0A=
//=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0A=
function startTarget(link,windowname,width,height, additional)=0A=
{=0A=
=0A=
    if(! window.focus)=0A=
        return;=0A=
=0A=
    var sizestring =3D ",width=3D" + width + ",height=3D" + height;=0A=
	var opt =3D =
"menubar=3Dno,toolbar=3Dno,status=3Dno,scrollbars=3Dyes,resizable=3Dyes,d=
ependent=3Dyes,location=3Dno";=0A=
    var allOptions =3D opt + sizestring;=0A=
    if (additional) { allOptions =3D allOptions + ',' + additional; }=0A=
=0A=
    windowname =3D String(windowname).replace(/-/g, "_")=0A=
    var moveToXDefault =3D 75=0A=
    var moveToYDefault =3D 50=0A=
=0A=
    var moveToX =3D moveToXDefault=0A=
    var moveToY =3D moveToYDefault=0A=
    var yAdj =3D 50=0A=
    var yAdjDelta =3D 25=0A=
=0A=
    var barNames =3D ['menubar', 'toolbar', 'statusbar']=0A=
    for (var idx in barNames)=0A=
    {=0A=
	if (String(allOptions).lastIndexOf(barNames[idx] + '=3Dyes') >=0A=
	    String(allOptions).lastIndexOf(barNames[idx] + '=3Dno'))=0A=
		yAdj +=3D yAdjDelta=0A=
    }=0A=
=0A=
    try {=0A=
        if (window.screen.width && width > 0)=0A=
            moveToX =3D Math.ceil((window.screen.width - width)) - 15=0A=
        moveToX =3D (moveToX > 0 ? moveToX : moveToXDefault)=0A=
=0A=
        if (window.screen.height && height > 0)=0A=
            moveToY =3D Math.ceil((window.screen.height - height)) - yAdj=0A=
        moveToY =3D (moveToY > 0 ? moveToY : moveToYDefault)=0A=
    }=0A=
    catch (e) {}=0A=
=0A=
    var wLeftTopCornerOptions =3D ',left=3D' + moveToX + ',top=3D' + =
moveToY + ',screenX=3D' + moveToX + ',screenY=3D' + moveToY=0A=
=0A=
    allOptions =3D allOptions + wLeftTopCornerOptions=0A=
=0A=
    w =3D window.open (link, windowname, allOptions)=0A=
    w.focus()=0A=
=0A=
    link.target=3Dwindowname=0A=
=0A=
    return false;=0A=
}=0A=
=0A=
=0A=
//=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0A=
function focuswin(windowname)=0A=
{=0A=
    windowname =3D String(windowname).replace(/-/g, "_")=0A=
    w =3D =
window.open("",windowname,"menubar=3Dyes,scrollbars=3Dyes,toolbar=3Dyes,l=
ocation=3Dyes,status=3Dyes,directories=3Dyes,resizable=3Dyes");=0A=
    w.focus();=0A=
=0A=
    return true;=0A=
}=0A=
=0A=
=0A=
//=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0A=
function reverseString (inStr)=0A=
{=0A=
    var outStr =3D ''=0A=
=0A=
    for (i =3D0; i <=3D inStr.length; i++)=0A=
    {=0A=
	outStr =3D inStr.charAt(i) + outStr=0A=
    }=0A=
=0A=
    return outStr=0A=
}=0A=
=0A=
=0A=
//=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0A=
function reverseAndReplaceString (inStr, findStr, newStr)=0A=
{=0A=
    return reverseString(inStr).replace(findStr, newStr)=0A=
}=0A=
=0A=
//=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0A=
function initUnObscureEmail (className, innerHTML)=0A=
{=0A=
=0A=
    try{=0A=
        if (window.addEventListener)=0A=
            window.addEventListener('load', function() {unObscureEmail =
(className, innerHTML)}, false)=0A=
        else if (window.attachEvent)=0A=
            window.attachEvent('onload', function() {unObscureEmail =
(className, innerHTML)})=0A=
    }catch(e){=0A=
    }=0A=
}=0A=
=0A=
//=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0A=
function unObscureEmail (className, innerHTML)=0A=
{=0A=
    try {=0A=
        if (typeof(unObscuredEmails) =3D=3D 'undefined')=0A=
            unObscuredEmails =3D new Array()=0A=
=0A=
        if (! unObscuredEmails[className])=0A=
        {=0A=
=0A=
            var elmnts =3D document.getElementsByTagName("span")=0A=
            for (var i =3D 0, len =3D elmnts.length; i < len; i++)=0A=
            {=0A=
                if (elmnts.item(i).className.indexOf(className, " ") =
!=3D -1)=0A=
                {=0A=
                    elmnts.item(i).innerHTML     =3D innerHTML;=0A=
                    unObscuredEmails[className]  =3D true=0A=
=0A=
                }=0A=
            }=0A=
        }=0A=
    }=0A=
    catch(e){=0A=
    }=0A=
}=0A=
=0A=
//=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0A=
function pubMedDbLinkSubmit(control) {=0A=
    try{=0A=
        if (control.pubmedOption)=0A=
            control =3D control.pubmedOption=0A=
        if (control.options)=0A=
            location.href =3D =
control.options[control.options.selectedIndex].value;=0A=
    }=0A=
    catch(e){}=0A=
    return false;=0A=
}=0A=
=0A=
//=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0A=
// elements "a", "area" with "ref" attribute report to redirect utility =
before dereferencing link=0A=
//=0A=
function initRedirectClicks(report_url) {=0A=
=0A=
    if (report_url && typeof jQuery !=3D 'undefined')=0A=
        jQuery(document).click(function(e) {=0A=
=0A=
            //=0A=
            if (!e) return true;=0A=
            //=0A=
            if (e.shiftKey || e.altKey || e.ctrlKey) return true;=0A=
            //=0A=
            var target =3D jQuery(e.target).closest("a[ref], area[ref]");=0A=
            if (!target || target.length =3D=3D 0) return true;=0A=
            //=0A=
            var ref  =3D target.attr("ref");=0A=
            var href =3D target.attr("href")=0A=
=0A=
            // special processing of href element for pubmed's authors=0A=
            if (typeof (href) !=3D 'undefined' && =
href.indexOf('sites/entrez') && href.indexOf('%5Bauth%5D'))=0A=
            {=0A=
                var newHref =3D replacePubMedUnsupportedChars(href);=0A=
                if (newHref !=3D href)=0A=
                    target.attr("href", newHref)=0A=
            }=0A=
=0A=
            // append ref with value of href if 'redirect-to-url' is =
missing in ref.=0A=
            if (typeof (ref) !=3D 'undefined' && =
ref.indexOf('redirect-to-url') =3D=3D -1)=0A=
            {=0A=
                ref =3D ref + '&redirect-to-url=3D' + =
encodeURIComponent(href)=0A=
                //=0A=
                jQuery.ajax({=0A=
                   type:    "HEAD",=0A=
                   url:     report_url + '?' + ref,=0A=
                   timeout: 1000,=0A=
                   async:   false=0A=
                });=0A=
            }=0A=
=0A=
            return true;=0A=
        });=0A=
};=0A=
=0A=
// function to replace unsupported charachters in author names to be =
searchable in PubMed database.=0A=
function replacePubMedUnsupportedChars (str)=0A=
{=0A=
    // replace low 128 chars automatically=0A=
    str =3D str.replace(/%26%23(x000[0-7][0-9a-f])%3b/ig,=0A=
        function($0, $1){=0A=
            return (String.fromCharCode('0' + $1))=0A=
        }=0A=
    )=0A=
    // replace others based on map and if it is not in the map replace =
with empty string.=0A=
    str =3D =
str.replace(/%26%23(x[0-9a-f][0-9a-f][0-9a-f][0-9a-f][0-9a-f])%3b/ig,=0A=
        function($0, $1){=0A=
            return (pubmedUnsupportedCharMap[$1] ? =
pubmedUnsupportedCharMap[$1] : '')=0A=
        }=0A=
    )=0A=
    return str;=0A=
}=0A=
//=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0A=
// Based on script written by Dean Edwards, 2005=0A=
// http://dean.edwards.name/=0A=
=0A=
var pmc_script =3D {=0A=
	addEvent: function(element, type, handler) {=0A=
		// assign each event handler a unique ID=0A=
		if (!handler.$$guid) handler.$$guid =3D this.addEvent_guid++;=0A=
		// create a hash table of event types for the element=0A=
		if (!element.events) element.events =3D {};=0A=
		// create a hash table of event handlers for each element/event pair=0A=
		var handlers =3D element.events[type];=0A=
		if (!handlers) {=0A=
			handlers =3D element.events[type] =3D {};=0A=
			// store the existing event handler (if there is one)=0A=
			if (element["on" + type]) {=0A=
				handlers[0] =3D element["on" + type];=0A=
			}=0A=
		}=0A=
		// store the event handler in the hash table=0A=
		handlers[handler.$$guid] =3D handler;=0A=
		// assign a global event handler to do all the work=0A=
		element["on" + type] =3D handleEvent;=0A=
=0A=
=0A=
		function handleEvent(event) {=0A=
			var returnValue =3D true;=0A=
			// grab the event object (IE uses a global event object)=0A=
			event =3D event || fixEvent(window.event);=0A=
			// get a reference to the hash table of event handlers=0A=
			var handlers =3D this.events[event.type];=0A=
			// execute each event handler=0A=
			for (var i in handlers) {=0A=
				this.$$handleEvent =3D handlers[i];=0A=
				if (this.$$handleEvent(event) =3D=3D=3D false) {=0A=
					returnValue =3D false;=0A=
				}=0A=
			}=0A=
			return returnValue;=0A=
		};=0A=
=0A=
		function fixEvent(event) {=0A=
			// add W3C standard event methods=0A=
			event.preventDefault =3D fixEvent.preventDefault;=0A=
			event.stopPropagation =3D fixEvent.stopPropagation;=0A=
			return event;=0A=
		};=0A=
=0A=
		fixEvent.preventDefault =3D function() {=0A=
			this.returnValue =3D false;=0A=
		};=0A=
=0A=
		fixEvent.stopPropagation =3D function() {=0A=
			this.cancelBubble =3D true;=0A=
		};=0A=
	},=0A=
=0A=
	// a counter used to create unique IDs=0A=
	addEvent_guid: 1,=0A=
=0A=
	removeEvent: function(element, type, handler) {=0A=
		// delete the event handler from the hash table=0A=
		if (element.events && element.events[type]) {=0A=
			delete element.events[type][handler.$$guid];=0A=
		}=0A=
	}=0A=
}=0A=
=0A=
=0A=
// =
*************************************************************************=
***=0A=
//  implementation of figure's popup using jQuery and =
jQuery.fn.hoverIntent lib=0A=
//  it set appropriate handlers for all "a" elements with "figpopup" =
class name.=0A=
// =
*************************************************************************=
***=0A=
if (typeof jQuery !=3D 'undefined' && typeof jQuery.fn.hoverIntent !=3D =
'undefined') {=0A=
    (function($j) {=0A=
        // =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D  hoverHandlers =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=0A=
        var hoverHandlers =3D function  (opts) {=0A=
            this.config =3D {}=0A=
            this.self =3D this;=0A=
            this.__init(opts)=0A=
        }=0A=
=0A=
         $j.fn.extend(hoverHandlers.prototype,  {=0A=
                //=0A=
                __init: function(opts) {=0A=
                    $j.fn.extend(this.config, opts)=0A=
                },=0A=
                //=0A=
                over: function (el) {=0A=
                    var canvas =3D $j('.large-thumb-canvas', el)=0A=
                    var prnt =3D  canvas.parent();=0A=
                    var win =3D $j(window)=0A=
=0A=
                    //=0A=
                    if (canvas && prnt && win)=0A=
                    {=0A=
=0A=
                        // collect necessary coordinates from all =
intresting objects=0A=
                        canvas.coords =3D this._x_coords(canvas, =
'canvas')=0A=
                        prnt.coords   =3D this._x_coords(prnt,   =
'parent')=0A=
                        win.coords    =3D this._x_coords(win,    =
'window')=0A=
=0A=
                        // replace @src with value of @hires, because =
href hold high resolution image and src low one.=0A=
                        $j('img', canvas).attr('src',=0A=
                                function(){=0A=
                                    var hires =3D $j(this).attr("hires");=0A=
                                    return (typeof (hires) !=3D =
'undefined' && hires !=3D this.src)=0A=
                                            ? hires : this.src=0A=
                                }=0A=
                        )=0A=
=0A=
                        // make arrangement of canvas in the view port =
nearby parent element.=0A=
                        var cnvsRltvToPrnt =3D =
this._x_arrange_canvas(canvas.coords, prnt.coords, win.coords)=0A=
=0A=
                        // visualize the canvas with images.=0A=
                        canvas.css('top', cnvsRltvToPrnt.top + 'px')=0A=
                        canvas.css('left', cnvsRltvToPrnt.left + 'px')=0A=
                        canvas.css('display', 'block')=0A=
                    } // canvas=0A=
                }, // over=0A=
                //=0A=
                out: function (el) {=0A=
                    var canvas =3D $j('.large-thumb-canvas', el)=0A=
                    canvas.css('display', 'none')=0A=
                },=0A=
                //=0A=
                _x_offset:                     function(el, elname) {=0A=
                    var c =3D {}=0A=
                    if (el[0] =3D=3D window )=0A=
                        c =3D this._x_scroll(el, elname)=0A=
                    else=0A=
                        c =3D el.offset()=0A=
                    //console.info('%s.offset {top,left} =3D {%s, %s}', =
elname, c.top, c.left)=0A=
                    return c=0A=
                },=0A=
                _x_scroll:                     function(el, elname) {=0A=
                    var c =3D {top: el.scrollTop(), left: =
el.scrollLeft()}=0A=
                    //console.info('%s.scroll {top,left} =3D {%s, %s}', =
elname, c.top, c.left)=0A=
                    return c=0A=
                },=0A=
                _x_width:                     function(el, elname) {=0A=
                    var w =3D el.outerWidth() || el.width()=0A=
                    //console.info('%s.width      =3D %s; outerWidth =3D =
%s; width =3D %s', elname, w, el.outerWidth(), el.width())=0A=
                    //IE: alert(elname + '.width      =3D ' + w + '; =
outerWidth =3D ' + el.outerWidth() + 'width =3D ' + el.width())=0A=
                    return w=0A=
                },=0A=
                _x_height:                     function(el, elname) {=0A=
                    var h =3D el.outerHeight() || el.height()=0A=
                    // console.info('%s.height =3D %s', elname, h)=0A=
                    return h=0A=
                },=0A=
                _x_coords:                    function(el, elname) {=0A=
                    var size =3D { width: this._x_width (el, elname), =
height:  this._x_height(el, elname)}=0A=
                    var coords =3D {=0A=
                            scroll:  this._x_scroll(el, elname),=0A=
                            width:   size.width,=0A=
                            height:  size.height,=0A=
                            offset:  this._x_offset(el, elname),=0A=
                            size:    size=0A=
                        }=0A=
                    return coords=0A=
                },=0A=
                _x_get_rltv_coord:            function(trgtObj, baseObj, =
label) {=0A=
                    var c =3D {top: trgtObj.top - baseObj.top, left: =
trgtObj.left - baseObj.left}=0A=
                    //console.info("%s {top: %s, left: %s}", label, =
c.top, c.left)=0A=
                    return c=0A=
                },=0A=
                //=0A=
                _x_get_empty_space:            function(objCoords, =
objSize, viewPortCoords, viewPortSize, label) {=0A=
                    var objRelToViewPort =3D =
this._x_get_rltv_coord(objCoords, viewPortCoords, '_x_get_empty_space: =
for ' + label);=0A=
                    var c =3D {above: objRelToViewPort.top,=0A=
                             below: viewPortSize.height - =
(objRelToViewPort.top + objSize.height),=0A=
                             left: objRelToViewPort.left,=0A=
                             right: viewPortSize.width - =
(objRelToViewPort.left + objSize.width)}=0A=
                    $j.each(c, function(k, v){c[k] =3D (v < 0 ? 0 : v)})=0A=
                    //console.info("%s {above: %s, below: %s, left: %s, =
right: %s}", label, c.above, c.below, c.left, c.right)=0A=
                    return c=0A=
                },=0A=
                //=0A=
                _x_get_bigest_space_area_name: function(spaces, label) {=0A=
                    var sArr =3D [];=0A=
                    for (k in spaces){ sArr[sArr.length] =3D {k: k, v: =
spaces[k]} }=0A=
                    // sort in reverse order=0A=
                    sArr.sort (function(a,b){return ( a.v < b.v ? 1 : ( =
a.v > b.v ?  - 1 : 0 ) )})=0A=
                    // console.info('%s: %s', label, sArr[0].k)=0A=
                    return sArr[0].k=0A=
                },=0A=
                //=0A=
                _x_get_space_ratios:             function(spaces, =
viewPortSize, label) {=0A=
                    var ratios =3D {above: 0, left: 0}=0A=
                    if (viewPortSize.height > 0)=0A=
                        ratios.above =3D spaces.above / =
viewPortSize.height=0A=
                    if (viewPortSize.width > 0)=0A=
                        ratios.left =3D spaces.left / viewPortSize.width=0A=
                    // console.info('ratio: %s {above: %s, left: %s}', =
label, ratios.above, ratios.left)=0A=
                    return ratios=0A=
                },=0A=
                _x_arrange_canvas:                function(c_c, prnt_c, =
viewp_c) {=0A=
                // then calculate empty space areas around parent =
element of the canvas, which is ususally an anchor ("a" element)=0A=
                    var emptySpacesArndPrntInViewPort =3D =
this._x_get_empty_space (prnt_c.offset, prnt_c.size, viewp_c.offset, =
viewp_c.size, 'emptySpacesArndPrntInWinPort')=0A=
=0A=
                    // get the area name, where the most linear space =
avaiable=0A=
                    var areaName =3D =
this._x_get_bigest_space_area_name(emptySpacesArndPrntInViewPort, =
viewp_c.size, 'spacios areaName')=0A=
=0A=
                    // calculate the proportions of area to be taken by =
canvas in empty space area=0A=
                    // relativly to the parent element.=0A=
                    var ratios =3D =
this._x_get_space_ratios(emptySpacesArndPrntInViewPort, viewp_c.size, =
'ratios')=0A=
=0A=
                    // calculate parent's coordinates relative to view =
port=0A=
                    var prntRltvToViewPort =3D =
this._x_get_rltv_coord(prnt_c.offset, viewp_c.offset, =
'prntRltvToViewPort')=0A=
=0A=
                    // declare canvas relative coordinates=0A=
                    var cnvsRltvToPrnt =3D {top: 0, left: 0}=0A=
=0A=
                    // choose appropriate location for placing canvas.=0A=
                    // and choose the 1st element of an array as the one =
with the biggest area around parent of canvas.=0A=
                    // console.info ('place it at the %s', =
bigestEmptySpaceAreaName)=0A=
                    // calculations are relative to the left corner of =
the parent element of canvas. (it has to have the css property =
position:relative)=0A=
                    switch (areaName)=0A=
                    {=0A=
                        case 'above':=0A=
                            cnvsRltvToPrnt.top  =3D - c_c.height=0A=
                            cnvsRltvToPrnt.left =3D prnt_c.width * 0.5 - =
c_c.width * ratios.left=0A=
                        break;=0A=
                        case 'below':=0A=
                            cnvsRltvToPrnt.top  =3D prnt_c.height=0A=
                            cnvsRltvToPrnt.left =3D prnt_c.width * 0.5 - =
c_c.width * ratios.left=0A=
                        break;=0A=
                        case 'left':=0A=
                            cnvsRltvToPrnt.left =3D - c_c.width=0A=
                            cnvsRltvToPrnt.top  =3D prnt_c.height * 0.5 =
- c_c.height * ratios.above=0A=
                        break;=0A=
                        case 'right':=0A=
                            cnvsRltvToPrnt.left =3D prnt_c.width=0A=
                            cnvsRltvToPrnt.top  =3D prnt_c.height * 0.5 =
- c_c.height * ratios.above=0A=
                        break;=0A=
                    }=0A=
=0A=
                    // recalculate canvas' coordinates relative to =
parent into coordinates relative to view port.=0A=
                    var cnvsRltvToViewPort =3D {=0A=
                        top:  prntRltvToViewPort.top + =
cnvsRltvToPrnt.top,=0A=
                        left: prntRltvToViewPort.left + =
cnvsRltvToPrnt.left=0A=
                    }=0A=
                    //console.info("cnvsRltvToPrnt {top:%s, left: %s}", =
cnvsRltvToPrnt.top, cnvsRltvToPrnt.left)=0A=
                    //console.info("cnvsRltvToViewPort {top:%s, left: =
%s}", cnvsRltvToViewPort.top, cnvsRltvToViewPort.left)=0A=
=0A=
                    // adjust relative position of canvas to the window =
if calculated values=0A=
                    // are forcing canvas go out of view port=0A=
                    // next order should be preserved to keep left top =
corner visible always=0A=
=0A=
                    // adjust right side and move a bit to the left=0A=
                    if (cnvsRltvToViewPort.left + c_c.width > =
viewp_c.width)=0A=
                    {=0A=
                         var horAdj =3D c_c.width - (viewp_c.width - =
cnvsRltvToViewPort.left)=0A=
                         cnvsRltvToPrnt.left     -=3D horAdj=0A=
                         cnvsRltvToViewPort.left -=3D horAdj=0A=
                         //console.log('adjust right side and move to =
the left %spx', horizontalAdjustment)=0A=
                    }=0A=
=0A=
                    // adjust below side and move to the top=0A=
                    if (cnvsRltvToViewPort.top + c_c.height > =
viewp_c.height)=0A=
                    {=0A=
                        var vertAdj =3D c_c.height - (viewp_c.height - =
cnvsRltvToViewPort.top)=0A=
                        cnvsRltvToPrnt.top     -=3D vertAdj=0A=
                        cnvsRltvToViewPort.top -=3D vertAdj=0A=
                        // console.log('adjust below side and move to =
the top %spx', verticalAdjustment)=0A=
                    }=0A=
=0A=
                    // adjust left side and move to the right=0A=
                    if (cnvsRltvToViewPort.left < 0)=0A=
                    {=0A=
                        // console.log('adjust left side and move to the =
right %spx', -(cnvsLeftRelativeToWindowPort))=0A=
                        cnvsRltvToPrnt.left    -=3D =
cnvsRltvToViewPort.left=0A=
                        cnvsRltvToViewPort.left =3D 0=0A=
                    }=0A=
                    // adjust above side and move to the bottom=0A=
                    if (cnvsRltvToViewPort.top < 0)=0A=
                    {=0A=
                        // console.log('adjust above side and move to =
the bottom %spx', -(cnvsTopRelativeToWindowPort))=0A=
                        cnvsRltvToPrnt.top          -=3D =
cnvsRltvToViewPort.top=0A=
                        cnvsRltvToViewPort.top =3D 0=0A=
                    }=0A=
                    // console.info("cnvsRltvToPrnt adjusted {top: %s, =
left: %s}", cnvsRltvToPrnt.top, cnvsRltvToPrnt.left)=0A=
                    // console.info("cnvsRltvToViewPort adjusted {top: =
%s, left: %s}", cnvsRltvToViewPort.top, cnvsRltvToViewPort.left)=0A=
                    return cnvsRltvToPrnt=0A=
                }=0A=
        })=0A=
         // =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D  end of hoverHandlers =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0A=
=0A=
=0A=
         // =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D  $j.fn.figPopup =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=0A=
        function  hoverOverHandler  () {=0A=
            var h =3D new hoverHandlers();=0A=
            h.over(this)=0A=
        }=0A=
=0A=
        function hoverOutHandler () {=0A=
            var h =3D new hoverHandlers();=0A=
            h.out(this)=0A=
        }=0A=
=0A=
        $j.fn.figPopup =3D function(opts){=0A=
            var config =3D {=0A=
                interval:      500,=0A=
                timeout:       0,=0A=
                over:          hoverOverHandler, // handler onMouseOver=0A=
                out:           hoverOutHandler    // handler  onMouseOut=0A=
            }=0A=
            $j.extend(config, opts)=0A=
            return  config=0A=
        }=0A=
=0A=
        // =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D  end of $j.fn.figPopup =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0A=
=0A=
    }) (jQuery) // end of extention of jQuery with figPopup=0A=
=0A=
=0A=
=0A=
    jQuery(document).ready( function () {=0A=
        var fp_cfg =3D new jQuery.fn.figPopup()=0A=
        jQuery('a.figpopup').hoverIntent(fp_cfg)=0A=
    });=0A=
}=0A=
=0A=
// end of hoverIntent routines for figures' popups=0A=
// =
*************************************************************************=
***=0A=
//  implementation of ....=0A=
// =
*************************************************************************=
***=0A=

------=_NextPart_000_0000_01CA72A3.109DE760
Content-Type: application/octet-stream
Content-Transfer-Encoding: quoted-printable
Content-Location: http://www.ncbi.nlm.nih.gov/corehtml/pmc/js/noext.menu.js

if (typeof(noext) =3D=3D=3D 'undefined') {
   noext =3D {};=20
}

if (typeof jQuery =3D=3D=3D 'undefined') {
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}

// Constructor
noext.Menu =3D function (n, subMenuStyle) {
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    this.subMenuStyle =3D (subMenuStyle =3D=3D=3D 'ext') ? 'opened-ext' =
: 'opened';
    this.firstLi =3D this.n.children('li');
    this.subMenu =3D this.firstLi.find('ul');
    this.subMenuItems =3D this.subMenu.find('li');
    this.init();
    noext.Menu.menuInstances.push(this);
};
noext.Menu.menuInstances =3D [];

noext.Menu.prototype =3D {
    init: function () { // add events to what we need
        var that =3D this;
        this.subMenuItems.mouseover( this.hover); // do mouseovers for =
ie6
        this.subMenuItems.mouseout( this.unHover);
        this.n.click( function (event) { that.update(event);}); // =
update the menu
       =20
        jQuery(document).click( function (event) { =
that.closeAllSubMenus(event); }); // close other menus when we click one
    },
    update: function (e) {
            var t =3D jQuery(e.target);         =20
            // don't follow link if first item, whose target is '<u>'
            if (t.hasClass('first-link') ) {
                e.preventDefault();
            }

            var sm =3D this.subMenu;
            // close other menus
            this.closeOtherSubMenus(sm);
      =20
            var subMenuStyle =3D this.subMenuStyle;
           =20
            if ( !sm.hasClass(subMenuStyle)) {
                sm.addClass(subMenuStyle);
            } else {
                sm.removeClass(subMenuStyle);
            }
            e.stopPropagation(); // don't let default event occur =
(removeMenus from document.click)

           =20

    },
    hover: function () {
        jQuery(this).addClass('active-item');

    },
    unHover: function () {
        jQuery(this).removeClass('active-item');

    },
    closeOtherSubMenus: function (currentSubMenu) {
        // close all menu's submenus, that are different than currently =
clicked menu's submenu
        var subMenuStyle =3D this.subMenuStyle;
        currentSubMenu =3D this.subMenu;
        var menuInstances =3D noext.Menu.menuInstances;
        for (var i =3D 0; i < menuInstances.length; i++) {
            var menuInstance =3D menuInstances[i];
    =20
            if (currentSubMenu !=3D=3D menuInstance.subMenu && =
menuInstance.subMenu.hasClass(subMenuStyle)) {
                menuInstance.subMenu.removeClass(subMenuStyle);
            }=20
        }
    },
    closeAllSubMenus: function (event) {
        // for when user clicks on document
        var menuInstances =3D noext.Menu.menuInstances;
        for (var i =3D 0; i < menuInstances.length; i++) {
            var subMenu =3D this.subMenu;
            subMenu.removeClass(this.subMenuStyle);
        }
    }
};
// end of menu objecta


jQuery(document).ready( function () {
    jQuery('ul.noext-menu').removeClass('noext-menu-hidden').each( =
function () {
        noext.Menu.menuInstances.push( new noext.Menu( jQuery(this) ) );
    });
});
------=_NextPart_000_0000_01CA72A3.109DE760
Content-Type: application/octet-stream
Content-Transfer-Encoding: quoted-printable
Content-Location: http://www.ncbi.nlm.nih.gov/portal/js/portal.js

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e{return =
x_setListener(oListener,sMessage,fFunction,oNotifier);}};Notifier.prototy=
pe.Notify=3Dfunction(oNotifier,sMessage,oComment,oListener){var =
sAnyMessage=3D"*";for(var i in =
this.oQuee[sAnyMessage]){if(null=3D=3DoListener||this.oQuee[sAnyMessage][=
i].obj=3D=3DoListener){if(this.oQuee[sAnyMessage][i].ntf=3D=3Dnull||this.=
oQuee[sAnyMessage][i].ntf=3D=3D=3DoNotifier){if("function"=3D=3Dtypeof =
this.oQuee[sAnyMessage][i].fun){var =
fun=3Dthis.oQuee[sAnyMessage][i].fun;fun(this.oQuee[sAnyMessage][i].obj,o=
Comment,sMessage,oNotifier);}}}}=0A=
for(i in =
this.oQuee[sMessage]){if(null=3D=3DoListener||this.oQuee[sMessage][i].obj=
=3D=3DoListener){if(this.oQuee[sMessage][i].ntf=3D=3Dnull||this.oQuee[sMe=
ssage][i].ntf=3D=3D=3DoNotifier){if("function"=3D=3Dtypeof =
this.oQuee[sMessage][i].fun){if(this.oQuee[sMessage][i].fun(this.oQuee[sM=
essage][i].obj,oComment,sMessage,oNotifier)){return;}}}}}};Notifier.getIn=
stance=3Dfunction(){if(!Notifier.instance){Notifier.instance=3Dnew =
Notifier();}=0A=
return =
Notifier.instance;};Dispatcher=3DBase.extend({constructor:function(oRules=
,oHierarchy){this.init();},init:function(){this.oNotifier=3Dnew =
Notifier();this.submitOK=3Dtrue;this.submitter=3Dfalse;this.submitRequest=
ed=3Dfalse;this.submitChecking=3Dfalse;this._rules=3D{};},initDataExchang=
e:function(oRules){var oThis=3Dthis;var activenames=3DActiveNames;var =
i,j;var =
rulehash=3D{};activenames=3DActiveNames;this.submitOK=3Dtrue;this.submitR=
equested=3Dfalse;this.submitter=3Dnull;this.oRules=3DoRules;for(i=3D0;i<o=
Rules.length;i++){var =
name=3DoRules[i].ename;rulehash[name]=3D(rulehash[name]||[]);rulehash[nam=
e][rulehash[name].length]=3DoRules[i];}=0A=
var =
links=3Ddocument.links;for(i=3D0;i<links.length;i++){initializeControl(li=
nks[i]);}=0A=
for(name in ActiveNames){var ctrl;var =
elems=3Ddocument.getElementsByName(name);for(i=3D0;i<elems.length;i++){in=
itializeControl(elems[i]);}}=0A=
for(var fname in =
this.dataExchangeFunctions){this.setListener(this,fname,this.dataExchange=
Functions[fname],null);}=0A=
function initializeControl(domCtrl){var thisName=3DdomCtrl.name;var =
j,oRule;if(!(thisName&&typeof =
activenames[thisName]!=3D=3D'undefined')){return;}=0A=
console&&console.group&&console.group(thisName+"["+domCtrl.getAttribute("=
sid")+"]");try{var =
sActionEvent=3DoThis.actionEventName(domCtrl);if(sActionEvent>""){if(rule=
hash[thisName]){oThis.addRule(oThis,sActionEvent,thisName,oThis.doDataExc=
hange,rulehash[thisName]);console&&console.info("Rule: =
"+thisName+"."+sActionEvent+": "+rulehash[thisName].m);}=0A=
if(activenames[thisName]){oThis.addRule(oThis,sActionEvent,thisName,oThis=
.doSubmitAttribute,null);console&&console.info("Rule: =
"+thisName+"."+sActionEvent+": doSubmit");}=0A=
oThis.listenForEvents(domCtrl,sActionEvent);}}finally{console&&console.gr=
oupEnd&&console.groupEnd();}};},addRule:function(oThis,sEvent,sName,fFunc=
,oArg){var rules=3Dthis._rules;var ename=3DsName+"$"+sEvent;var =
i;if(typeof(rules[ename])!=3D'undefined'){for(i=3D0;i<rules[ename].length=
;i++){if(rules[ename][i].func=3D=3DfFunc){return;}}}else{rules[ename]=3D[=
];}=0A=
rules[ename][rules[ename].length]=3D{'thisptr':oThis,'func':fFunc,'arg':o=
Arg};},getRulesFor:function(sName,sEvent){return =
this._rules[sName+"$"+sEvent];},listenForEvents:function(domCtrl,sEventNa=
me){domCtrl._i_=3D(domCtrl._i_||[]);if(!domCtrl._i_[sEventName]){domCtrl.=
_i_[sEventName]=3D1;utils.addEvent(domCtrl,sEventName,this.handleAction);=
}},doDataExchange:function(eEvent,domTarget,oArg){var =
d=3DDispatcher.getInstance();var rules=3DoArg;if(!rules){return;}=0A=
for(var =
k=3D0;k<rules.length;k++){d.notify(domTarget,rules[k].m,rules[k]);}},doSu=
bmitAttribute:function(eEvent,domTarget,oArg){eEvent.preventDefault();eEv=
ent.stopPropagation();console&&console.info("Submitting request because =
submit attribute set");var =
realname=3DdomTarget.getAttributeNode("realname");realname=3Drealname?rea=
lname.value:null;if(domTarget.name||realname){this.setSubmitSource(realna=
me||domTarget.name);}=0A=
if(domTarget.name=3D=3D"p$ExL"){el=3Ddocument.getElementsByName('p$el');i=
f((typeof(el)!=3D'undefined')&&(el.length>0)){el[0].value=3DdomTarget.get=
Attribute("href");}}=0A=
Dispatcher.getInstance().requestSubmit();},handleAction:function(e){var =
d=3DDispatcher.getInstance();var t=3Dthis;var =
i;if(t.tagName&&t.tagName.toLowerCase()=3D=3D'a'){e.preventDefault();e.st=
opPropagation();}=0A=
var =
realname=3Dthis.getAttributeNode("realname");realname=3Drealname?realname=
.value:null;if(this.name||realname){d.setSubmitSource(realname||this.name=
);}=0A=
d.submitCheckBegin();try{console&&console.info("Executing rule =
"+t.name+"."+e.type);var =
rules=3Dd.getRulesFor(t.name,e.type);for(i=3D0;rules&&(i<rules.length);i+=
+){var =
rule=3Drules[i];try{rule.func.call(rule.thisptr,e,t,rule.arg);}catch(err)=
{console&&console.error("Dispatcher.handleAction: rule failed: =
"+t.name+"$"+e.type+": =
"+err);}}}catch(err){console&&console.error("Error: handleAction: =
"+err);}finally{d.submitCheckEnd();}},actionEventName:function(t){var =
ttype=3D(t.getAttribute("type")||'').toLowerCase();switch(t.tagName.toLow=
erCase()){case'select':case'textarea':return'change';case'form':return'';=
case'input':if(ttype=3D=3D'text'){return'change';}}=0A=
return'click';},initHierarchy:function(oTree){if(!oTree||!oTree.name){ret=
urn;}=0A=
var =
sname=3DoTree.shortname||oTree.name.substring(1+oTree.name.lastIndexOf(".=
"));try{var =
c=3DPortal.Component.create(oTree.type,oTree.name,sname,this.oNotifier);c=
.realname=3DoTree.realname;}catch(e){console&&console.group&&console.grou=
p("Exception creating portlet =
"+oTree.name);console&&console.info("Message: =
"+e.toString());if(typeof(e)!=3D'string'){console&&console.group&&console=
.group("Details");console&&console.dir&&console.dir(e);console&&console.g=
roupEnd&&console.groupEnd();}=0A=
console&&console.group&&console.group("Trace")=0A=
console&&console.trace&&console.trace();console&&console.groupEnd&&consol=
e.groupEnd();console&&console.groupEnd&&console.groupEnd();}=0A=
if(oTree.children){for(var =
i=3D0;i<oTree.children.length;i++){this.initHierarchy(oTree.children[i]);=
}}},submit:function(){if(this.submitCheck()){if(xmlHttpCall&&xmlHttpCall.=
abortCalls){xmlHttpCall.abortCalls();}=0A=
document.forms[0]._submit();}},submitCheck:function(){var =
oThis=3Dthis;var =
thisForm=3Ddocument.forms[0];this.submitOK=3Dtrue;this.vetoWhy=3Dnull;thi=
s.notify(this,"portal$beforesubmit",{form:thisForm},null);return =
this.submitOK;},veto:function(whydata){this.submitOK=3Dfalse;this.vetoWhy=
=3Dwhydata;},isVetoed:function(){return!this.submitOK;},setSubmitSource:f=
unction(sourceName){var =
el=3Ddocument.getElementsByName('p$a');if((typeof(el)!=3D'undefined')&&(e=
l.length>0)){if(typeof(sourceName)=3D=3D'undefined'){console&&console.war=
n("Warning: Can't identify submitter: using =
p$a=3D''");}else{el[0].value=3DsourceName;}}},getSrcDst:function(oRule,oN=
otifierObj){function x_FindObj(name,sid){var oResult=3D[];var =
oControls=3D$N(name);for(var =
i=3D0;i<oControls.length;i++){if("*"=3D=3Dsid||oControls[i].getAttribute(=
"sid")=3D=3Dsid){oResult[oResult.length]=3DoControls[i];}}=0A=
return oResult;}=0A=
var oThis=3Dthis;var name=3DoRule.sname;var =
sid=3DoRule.ssid;if("#"=3D=3Dname){name=3DoRule.ename;}=0A=
if("#"=3D=3Dsid){sid=3DoRule.esid;sid=3DoNotifierObj.getAttribute("sid");=
}=0A=
var =
oSrc=3Dx_FindObj(name,sid);name=3DoRule.dname;sid=3DoRule.dsid;if("#"=3D=3D=
name){name=3DoRule.ename;}=0A=
if("#"=3D=3Dsid){sid=3DoRule.esid;sid=3DoNotifierObj.getAttribute("sid");=
}=0A=
var =
oDst=3Dx_FindObj(name,sid);return{src:oSrc,dst:oDst};},setListener:functi=
on(oListener,sMessage,fFunction,oNotifier){return =
this.oNotifier.setListener(oListener,sMessage,fFunction,oNotifier);},noti=
fy:function(oNotifier,sMessage,oComment,oListener){return =
this.oNotifier.Notify(oNotifier,sMessage,oComment,oListener);},dataExchan=
geFunctions:{CopyValue:function(oListener,oRule,sMessage,oNotifierObj){va=
r dispatcher=3DoListener;var =
oSrcDst=3Ddispatcher.getSrcDst(oRule,oNotifierObj);for(var =
j=3D0;j<oSrcDst.dst.length;j++){for(var =
i=3D0;i<oSrcDst.src.length;i++){oSrcDst.dst[j].value=3DoSrcDst.src[i].val=
ue;}}},AddValue:function(oListener,oRule,sMessage,oNotifierObj){var =
dispatcher=3DoListener;var =
oSrcDst=3Ddispatcher.getSrcDst(oRule,oNotifierObj);for(var =
j=3D0;j<oSrcDst.dst.length;j++){for(var =
i=3D0;i<oSrcDst.src.length;i++){oSrcDst.dst[j].value+=3D(oSrcDst.dst[j].v=
alue>""?", =
":"")+oSrcDst.src[i].value;}}},SetValue:function(oListener,oRule,sMessage=
,oNotifierObj){var dispatcher=3DoListener;var =
oSrcDst=3Ddispatcher.getSrcDst(oRule,oNotifierObj);for(var =
j=3D0;j<oSrcDst.dst.length;j++){var =
dst=3DoSrcDst.dst[j];if(Dispatcher.isCheckable(dst)){dst.checked=3DoRule.=
p[0];}else{dst.value=3DoRule.p[0];}}},ItemToList:function(oListener,oRule=
,sMessage,oNotifierObj){var dispatcher=3DoListener;var =
oSrcDst=3Ddispatcher.getSrcDst(oRule,oNotifierObj);for(var =
j=3D0;j<oSrcDst.dst.length;j++){var dst=3DoSrcDst.dst[j];var =
dstval=3Ddst.value.replace(/^\s+/,"").replace(/\s+$/,"");var =
dstItems=3Ddstval.split(/\s*,\s*/).filter(function(s){return =
s!=3D=3D"";});for(var i=3D0;i<oSrcDst.src.length;i++){var =
src=3DoSrcDst.src[i];var sc=3DDispatcher.isCheckable(src);var =
checked=3D(sc?src.checked:(src.value!=3D=3D""));var =
position=3DdstItems.indexOf(src.value);if(checked&&position<0){dstItems[d=
stItems.length]=3Dsrc.value;}=0A=
if(!checked&&position>=3D0){dstItems.splice(position,1);}}=0A=
dst.value=3DdstItems.join(", =
");}},PropertyToValue:function(oListener,oRule,sMessage,oNotifierObj){var=
 dispatcher=3DoListener;var =
oSrcDst=3Ddispatcher.getSrcDst(oRule,oNotifierObj);for(var =
j=3D0;j<oSrcDst.dst.length;j++){for(var =
i=3D0;i<oSrcDst.src.length;i++){oSrcDst.dst[j].value=3DoSrcDst.src[i].get=
Attribute(oRule.p[0]);}}},PropertyToList:function(oListener,oRule,sMessag=
e,oNotifierObj){var dispatcher=3DoListener;var =
oSrcDst=3Ddispatcher.getSrcDst(oRule,oNotifierObj);for(var =
j=3D0;j<oSrcDst.dst.length;j++){var dst=3DoSrcDst.dst[j];var o=3D{};var =
values=3D[];var propname=3DoRule.p[0];for(var =
i=3D0;i<oSrcDst.src.length;i++){var src=3DoSrcDst.src[i];var =
prop=3Dsrc.getAttribute(propname);if(!prop){continue;}=0A=
var =
sc=3DDispatcher.isCheckable(src);if(sc?src.checked:(prop&&prop!=3D=3D""))=
{if(!o[prop]){values[values.length]=3Dprop;}=0A=
o[prop]=3D1;}}=0A=
dst.value=3Dvalues.join(", =
");}}},requestSubmit:function(src){console&&console.info("Request =
submitted");this.submitter=3Dsrc;this.submitRequested=3Dtrue;},submitChec=
kBegin:function(){if(this.submitChecking){throw"ERRINTERNAL: recursive =
submit check";}=0A=
this.submitChecking=3Dtrue;this.submitter=3Dnull;this.submitRequested=3Df=
alse;},submitCheckEnd:function(){if(this.submitRequested){this.submit();}=0A=
this.submitChecking=3Dfalse;this.submitter=3Dnull;this.submitRequested=3D=
false;}},{_instance:null,getInstance:function(){return =
Dispatcher._instance||(Dispatcher._instance=3Dnew =
Dispatcher());},onload:function(){var sc=3D"Create components";var =
si=3D"Initialize components";var =
d=3DDispatcher.getInstance();console&&console.group&&console.group(sc);co=
nsole&&console.time&&console.time(sc);d.initHierarchy(objHierarchy);conso=
le&&console.timeEnd&&console.timeEnd(sc);console&&console.groupEnd&&conso=
le.groupEnd();console&&console.group&&console.group(si);console&&console.=
time&&console.time(si);d.initDataExchange(ObjectLinks);d.setListener(d,'p=
ortal$vetosubmit',function(dst,data,message,src){d.veto(data);},null);var=
 =
theForm=3Ddocument.forms[0];if(theForm&&!theForm._submit){theForm._submit=
=3DtheForm.submit;theForm.submit=3Dfunction(){Dispatcher.getInstance().re=
questSubmit();};}=0A=
console&&console.timeEnd&&console.timeEnd(si);console&&console.groupEnd&&=
console.groupEnd();},isCheckbox:function(node){var =
t=3Dnode.getAttribute("type");return =
t&&(t.toLowerCase()=3D=3D"checkbox");},isRadio:function(node){var =
t=3Dnode.getAttribute("type");return =
t&&(t.toLowerCase()=3D=3D"radio");},isCheckable:function(node){return =
this.isRadio(node)||this.isCheckbox(node);}});utils.addEvent(window,"load=
",Dispatcher.onload,false);Portal=3DBase.extend({constructor:function(){t=
his.init();},init:function(){}},{_instance:null,getInstance:function(){re=
turn Portal._instance||(Portal._instance=3Dnew =
Portal());},requestSubmit:function(){Dispatcher.getInstance().requestSubm=
it();},$send:function(sMessage,oData,oDst){var =
d=3DDispatcher.getInstance();d.submitCheckBegin();d.notify(null,sMessage,=
oData,oDst);d.submitCheckEnd();}});Portal.Component=3DBase.extend({constr=
uctor:function(path,name,notifier){this.init(path,name,notifier);},init:f=
unction(path,name,notifier){this.name=3Dname;this.path=3Dpath;this.notifi=
er=3Dnotifier;if(this.listen){var msg;var isEvent=3Dnew =
RegExp(/^([^<]+)<([^>]+)>/);var m;var =
d=3DDispatcher.getInstance();for(msg in =
this.listen){m=3DisEvent.exec(msg);if(m){this.addEvent(m[1],m[2],this.lis=
ten[msg],false);}else{this._listen(msg,this.listen[msg],null);}}}=0A=
if(this.send){for(msg in =
this.send){if(this.send[msg]=3D=3Dnull){this.send[msg]=3Dthis.makeSender(=
this,msg);}}}},makeSender:function(sender,msg){return =
function(obj){return =
sender._send(msg,obj,null);};},getValue:function(attr){var =
prop=3Dnull;var ix;if(typeof =
attr=3D=3D=3D"object"){prop=3Dattr.prop;attr=3Dattr.attr;}=0A=
else =
if((ix=3Dattr.indexOf(":"))>=3D0){prop=3Dattr.substring(ix+1);attr=3Dattr=
.substring(0,ix);}=0A=
var inp=3Dthis.getInputs(attr);if(!inp){return null;}=0A=
if(inp.length=3D=3D1){inp=3Dinp[0];return(prop&&prop.toLowerCase()!=3D=3D=
"value")?inp.getAttribute(prop):htmlutils.getValue(inp);}=0A=
var result=3D[];for(var =
i=3D0;i<inp.length;i++){if(prop&&prop.toLowerCase()!=3D=3D"value"){if(typ=
eof(inp[i][prop])!=3D'undefined'){result[result.length]=3Dinp[i][prop];}e=
lse{result[result.length]=3Dinp[i].getAttribute(prop);}}else{result[resul=
t.length]=3Dhtmlutils.getValue(inp[i]);}}=0A=
return result;},getList:function(attr){var ix;var =
prop=3Dnull;if((ix=3Dattr.indexOf(":"))>=3D0){prop=3Dattr.substring(ix+1)=
;attr=3Dattr.substring(0,ix);}=0A=
if(prop){throw"UNIMPLEMENTED: Component.getList: Getting list by =
property";}=0A=
var inp=3Dthis.getInputs(attr);if(!inp){return null;}=0A=
if(inp.length=3D=3D1){inp=3Dinp[0];return htmlutils.getList(inp);}=0A=
var result=3D[];for(var =
i=3D0;i<inp.length;i++){result[result.length]=3Dhtmlutils.getList(inp[i])=
;}=0A=
return result;},setValue:function(attr,value){var prop=3Dnull;var =
ix;if((ix=3Dattr.indexOf(":"))>=3D0){prop=3Dattr.substring(ix+1);attr=3Da=
ttr.substring(0,ix);}=0A=
var =
inp=3Dthis.getInputs(attr);if(inp.length=3D=3D1){inp=3Dinp[0];if(prop){if=
(typeof(inp[prop])!=3D'undefined'){inp[prop]=3Dvalue;}else{inp.setAttribu=
te(prop,value);}}else{inp.value=3Dvalue;}}else{throw"UNIMPLEMENTED: =
Cannot (yet) set vector values from =
scalar";}},getInputs:function(name){var =
inp=3Ddocument.getElementsByName(this.path+"."+name);if(!inp||inp.length=3D=
=3D=3D0){inp=3Dnull;}=0A=
return inp;},getInput:function(name){var =
inp=3Dthis.getInputs(name);return((inp&&inp.length>0)?inp[0]:null);},has:=
function(attrname){var =
inp=3Ddocument.getElementsByName(this.path+"."+attrname);return(inp&&(inp=
.length>0));},addEvent:function(inputName,eventName,f,flag){var =
inputs;var =
oThis=3Dthis;if(typeof(inputName)=3D=3D'string'){inputs=3Dthis.getInputs(=
inputName);}else =
if(utils.isArray(inputName)){inputs=3DinputName;}else{inputs=3D[inputName=
];}=0A=
if(!inputs){console&&console.warn("Can't find: "+inputName);return;}=0A=
var =
d=3DDispatcher.getInstance();for(i=3D0;i<inputs.length;i++){d.addRule(oTh=
is,eventName,inputs[i].name,f,null);d.listenForEvents(inputs[i],eventName=
);}=0A=
return;},removeEvent:function(inputName,eventName,f,flag){var =
inputs=3Dthis.getInputs(inputName);for(var =
i=3D0;inputs&&(i<inputs.length);i++){utils.removeEvent(inputs[i],eventNam=
e,f,flag);}},iListen:0,iNextListen:function(){return"L$"+this.iListen++;}=
,_listen:function(sMessage,fFunction,sSource){var oThis=3Dthis;var =
fName=3Dthis.iNextListen()+"$"+sMessage;this[fName]=3DfFunction;var =
d=3DDispatcher.getInstance();d.setListener(oThis,sMessage,function(dst,da=
ta,message,src){oThis[fName](message,data,src);},sSource);},_send:functio=
n(sMessage,oData,oDst){var =
d=3DDispatcher.getInstance();d.notify(this,sMessage,oData,oDst);},getMeta=
Data:function(){var =
result=3D{};result.listensFor=3D[];if(this.listen){for(var msg in =
this.listen){result.listensFor[result.listensFor.length]=3Dmsg;}}=0A=
result.sends=3D[];if(this.send){for(msg in =
this.send){result.sends[result.sends.length]=3Dmsg;}}=0A=
result.attributes=3D[];for(var attr in =
this.getAttributes()){result.attributes[result.attributes.length]=3Dattr;=
}=0A=
return =
result;}},{$i:{},$$i:{},create:function(type,path,cname,notifier){var =
p=3DPortal.Component.$i;var pelem=3Dpath.split(".");for(var =
i=3D0;i<pelem.length-1;i++){p=3Dp[pelem[i]];}=0A=
var =
sname=3Dpath.substring(1+path.lastIndexOf("."));if(typeof(Portal[type])=3D=
=3D'undefined'){throw("No such portlet type: "+type);}=0A=
if(typeof(Portal[type][sname])=3D=3D'undefined'){p[sname]=3Dnew =
Portal[type](path,cname,notifier);}else{try{p[sname]=3Dnew =
Portal[type][sname](path,cname,notifier);}catch(e){console&&console.error=
("Creating Portlet."+type+"."+sname+": "+e.message);throw e;}}=0A=
var =
l;if(!(l=3DPortal.Component.$$i[sname])){l=3DPortal.Component.$$i[sname]=3D=
[];}=0A=
l[l.length]=3Dp[cname];if(p[cname].beforesubmit){var =
d=3DDispatcher.getInstance();var =
oThis=3Dthis;d.setListener(oThis,"portal$beforesubmit",function(dst,data,=
message,src){var =
whydata=3Dp[cname].beforesubmit();if(typeof(whydata)=3D=3D'boolean'){retu=
rn whydata;}else =
if(typeof(whydata)=3D=3D'object'){d.notify(this,'portal$vetosubmit',whyda=
ta,null);return true;}=0A=
throw cname+".beforesubmit: returned "+typeof(whydata);},null);}=0A=
return p[cname];},get:function(path){return =
eval("Portal.Component.$i."+path);},getByShortName:function(name){return =
eval("Portal.Component.$$i."+name);},classExists:function(name){return(ty=
peof(Portal.Component[name])!=3D"undefined");},instanceExists:function(pa=
th){try{eval("Portal.Component.$i"+path);return true;}catch(e){}=0A=
return =
false;}});Portal.Layout=3DPortal.Component.extend({constructor:function(p=
ath,name,notifier){this.base(path,name,notifier);console&&console.info("C=
reated Layout: =
"+path);}});Portal.Cluster=3DPortal.Component.extend({constructor:functio=
n(path,name,notifier){this.base(path,name,notifier);console&&console.info=
("Created Cluster: =
"+path);}});Portal.Portlet=3DPortal.Component.extend({getAttributes:funct=
ion(){var t=3Ddocument.getElementsByTagName("input");var result=3D{};var =
pathlen=3Dthis.path.length;for(var i=3D0;i<t.length;i++){var =
it=3Dt[i];var itn=3Dit.getAttribute("name");if(!itn){continue;}=0A=
var prefixlen=3Ditn.lastIndexOf(".");var =
samePrefix=3D(itn.substring(0,this.path.length)=3D=3Dthis.path);if((prefi=
xlen=3D=3Dpathlen)&&samePrefix){result[itn.substring(1+prefixlen)]=3Dit.v=
alue;}}=0A=
return result;}});$PI=3Dfunction(path){return =
Portal.Component.get(path);};$PN=3Dfunction(name){var =
c=3DPortal.Component.getByShortName(name);if(typeof(c)=3D=3D"undefined"){=
return null;}=0A=
return(c.length=3D=3D1)?c[0]:c;};htmlutils=3D{accessors:{select:{getValue=
:function(node){return this.getList(node).join(", =
");},getList:function(node){var opts=3Dnode.options;var r=3D[];for(var =
i=3D0;i<opts.length;i++){if(opts[i].selected){r[r.length]=3Dopts[i].value=
;}}=0A=
return r;}},button:{getValue:function(node){var =
attrNode=3Dnode.getAttributeNode('value');return(attrNode!=3D=3Dnull)?att=
rNode.nodeValue:null;}}},getValue:function(elem){var =
v=3Dthis.accessors[elem.tagName.toLowerCase()];return =
v&&v.getValue?v.getValue(elem):elem.value;},getList:function(elem){var =
v=3Dthis.accessors[elem.tagName.toLowerCase()];return =
v&&v.getList?v.getList(elem):(elem.value?[elem.value]:[]);}};utils.addEve=
nt(window,"load",function(){Portal.getInstance();},false);
------=_NextPart_000_0000_01CA72A3.109DE760
Content-Type: application/octet-stream
Content-Transfer-Encoding: quoted-printable
Content-Location: http://www.ncbi.nlm.nih.gov/portal/portalrc.fcgi/37359/js/15394/28968/29966/27166/30783/28669/27885/27590/29994/24519/29669/31945.js

//=0A=
//		 PAFAppResources: Initialize client side of Portlet Application =
Framework=0A=
//=0A=
=0A=
Portal.Portlet.PAFAppResources =3D Portal.Portlet.extend({=0A=
=0A=
   // In PAF, the form always posts to itself. It should update and =
interpret data, and=0A=
   // then *redirect* to another page if necessary.=0A=
   =0A=
   // This code fixes up the EntrezForm in PAF templates to =
automatically post=0A=
   // to the current window pathname.=0A=
   =0A=
   // If the programmer specifies a hidden input with =
id=3D"entrez-action",=0A=
   // that action (instead of POST) is used for the form.=0A=
   =0A=
   // If the programmer specifies a hidden input with =
id=3D"entrez-method",=0A=
   // that method is used for the form. =0A=
       =0A=
   // FIXME: This is a hack. EntrezForm should default to posting to =
same page,=0A=
   // and there should be some way of indicating how to post (or get) =
elsewhere.=0A=
   // The problem here is that we've mixed Entrez into PAF. This should =
be refactored.=0A=
   =0A=
   init: function(path, name, notifier) {=0A=
      var oThis =3D this;  // Use <oThis> instead of <this> for =
registering callbacks=0A=
      this.base(path, name, notifier);  // Call superclass constructor=0A=
      =0A=
      if (!document.forms[0]) return; // Do nothing if no form.=0A=
      =0A=
      var getNodeValue =3D function(id, dfl) {=0A=
         var node =3D $(id);=0A=
         return node ? node.value : dfl;=0A=
      };=0A=
      =0A=
      var entrezAction =3D getNodeValue('entrez-action', =
window.location.pathname);=0A=
      var entrezMethod =3D getNodeValue('entrez-method', null);=0A=
      var entrezSubmit =3D getNodeValue('entrez-submit', false);=0A=
      =0A=
      document.forms[0].action =3D entrezAction;=0A=
      =0A=
      // FIXME: We need to include query string here, too, I think... At =
least for POST...      =0A=
      if (entrezMethod) {=0A=
         document.forms[0].method =3D entrezMethod;=0A=
      }=0A=
=0A=
      // By default, entrez form ignores submits. Setting "entrezSubmit" =
to "true" means let Entrez form=0A=
      // actually process the submit. This probably will only work =
correctly for action=3D"get"       =0A=
      if (entrezSubmit) {=0A=
         document.forms[0].onsubmit=3D"return true;"=0A=
      }=0A=
   }=0A=
});=0A=
=0A=
// makes an ext js looking portlet w/o using extjs
if (typeof(noext) =3D=3D 'undefined') {
    noext =3D {};
}
noext.parseConfig =3D function(n) {
    var configStr =3D n.getAttribute('config') || '';
    try {
        var jsonObj =3D eval('({' + configStr + '})');
    }
    catch(e) {
        if (window.console) {
            console.error(e.message + ' in local config object in =
noext.Portlet: file: ' + e.fileName + ', line ' + e.lineNumber + '.' );
        }
    }
    return jsonObj;
};
noext.getClassArray =3D function(n) {
    var classNameStr =3D n.className;
    return classNameStr.split(' ');
};
noext.getFirstHeader =3D function(n) {
    var fc =3D utils.getFirstChild(n);
    if(fc.tagName.search(/^h\d/i) !=3D -1) {
        return fc;
    }
};
noext.Portlet =3D function(n, beenClassed) {
    this.n =3D n;=0A=
    this.beenClassed =3D beenClassed;=0A=
    if (!beenClassed) {
        this.headerNode =3D noext.getFirstHeader(this.n);
        this.headerDiv =3D document.createElement('div');
        this.bodyDiv =3D document.createElement('div');
        utils.addClass(this.bodyDiv, 'x-panel-body');=0A=
    }=0A=
    else {=0A=
        var divNodes =3D n.getElementsByTagName("div");=0A=
        for (var i =3D 0; i < divNodes.length; ++i) {=0A=
            var divNode=3D divNodes[i];=0A=
            if (utils.hasClass(divNode, 'x-panel-header')) {=0A=
                this.headerDiv =3D divNode;=0A=
            }=0A=
            else if (utils.hasClass(divNode, 'x-panel-body')) {=0A=
                this.bodyDiv =3D divNode;=0A=
            }=0A=
        }=0A=
    }
    var configObj =3D noext.parseConfig(this.n);
    this.collapsible =3D configObj.collapsible =3D=3D false ? false : =
true;=20
    this.closeable =3D configObj.closeable =3D=3D false ? false : true;=20
    this.collapsed =3D configObj.collapsed =3D=3D true ? true : false;
    if (this.collapsed =3D=3D true) {
        utils.addClass(this.n, 'x-panel-collapsed');
        this.bodyDiv.style.display =3D 'none';
    }
    this.make();
};

noext.Portlet.instances =3D [];
noext.Portlet.ready =3D function() {
    var nodes =3D $C('port', 'class', document, 'div');
    for (var i =3D 0; i < nodes.length; i++) {
        var n =3D nodes[i];
        if (utils.hasClass(n, 'norender')) {
            continue;
        }=0A=
        // CFM:  If the top-level div already has the 'x-panel' class, =
then =0A=
        // assume that it has been completely "classed up".=0A=
        var beenClassed =3D utils.hasClass(n, 'x-panel');
        portlet =3D new noext.Portlet(n, beenClassed);
    }
}
noext.Portlet.prototype =3D {
    make: function() {=0A=
        var beenClassed =3D this.beenClassed;=0A=
        =0A=
        var toolCloseA, toggleA;=0A=
        if (!beenClassed) {
            // put a parent around body content
            //var innerContainingDiv =3D document.createElement('div');
            utils.addClass(this.n, 'x-panel');
            //this.n.style.width =3D 'auto';
            utils.addClass(this.headerDiv, 'x-panel-header');
            utils.addClass(this.headerDiv, 'x-unselectable');
            if (this.headerNode) {=20
                this.n.insertBefore(this.headerDiv, this.headerNode);
                var header =3D this.n.removeChild(this.headerNode);
            }
            toolCloseA =3D document.createElement('a');
            toolCloseA.setAttribute('href', '#');
            utils.addClass(toolCloseA, 'x-tool');
            utils.addClass(toolCloseA, 'x-tool-close');
            toggleA =3D document.createElement('a');
            toggleA.setAttribute('href', '#');
            utils.addClass(toggleA, 'x-tool');
            utils.addClass(toggleA, 'x-tool-toggle');
            if (this.closeable =3D=3D true) {
                this.headerDiv.appendChild(toolCloseA);
            }
            if (this.collapsible) {
                this.headerDiv.appendChild(toggleA);
            }
            if (this.headerNode) {
                this.headerDiv.appendChild(header);
                utils.addClass(this.headerNode, 'x-panel-header-text');
            }=0A=
        }=0A=
        else {=0A=
            // Find the close and toggle <a> elements, if they exist.  =
To do this, we=0A=
            // iterate through all the <a> children, looking for the =
right classes.=0A=
            var aKids =3D this.n.getElementsByTagName("a");=0A=
            for (var i =3D 0; i < aKids.length; ++i) {=0A=
                var aKid =3D aKids[i];=0A=
                if (utils.hasClass(aKid, 'x-tool-close')) {=0A=
                    toolCloseA =3D aKid;=0A=
                }=0A=
                else if (utils.hasClass(aKid, 'x-tool-toggle')) {=0A=
                    toggleA =3D aKid;=0A=
                }=0A=
            }=0A=
        }=0A=
        this.toolCloseA =3D toolCloseA;
        this.toggleA =3D toggleA;=0A=
        if (!beenClassed) {
            this.reParent();=0A=
        }
        this.setEvents();
    },=20
    reParent: function() {
        var bodyElems =3D [];
        utils.insertAfter(this.n, this.bodyDiv, this.headerDiv);
        for (var i =3D this.n.childNodes.length -1; i >=3D 0; i--) {
            var fc =3D this.n.childNodes[i];
            if (fc !=3D this.headerDiv && fc !=3D this.bodyDiv) {=20
                bodyElems.push(this.n.removeChild(fc));
            }
            for (var j =3D 0; j < bodyElems.length; j++) {
                this.bodyDiv.appendChild(bodyElems[j]);
            }
        }
    },
    setEvents: function(toggleA) {
        var that =3D this;=0A=
        if (this.toggleA) {
            utils.addEvent(this.toggleA, 'click', function(e) { =
that.toggle(e)});=0A=
        }=0A=
        if (this.toolCloseA) {
            utils.addEvent(this.toolCloseA, 'click', function(e) { =
that.close(e)});=0A=
        }
    },=20
    toggle: function(e) {
        utils.preventDefault(e);
        if (utils.hasClass(this.n, 'x-panel-collapsed')) {
            utils.removeClass(this.n, 'x-panel-collapsed')
            this.bodyDiv.style.display =3D 'block';
        } else {
            utils.addClass(this.n, 'x-panel-collapsed');
            this.bodyDiv.style.display =3D 'none';
        }
    },
    close: function(e) {
        utils.preventDefault(e);=20
        this.n.parentNode.removeChild(this.n);
    }
};

utils.addEvent(window, 'load', noext.Portlet.ready);
=0A=
// This 2.x branch of this file was to add a brief delay to the pop-up, =
but it=0A=
// was decided not to merge this change into the main trunk.  I.e. this =
branch=0A=
// is PMC specific.  See PP-207.=0A=
=0A=
Portal.Portlet.BriefLinkPageSection =3D Portal.Portlet.extend({

	init: function(path, name, notifier) {=0A=
	    console.info("Created BriefLinkPageSection");
		this.base(path, name, notifier);
        =0A=
        this.SetPortletName();=0A=
        if (Portal.Portlet.BriefLinkPageSection.portletname !=3D ''){=0A=
            Portal.Portlet.BriefLinkPageSection.portletname =3D "." + =
Portal.Portlet.BriefLinkPageSection.portletname;=0A=
        }=0A=
        =0A=
        this.CreatePopNodes();=0A=
       =20
	},=0A=
	=0A=
	SetPortletName: function(){=0A=
	    // derived portlet should override and provide portlet name;=0A=
	},=0A=
	=0A=
    popNodeDelay: 0,
=0A=
    CreatePopNodes: function(){=0A=
        var pop =3D cssQuery("div.brieflink div" + =
Portal.Portlet.BriefLinkPageSection.portletname + " ul");
        var poptype =3D pop[0].className;
       =20
        // when value is pop0
        if (poptype.match(/pop0/)){
            // no popnodes need to be created
        }
        // for all other cases try to create popnode
        else{
            // Create ElementPopper for each li.item
    		var elemid =3D "div.brieflink div" + =
Portal.Portlet.BriefLinkPageSection.portletname + " li.item";
    		var elements =3D cssQuery(elemid);=20
    	=09
    		// go through the list of elements
    		for (var i =3D 0; i < elements.length; i++) {
                var elem =3D elements[i];
                var content =3D "";=20
               =20
                // when value is pop1
                if (poptype.match(/pop1/)){
                    // create pop with title + desc
                    var linktext =3D cssQuery("a", elem);
                    if (linktext && linktext.length > 0){
                        content +=3D linktext[0].innerHTML + "<br/>";
                    }
                }
                // default case - when value is pop2 or anything else =
but pop3
                else if (!poptype || !poptype.match(/pop3/)){
                    // if visible content length is larger than 105, =
then show the entire text in popup,
                    // followed by any included link description.
                    var linktext =3D cssQuery("a", elem);
                    var note =3D cssQuery("p.note", elem);
                    var content =3D "";=20
                    var linklength =3D 0;
                    if (linktext && linktext.length > 0){
                       linklength +=3D linktext[0].innerHTML.length;
                    }
                    if (note && note.length > 0){
                       linklength +=3D note[0].innerHTML.length;
                    }
                    if (linklength > 100){
                       content +=3D linktext[0].innerHTML + "<br/>";
                    }
                } // end default case
	          =20
	          =20
                // add Description to pop node when it exists for all =
popnode cases	          =20
	            var desc =3D cssQuery("p.desc", elem);
                if (desc && desc.length > 0){
                   content +=3D desc[0].innerHTML;
                }
               =20
                // create popnode when content is present
                if (content && content.length > 0) {
                  var elemclass =3D elem.className;
                  if (!elemclass.match(/popnode/)){
                      elem.className =3D elemclass + " popnode";
                  }
                  //new ElementPopper(elem, content);
                  new ElementPopper(elem, {=20
                      content: content,
                      delay: this.popNodeDelay=20
                  });
                }
               =20
            } // end for=20
        } // end else=0A=
	} // end CreatePopNodes function
},=0A=
{=0A=
portletname: '' =0A=
=0A=
});=0A=
//=0A=
// Java Module PopDiv_JS=0A=
//=0A=
=0A=
//=0A=
// Shows and hides a div at a specific location, either (x,y), or =
relative to=0A=
// an element in a specific direction.=0A=
//=0A=
// Limitations:=0A=
//  - height or width must be set on the popper div, or it may not =
position correctly.=0A=
//=0A=
// You're probably better off using ElementPopper instead of PopDiv for =
hover pops. Popper handles mouse events=0A=
// correctly.=0A=
//=0A=
// Arguments:=0A=
//   divId: the id of the div to use for the popper. You can also pass a =
DOM node, and PopDiv will use that node.=0A=
//       The default is "popperDiv".=0A=
//   className: Add this className to the popper div. Optional--no =
default. This is useful for setting up default state.=0A=
//=0A=
// It's preferable to use a single PopDiv to render popups all over=0A=
// a single page. You only need as many PopDivs as the maximum number of =
popups you may=0A=
// ever have open at once. See ElementPopper for details.=0A=
=0A=
var PopDiv =3D function(divId, className) {=0A=
=0A=
   var innerdiv =3D null;=0A=
   =0A=
   // default is a string=0A=
   if (typeof(divId) =3D=3D 'undefined') {=0A=
      divId =3D "popperDiv";=0A=
   }=0A=
   =0A=
   // Find or make popper div=0A=
   if ((this.div =3D document.getElementById(divId)) =3D=3D null) {=0A=
   =0A=
      this.div =3D document.createElement("div");=0A=
      this.div.id =3D divId;=0A=
      this.div.className =3D "popper";=0A=
      if (className) {=0A=
         this.div.className +=3D " " + className;=0A=
      }=0A=
      document.body.appendChild(this.div);=0A=
      this.div.innerHTML =3D "<div class=3D'popperInnerDiv'/>";=0A=
   } else {=0A=
      utils.addClass(this.div, "popper"); // Be sure it has this=0A=
   }=0A=
=0A=
   // this.innerdiv is first element of this.div=0A=
   for (this.innerdiv =3D this.div.firstChild;=0A=
      this.innerdiv && this.innerdiv.nodeType !=3D 1;=0A=
      this.innerdiv =3D this.innerdiv.nextSibling) {=0A=
   }=0A=
   =0A=
   // If caller provided a div with no inner divs, add one.=0A=
   if (!this.innerdiv) {=0A=
       this.innerdiv =3D document.createElement("div");=0A=
       this.innerdiv.className =3D "popperInnerDiv";=0A=
       this.div.appendChild(this.innerdiv);=0A=
   }=0A=
}=0A=
=0A=
PopDiv.POP_ABOVE =3D 0;=0A=
PopDiv.POP_RIGHT =3D 1;=0A=
PopDiv.POP_BELOW =3D 2;=0A=
PopDiv.POP_LEFT =3D 3;=0A=
PopDiv.POP_CLASSES =3D ['pop-above', 'pop-right', 'pop-below', =
'pop-left'];=0A=
=0A=
PopDiv.POPPED =3D 'popped';=0A=
PopDiv.POP_GETXY =3D 'pop-getxy';=0A=
=0A=
PopDiv.prototype =3D {=0A=
   // Show it at x, y=0A=
   showAt: function(html, x, y) {=0A=
=0A=
    //console.info("POP @ (" + x + ", " + y + ")");=0A=
    //console.info("----");=0A=
    =0A=
      // Set content if provided=0A=
      if (html) {=0A=
         this.innerdiv.innerHTML =3D html;=0A=
      }=0A=
=0A=
      this.div.style.left =3D x + "px";=0A=
      this.div.style.top =3D y + "px";=0A=
=0A=
      // Pop it=0A=
      utils.addClass(this.div, PopDiv.POPPED);=0A=
=0A=
   },=0A=
=0A=
   // Show it near element ("dir" indications direction)=0A=
   // Dimensions don't exist if element isn't shown.=0A=
   getXY: function() {=0A=
      var popped =3D utils.hasClass(this.div, PopDiv.POPPED);=0A=
=0A=
      if (!popped) {=0A=
         utils.addClass(this.div, PopDiv.POPPED);=0A=
      }=0A=
      var dim =3D utils.getXY(this.div);=0A=
      if (!popped) {=0A=
         utils.removeClass(this.div, PopDiv.POPPED);=0A=
      }=0A=
=0A=
      return dim;=0A=
   },=0A=
=0A=
   hide: function() {=0A=
      utils.removeClass(this.div, PopDiv.POPPED);=0A=
      if (this.popClass) {=0A=
         utils.removeClass(this.div, this.popClass);=0A=
         this.popClass =3D null;=0A=
         this.popnode =3D null;=0A=
      }=0A=
   },=0A=
=0A=
   // showBy shows a popper adjacent to another item.=0A=
   showBy: function(html, elem, dir) {=0A=
      var dx =3D 0;=0A=
      var dy =3D 0;=0A=
=0A=
      // Already popped over a particular popnode=0A=
      if (this.popnode && (this.popnode =3D=3D elem)) {=0A=
         return;=0A=
      }=0A=
      this.popnode =3D elem;=0A=
=0A=
      // Default direction=0A=
      if (typeof(dir) !=3D "number") {=0A=
         dir =3D PopDiv.POP_LEFT;=0A=
      }=0A=
=0A=
      // Set class "pop-<direction>": this determines margin=0A=
      this.popClass =3D PopDiv.POP_CLASSES[dir];=0A=
      //console.info("dir =3D " + dir +", popclass =3D " + =
this.popClass);=0A=
      utils.addClass(this.div, this.popClass);=0A=
      =0A=
      // Set text so that sizing is correct=0A=
      this.innerdiv.innerHTML =3D html;=0A=
=0A=
      // Get geometries of target and popper=0A=
      var thatdim =3D utils.getXY(elem);=0A=
      var popdim =3D this.getXY(this.div);=0A=
      //console.info("that =3D");=0A=
      //console.info(thatdim);=0A=
      //console.info("pop =3D ");=0A=
      //console.info(popdim);=0A=
=0A=
      // Calculate position=0A=
      switch (dir) {=0A=
      case PopDiv.POP_ABOVE: dy =3D -1*popdim.h;  break;=0A=
      case PopDiv.POP_LEFT:  dx =3D -1*popdim.w;  break;=0A=
      case PopDiv.POP_BELOW: dy =3D    thatdim.h; break;=0A=
      case PopDiv.POP_RIGHT: dx =3D    thatdim.w; break;=0A=
      default:=0A=
        throw "PopDiv: Invalid direction: " + dir;=0A=
      }=0A=
      //console.info("Popping at: [x=3D" + (thatdim.x + dx) + ", =
y=3D"+(thatdim.y + dy)+"]");=0A=
=0A=
      this.showAt(null, thatdim.x + dx, thatdim.y + dy);=0A=
   }=0A=
};=0A=
=0A=
=0A=
=0A=
// An ElementPopper shows a popup adjacent to a target element when the =
user mouses over the target.=0A=
// It handles browser events and manipulates a popper to show and hide =
detail data.=0A=
//=0A=
// When the mouse cursor enters the target, the content appears in the =
popper nearby.=0A=
//  When the mouse cursor leaves the target, the popper is hidden.=0A=
//=0A=
// This rather intense event handling code is necessary because =
mouseover and mouseout doesn't work=0A=
// as expected--mouseouts occur when moving over child nodes. The =
"relatedTarget" trick described=0A=
// by PPK (quirksmode.org) doesn't work either, because browsers =
sometimes drop events=0A=
// with related targets. So the only option is to capture =
document.onmousemove, and detect when=0A=
// the mouse either exits document.body, or moves over something that is =
neither the target nor=0A=
// one of its children.=0A=
//=0A=
// "popnode" is the target node=0A=
// "content" is either a string (the content to show), a DOM node (show =
its innerHTML), or a function.=0A=
// "config" is configuration; if it's just a number, then it's =
"direction" (PopDiv.POP_*); otherwise, it's a JS object with =0A=
//     attribute/value pairs=0A=
// "popperId" is the ID to assign to the popper; default is to make one =
up.=0A=
//=0A=
// When used with Ext.Ncbi, the popper should initialize itself on the =
page a few hundred=0A=
// ms after the page loads. IE apparently creates a race condition where =
popper and Ext.Ncbi initialization=0A=
// throw away the event handlers on which ElementPopper depends.=0A=
//=0A=
// So in that case, instead of new ElementPopper(a,b), you want to do:=0A=
//     setTimeout(function() {new ElementPopper(a,b);}), 500);=0A=
=0A=
//=0A=
var ElementPopper =3D function(popnode, content, config, popperId) {=0A=
=0A=
    var that =3D this;=0A=
=0A=
    // Inner functions=0A=
    // If target is popnode or one of its children, returns popnode; =
otherwise, null=0A=
    function getPopTarget(target) {=0A=
       while (target && !utils.hasClass(target, "popnode")) {=0A=
          target =3D target.parentNode;=0A=
       }=0A=
       return target;=0A=
    };=0A=
=0A=
    // Use inner functions here because removeEvent requires a reference =
to the=0A=
    // function object passed to addEvent, and we need to use closure to =
maintain scope.=0A=
=0A=
    // Show popper and start tracking mouse motions=0A=
    var handlePop =3D function(e) {=0A=
       var target =3D getPopTarget(utils.getTargetObj(e));=0A=
       =0A=
       if (target) {=0A=
	       // If Ajax URL is supplied, then fetch URL.=0A=
	       //   If AJAX URL is a function, the URL is the return value of =
the function=0A=
	       //   Otherwise AJAX URL must be a string=0A=
	       // When AJAX call succeeds, pop up the content. If there's a =
contentFunction, the content is=0A=
	       // the result of applying the contentFunction to the AJAX return =
data; otherwise, it's just=0A=
	       // the AJAX return data itself.=0A=
	       //=0A=
	       if (that.url) {=0A=
	          var url =3D (typeof(that.url) =3D=3D 'function') ? =
that.url(target) : that.url;=0A=
	=0A=
	          jQuery.ajax({=0A=
	             cache: false,=0A=
	             'url': url,=0A=
	             success: function(data, textStatus) {=0A=
	                doPop(target, data, textStatus);=0A=
	             }=0A=
	          });=0A=
	       } else {=0A=
	          doPop(target);=0A=
	       }=0A=
	       =0A=
	       // Set up to listen for mouse out=0A=
	       // This is the node currently being handled; it's cleared when=0A=
	       // the user mouses out.=0A=
	       that.handlingNode =3D target;=0A=
	    =0A=
           utils.removeEvent(target, "mousemove", handlePop);=0A=
           utils.addEvent(document.body, "mousemove", trackMouse);=0A=
           utils.addEvent(document.body, "mouseout", trackMouse);=0A=
       }=0A=
    }=0A=
    =0A=
    var doPop =3D function(target, data, status) {=0A=
       =0A=
       // Pop, shift listener to document body=0A=
       if (target) {=0A=
          that.timer =3D setTimeout(function() {=0A=
             // If we're still waiting for a pop, do the pop.=0A=
             // We're only waiting for a pop when handlingNode is set.=0A=
             if (target =3D=3D that.handlingNode) {=0A=
                that.thePopper.showBy(that.contentFunction(target, data, =
status), target, that.direction);=0A=
             } else {=0A=
               // Ignore the pop request, because we're no longer =
interested in this pop.=0A=
             }=0A=
             that.timer =3D null;             =0A=
          }, that.delay);=0A=
=0A=
       }=0A=
    };=0A=
=0A=
    // Unpop, shift listener back to popnode=0A=
    var trackMouse =3D function(e) {=0A=
       var target =3D getPopTarget(utils.getTargetObj(e));=0A=
=0A=
       // If mouse left document.body, or the target's not over the =
popnode, hide.=0A=
       if (e.type =3D=3D "mouseout" || target =3D=3D null) {=0A=
          // Clear pop timer if it hasn't popped=0A=
          if (that.timer) {=0A=
             window.clearTimeout(that.timer);=0A=
             that.timer =3D null;=0A=
          }=0A=
          that.thePopper.hide();=0A=
          that.handlingNode =3D null;=0A=
          =0A=
          utils.removeEvent(document.body, "mousemove", trackMouse);=0A=
          utils.removeEvent(document.body, "mouseout", trackMouse);=0A=
          utils.addEvent(popnode, "mousemove", handlePop);=0A=
       }=0A=
    };=0A=
=0A=
    // END inner functions=0A=
=0A=
    //=0A=
    // ctor main=0A=
    //=0A=
     =0A=
    // Support new signature ElementPopper(element, {config...}); in =
that case, "content" is a config object,=0A=
    // all other arguments are ignored, and config.content must be set =0A=
    if (typeof(content) =3D=3D 'object') {=0A=
       config =3D content;=0A=
       content =3D config.content;=0A=
    }=0A=
    =0A=
    // If a content URL is defined (AJAX URL string or function that =
returns URL), remember it=0A=
    if (config && config.url) {=0A=
       this.url =3D config.url;=0A=
    }=0A=
    =0A=
    // If content is a string, make it a function that returns the =
string.=0A=
    // If it's a dom node, make it a function that returns the dom =
node's innerHTML=0A=
    // If content is undefined, then assume data is coming from AJAX =
callback=0A=
    if (typeof(content) =3D=3D 'undefined') {=0A=
       this.contentFunction =3D function(target, data, status) { return =
data };=0A=
    } else if (typeof(content) =3D=3D 'string') {=0A=
       this.contentFunction =3D function() { return content; }=0A=
    } else if (content.innerHTML) {=0A=
       this.contentFunction =3D function() { return content.innerHTML; }=0A=
    } else if (typeof(content) =3D=3D 'function') {=0A=
       this.contentFunction =3D content; // Better be a function...=0A=
    }=0A=
    =0A=
    // Backward compatibility: "config" arg used to be "direction", so=0A=
    // interpret it as "direction" if config is a number.=0A=
    // Otherwise parse out config info=0A=
    if (typeof(config) =3D=3D=3D 'undefined') {=0A=
       config =3D {=0A=
          direction: PopDiv.POP_LEFT,=0A=
          delay: 0=0A=
       }=0A=
    }=0A=
    =0A=
    if (typeof(config) =3D=3D 'number') {=0A=
       this.direction =3D config;=0A=
    } else {=0A=
       this.direction =3D (typeof(config.direction) !=3D 'undefined') ? =
config.direction : PopDiv.POP_LEFT;=0A=
       this.delay =3D config.delay || 0;=0A=
    }=0A=
    this.popperId =3D config.popperId || popperId || ("popper" + =
(ElementPopper.popIndex++)); =0A=
=0A=
    // Create the popper=0A=
    this.thePopper =3D new PopDiv(this.popperId);=0A=
    var popdiv =3D $(this.popperId);=0A=
    =0A=
    // FIXME: Is this necessary? I think it's maybe wrong!=0A=
    if (popdiv) {=0A=
       utils.addClass(popdiv, "popnode");=0A=
    }=0A=
=0A=
    // Get popnode if it's an id string=0A=
    if (typeof(popnode) =3D=3D 'string') {=0A=
        popnode =3D $(popnode);=0A=
        if (!popnode) {=0A=
           throw "ElementPopper: id not found";=0A=
        }=0A=
    }=0A=
    this.popnode =3D popnode;=0A=
    this.timer =3D null; // Only exists when waiting for a pop=0A=
    =0A=
    // When the user mouses over target, pop it up=0A=
    utils.addEvent(popnode, "mousemove", handlePop);=0A=
}=0A=
=0A=
ElementPopper.popIndex =3D 0;=0A=
=0A=
ElementPopper.prototype =3D {=0A=
   setDelay: function(delay) {=0A=
      this.delay =3D delay;=0A=
   },=0A=
   getDelay: function() {=0A=
      return delay;=0A=
   }=0A=
};=0A=
=0A=
=0A=
=0A=
 utils.addEvent(window, "load", function(){     =0A=
     theDEP =3D new DeferredElementPopper("rapopper", { =0A=
          content: function(node) { =0A=
               var c =3D cssQuery(".hidden", node);               =0A=
               if (c && c.length > 0) {=0A=
                  var label =3D (c[0].textContent || c[0].innerText); =0A=
                  var cit =3D getCitation(node);=0A=
                  label =3D "<p id=3D'htbpoptext'>" + label + "</p>";=0A=
                  if (cit && cit > ""){ // avoid "undefined" value=0A=
                      label =3D label + "<p id=3D'htbpcit'>" + cit + =
"</p>";=0A=
                  } =0A=
                  return label;=0A=
               }                =0A=
          }, =0A=
          direction: PopDiv.POP_LEFT, =0A=
          popperId: "ppPopper", =0A=
          delay: 0 =0A=
     }); =0A=
});=0A=
=0A=
Portal.Portlet.HistoryDisplay =3D Portal.Portlet.extend({

	init: function(path, name, notifier) {
		console.info("Created History Ad...");
		this.base(path, name, notifier);   =20
	},
=09
	send: {
      'Cmd': null
      //'Recording': null
    },  =20
   =20
    receive: function(responseObject, userArgs) {  =0A=
         var cmd =3D userArgs.cmd;
         var rootNode =3D document.getElementById('HTDisplay'); =0A=
         var ul =3D document.getElementById('activity');=0A=
         var resp =3D responseObject.responseText;=0A=
             =0A=
         if (cmd =3D=3D 'HTOn') { =0A=
            rootNode.className =3D '';    // hide all msg and the turnOn =
link=0A=
            try {=0A=
                // Handle timeouts=0A=
                if (responseObject.status =3D=3D 408) { =0A=
                    rootNode.className =3D 'HTOn'; // so that the =
following msg will show up=0A=
                    rootNode.innerHTML =3D "<p class=3D'HTOn'>Your =
browsing activity is temporarily unavailable.</p>";=0A=
                    return;=0A=
                }=0A=
                   =0A=
                 // Looks like we got something...=0A=
                 resp =3D '(' + resp + ')';=0A=
                 var JSONobj =3D eval(resp);=0A=
                 =0A=
                 // Build new content (ul)=0A=
                 var newHTML =3D JSONobj.Activity;=0A=
                 var newContent =3D document.createElement('div');=0A=
                 newContent.innerHTML =3D newHTML;=0A=
                 var newUL =3D newContent.getElementsByTagName('ul')[0];=0A=
                 //alert(newHTML);=0A=
                 //alert(newContent.innerHTML);=0A=
                 //alert(newUL.innerHTML);=0A=
                 // Update content=0A=
                 rootNode.replaceChild(newUL, ul);=0A=
                 //XHR returns no activity (empty ul), e.g. activity =
cleared=0A=
                 if (newUL.className =3D=3D 'hide')                    =20
                     rootNode.className =3D 'HTOn';  // show "Your =
browsing activity is empty." message=0A=
                 =0A=
            }         =0A=
            catch (e) {=0A=
                //alert('error');=0A=
                rootNode.className =3D 'HTOn'; // so that the following =
msg will show up=0A=
                rootNode.innerHTML =3D "<p class=3D'HTOn'>Your browsing =
activity is temporarily unavailable.</p>";=0A=
           }=0A=
         }=0A=
         else if (cmd =3D=3D 'HTOff') {                         =0A=
             if (ul !=3D null) { =0A=
                 ul.className=3D'hide'; =0A=
                 ul.innerHTML =3D ''; // clear activity=0A=
             }=0A=
             rootNode.className =3D 'HTOff';    // make "Activity =
recording is turned off." and the turnOn link show up             =0A=
         }=0A=
         else if (cmd =3D=3D 'ClearHT') {     =0A=
             if ( rootNode.className =3D=3D '') { //                 =0A=
                 rootNode.className =3D 'HTOn';  // show "Your browsing =
activity is empty." message                                  =0A=
                 if (ul !=3D null) {=0A=
                     ul.className=3D'hide'; =0A=
                     ul.innerHTML =3D '';=0A=
                 }=0A=
             }            =0A=
         } =0A=
        =20
    },
   =20
	listen: {
	  'Cmd' : function(sMessage, oData, sSrc){
			console.info("Inside Cmd in HistoryDisplay: " + oData.cmd);
			this.setValue("Cmd", oData.cmd);
	  },	 =20
	=09
      "HistoryToggle<click>" : function(e, target, name){
         //alert(target.getAttribute("cmd"));
         this.send.Cmd({'cmd': target.getAttribute("cmd")});        =20
         console.info("Inside HistoryToggle in HistoryDisplay: " + =
target.getAttribute("cmd"));
        =20
         var site =3D document.forms[0]['p$st'].value;
         var cmd =3D  target.getAttribute("cmd");    =20
              =20
         // Issue asynchronous call to XHR service, callback is to =
update the portlet output
	     var resp =3D xmlHttpCall(site, this.path, cmd, {}, this.receive, =
{'cmd': target.getAttribute("cmd")}, this);
      },=20
     =20
      "HistoryOn<click>" : function(e, target, name){
         this.send.Cmd({'cmd': target.getAttribute("cmd")});
         =
//$PN('Pubmed_ResultsSearchController').getInput('RecordingHistory').valu=
e =3D 'yes';		=20
         console.info("Inside HistoryOn in HistoryDisplay: " + =
target.getAttribute("cmd"));
               =20
         var site =3D document.forms[0]['p$st'].value;  =20
	     var resp =3D xmlHttpCall(site, this.path, "HTOn", {}, =
this.receive, {'cmd': target.getAttribute("cmd")}, this);
	     //Portal.requestSubmit();
      },
     =20
      "ClearHistory<click>" : function(e, target, name){
         this.send.Cmd({'cmd': target.getAttribute("cmd")});=09
         var site =3D document.forms[0]['p$st'].value;  =20
	     var resp =3D xmlHttpCall(site, this.path, "ClearHT", {}, =
this.receive, {'cmd': target.getAttribute("cmd")}, this);	=20
      }
    }
});

function getCitation(node) {
   // var withHistorys =3D cssQuery("*[title]", node); does not work!!!  =
=20
   var withTitles =3D $AN('title', node, '*');
   //alert(withTitles.length + " " + withTitles[0].tagName + " " + =
withTitles[withTitles.length-1].tagName);
   //alert(withTitles[1].getAttribute('title'));
   if (withTitles.length > 0) {     =20
      var p =3D withTitles[0];
      var s =3D p.getAttribute("title");
      if (s && s > "") {=20
          //alert(s);
          p.setAttribute("title", "");
          node._title =3D s;
          for (var i =3D 0; i < withTitles.length; i++) {
              withTitles[i].removeAttribute("title");   =20
          }
      }
      /*else { //fixed in utils.js        =20
          s =3D node._title; // required for IE b/c of the bug in $AN
      }*/
   } else {
      s =3D node._title;
      //alert("old s "+ s);
   }
   return s;
}=0A=
// Requires: ElementPopper_JS, EventDispatcher_JS=0A=
=0A=
//=0A=
// A DeferredElementPopper creates an ElementPopper on any node with a =
given className the first time the=0A=
// node receives a mouseover event. It collects all of the poppers it =
creates (in an array), and=0A=
// remembers the dispatcher rule that invokes the initialization.=0A=
//=0A=
// "content" is the same as "content" for ElementPopper (see which)=0A=
//=0A=
DeferredElementPopper =3D function(className, config) {=0A=
   var that =3D this;=0A=
   this.config =3D config;=0A=
   this.poppers =3D [];=0A=
   this.dispatcher =3D new EventDispatcher("mouseover", className, =
function(event, udata, dispatcher) {=0A=
         if (!this._popup_init) {=0A=
            this._popup_init =3D 1;=0A=
            that.poppers[that.poppers.length] =3D new =
ElementPopper(this, that.config.content, that.config);=0A=
         }=0A=
    });=0A=
    =0A=
}=0A=
DeferredElementPopper.prototype =3D {=0A=
   debug: function() {=0A=
     var s =3D "";=0A=
     for (var i =3D 0; i < this.poppers.length; i++) {=0A=
        var z =3D this.poppers[i];=0A=
        s +=3D i + ": ";=0A=
        s +=3D z.popnode.innerText + "(" + =
z.popnode.getAttribute("title") +"); ";=0A=
     }=0A=
     alert(s);=0A=
   }=0A=
};=0A=
=0A=
=0A=
//=0A=
// A EventDispatcher does a popup on demand based on a classname on an =
element.=0A=
// Every mouse motion on the page notifies EventDispatcher that an event =
occurred.=0A=
// Any time an event occurs that has one of EventDispatcher's classnames =
on it,=0A=
// the handlers associated with that className are executed.=0A=
//=0A=
// EventDispatcher is designed for popups, but can be used for anything; =
the handler=0A=
// is a generic function:=0A=
//    handler(event, udata, dispatchrule)=0A=
// <event> is the platform event object; use utils.getTargetObj() to get =
its target=0A=
// <udata> is the udata that was passed when that handler was set up.=0A=
// <dispatchrule> is the EventDispatcher object; it is the dictionary=0A=
// {eventType, className, handler, udata} describing the popper behavior.=0A=
//=0A=
// dispatchrule.remove() [TBD] removes the rule from the event dispatcher=0A=
//=0A=
// When the callback occurs, <this> is the target element. =0A=
=0A=
EventDispatcher =3D function(eventType, className, handler, udata) {=0A=
=0A=
   // Start PP listening for this event=0A=
   if (!EventDispatcher.events) {=0A=
      EventDispatcher.events =3D {};=0A=
   }=0A=
=0A=
    // If first definition for this event type, listen for it=0A=
   if (!EventDispatcher.events[eventType]) {=0A=
      EventDispatcher.events[eventType] =3D {};=0A=
      utils.addEvent(document.body, eventType, =
EventDispatcher.handleEvent);=0A=
   }=0A=
   =0A=
   // Index of all class names managed by PP=0A=
   if (!EventDispatcher.classNames[className]) {=0A=
      EventDispatcher.classNames[className] =3D 1;=0A=
   }=0A=
=0A=
   // ev.classNames are the classes that listen for this event=0A=
   var ev =3D EventDispatcher.events[eventType];=0A=
   if (!ev.classNames) {=0A=
      ev.classNames =3D {};=0A=
   }=0A=
   =0A=
   // Add handler for this class=0A=
   if (!ev.classNames[className]) {=0A=
      ev.classNames[className] =3D [];=0A=
   }=0A=
   =0A=
   this.eventType =3D eventType;=0A=
   this.className =3D className;=0A=
   this.handler =3D handler;=0A=
   this.udata =3D udata || null;=0A=
   =0A=
   var c =3D ev.classNames[className];=0A=
   c[c.length] =3D this;=0A=
}=0A=
=0A=
EventDispatcher.events =3D {}=0A=
EventDispatcher.classNames =3D {}=0A=
=0A=
EventDispatcher.handleEvent =3D function(e) {=0A=
=0A=
   if (!EventDispatcher.events[e.type]) { return; } // TODO: Remove =
event listener here=0A=
   =0A=
   var t =3D utils.getTargetObj(e);=0A=
   if (t.className) {=0A=
      var theClasses =3D t.className.split(/\s+/);=0A=
      for (var c in theClasses) {=0A=
         if (EventDispatcher.classNames[theClasses[c]]) {=0A=
            EventDispatcher.dispatch(e, t, theClasses[c]);=0A=
         }=0A=
      }=0A=
   }=0A=
}=0A=
=0A=
EventDispatcher.dispatch =3D function(e, t, className) {=0A=
   if (!EventDispatcher.events[e.type]) return;=0A=
   var ev =3D EventDispatcher.events[e.type];=0A=
   if (!ev.classNames || !ev.classNames[className]) return;=0A=
   var poppers =3D ev.classNames[className];=0A=
   for (var i =3D 0; i < poppers.length; i++) {=0A=
      poppers[i].handleEvent(t, e);=0A=
   }=0A=
}=0A=
=0A=
EventDispatcher.prototype =3D {=0A=
   handleEvent: function(target, event) {=0A=
      this.handler.call(target, event, this.udata, this);=0A=
   }=0A=
}=0A=
=0A=
=0A=
=0A=
// PPMCRecentActivity=0A=
//=20
=0A=
Portal.Portlet.PPMCRecentActivity =3D =
Portal.Portlet.HistoryDisplay.extend({

    init: function(path, name, notifier) {
        console.info("Created PPMCRecentActivity");
        this.base(path, name, notifier);
    }
});=0A=
=0A=
=0A=
Portal.Portlet.Pubmed_Discovery_RA =3D =
Portal.Portlet.BriefLinkPageSection.extend({
   =20
    init: function(path, name, notifier) {
        console.info("Created Pubmed_Discovery_RA");
		this.base(path, name, notifier);
	},
=09
	SetPortletName: function(){
	    Portal.Portlet.BriefLinkPageSection.portletname =3D =
'Pubmed_Discovery_RA';
	}
});=0A=
Portal.Portlet.PPMCPubmedRA =3D =
Portal.Portlet.BriefLinkPageSection.extend({

    init: function(path, name, notifier) {=0A=
        console.info("Created PPMCPubmedRA");=0A=
        this.base(path, name, notifier);=0A=
    },=0A=
=0A=
    SetPortletName: function(){=0A=
        Portal.Portlet.BriefLinkPageSection.portletname =3D =
'PPMCPubmedRA';=0A=
    },=0A=
=0A=
    popNodeDelay: 500=0A=
});=0A=
// PPMCArticlePageJS=0A=
// This script does the following:=0A=
// - Positions reference portlets in the discovery column to the top of =
each paragraph;=0A=
// - Calculates how many references will fit;=0A=
// - Calculates whether it needs a "see all" link;=0A=
// - Adds mouseovers to links in paragraphs and reference portlet links=0A=
=0A=
// We use a self executing anonymous function in order to protect the =
global namespace from=0A=
// two top-level vars: '$j', and 'main'.=0A=
=0A=
( function() {=0A=
    var $j =3D jQuery;=0A=
=0A=
    // This main function runs when the DOM is ready to be queried; it =
gets attached to=0A=
    // the event down at the bottom of this module.=0A=
    var main =3D function() {=0A=
        //var start =3D new Date().getTime();=0A=
        var POPPER_DELAY =3D 500;=0A=
=0A=
        =
//////////////////////////////////////////////////////////////////////=0A=
        // Helper functions=0A=
=0A=
        =
//-------------------------------------------------------------------=0A=
        // This function determines if two rectangles intersect.=0A=
        // Two rectangles intersect if any point along their lines share =
a =0A=
        // point in space.  Because these portlets will be lined up =
vertically, =0A=
        // we only worry about one dimension.  The 'dims' parameter is =
an =0A=
        // object that contains top and bottom dimensions of the two =
rectangles.=0A=
=0A=
        var rectIntersect =3D function(dims) {=0A=
            // L1t is 'Line'1'Top' etc.=0A=
            var L1t =3D dims.L1t;=0A=
            var L1b =3D dims.L1b;=0A=
            var L2t =3D dims.L2t;=0A=
            var L2b =3D dims.L2b;=0A=
            return (=0A=
                (L2b > L1t && L2b < L1b) ||=0A=
                (L2t < L1b && L2t > L1t) ||=0A=
                (L2t > L1t && L2t < L1b) ||=0A=
                (L2t < L1t && L2b > L1b)=0A=
            );=0A=
        };=0A=
=0A=
        =
//-------------------------------------------------------------------=0A=
        // This function adds a popup to the links within the main =
article body.=0A=
        // It adds the popup to one element, and then queues itself up =
to add the=0A=
        // popup to the next element after a short delay.=0A=
=0A=
        var addPopper =3D function(elems, curr) {=0A=
            var currElem =3D elems[curr];=0A=
            var jqCurrElem =3D jQuery(currElem);=0A=
=0A=
            var rid =3D jqCurrElem.attr('rid');=0A=
            //console.info("rid is '" + rid + "'");=0A=
=0A=
            if (rid) {=0A=
                // Find the text for this popup from the element pointed =
to by =0A=
                // @rid.  This will be in the reference section of the =
article.=0A=
                // Some id's from the backend have special characters, =
so we=0A=
                // need to escape them, see PMC-6384 and =
http://tinyurl.com/2qfqgc=0A=
=0A=
                var ridEscaped =3D rid.replace(/:/g, "\\:")=0A=
                                    .replace(/\./g, "\\.")=0A=
                                    .replace(/=C2=B7/g, "\\=C2=B7");=0A=
                var refElem =3D jQuery('#' + ridEscaped);=0A=
                =0A=
                // Check to make sure that we found something=0A=
                if (refElem.length > 0) {=0A=
=0A=
                    var citeText =3D refElem.text();=0A=
                    //console.info("citeText is '" + citeText + "'");=0A=
=0A=
                    var popText =3D jQuery.trim(citeText);=0A=
                    //console.info("popText is '" + popText + "'");=0A=
    =0A=
                    // If the @href element of the current <a> tag =
(currElem)=0A=
                    // has a '#' portion, meaning that it is a link to =
the=0A=
                    // reference list in this same article, then =
indicate =0A=
                    // that in the popup text.=0A=
                    if (currElem.hash) {=0A=
                        popText +=3D ' [Reference List]';=0A=
                    }=0A=
    =0A=
                    new ElementPopper(currElem,=0A=
                        { content: popText, =0A=
                          direction: PopDiv.POP_ABOVE, =0A=
                          popperId: 'popper-para-links', =0A=
                          delay: POPPER_DELAY });=0A=
                }=0A=
            }=0A=
=0A=
            // Now arrange to have ourselves called for the next element =
that needs a popup,=0A=
            // after one millisecond.=0A=
            curr++;=0A=
            if (curr < elems.length) {=0A=
                var fnc =3D function(){=0A=
                    addPopper(elems, curr);=0A=
                }=0A=
                window.setTimeout(fnc, 1);=0A=
            }=0A=
        }; // end addPopper function=0A=
=0A=
        =
//-------------------------------------------------------------------=0A=
        // This function adds a popup to the links in the =
cited-reference blocks.=0A=
=0A=
        var addPopper2 =3D function(elems, curr) {=0A=
            var aDomElement =3D elems[curr];=0A=
            var aKids =3D aDomElement.childNodes;=0A=
            var aNumKids =3D aKids.length;=0A=
            //console.info("aDomElement is a " + aDomElement.toString() =
+ "; num kids is " + aNumKids);=0A=
=0A=
            // Generate the text that will go in the popup.=0A=
            // Get the text children of the <a> element.  This loop =
drops any element nodes;=0A=
            // in particular, the <span class=3D'flag'>Review</span> =
element, if present.=0A=
            var txt =3D "";=0A=
            for (var i =3D 0; i < aNumKids; ++i) {=0A=
                var kid =3D aKids[i];=0A=
                if (kid.nodeType !=3D 1) {=0A=
                    txt +=3D kid.nodeValue;=0A=
                }=0A=
            }=0A=
=0A=
            var l =3D jQuery(elems[curr]);=0A=
            txt +=3D "<br/>" + l.next('p')[0].innerHTML;=0A=
            new ElementPopper(l[0],=0A=
                { content: txt, direction: PopDiv.POP_LEFT, popperId: =
'popper-port-links', delay: POPPER_DELAY });=0A=
=0A=
            // Now arrange to have ourselves called for the next element =
that needs a popup,=0A=
            // after one millisecond.=0A=
            curr++;=0A=
            if (curr < elems.length) {=0A=
                var fnc =3D function(){=0A=
                    addPopper2(elems, curr);=0A=
                }=0A=
                window.setTimeout(fnc, 1);=0A=
            }=0A=
        }; // end addPopper2 function=0A=
=0A=
        // end helper function(s)=0A=
=0A=
        =
//////////////////////////////////////////////////////////////////////=0A=
        // In this space, we define and set variables that only need to =
be set once, not per paragraph.=0A=
=0A=
        // See if there any reference portlets in the page, by getting =
at least two reference=0A=
        // portlets. Later we will use these two portlets to make sure =
they do not interfere with=0A=
        // existing portlets in the column. It is unlikely that a third =
portlet would interfere=0A=
        // with anything, so let's make this as efficient as possible=0A=
        var portNodes =3D =
$j('#ArticleRefDocsums').find('div.cited-ref:lt(2)');=0A=
=0A=
        // If there is at least one portlet in the page, we need to get =
some initial information,=0A=
        // like sample portlet elements' sizes, information about =
existing portlet in page etc.=0A=
        var portsInPage =3D false;=0A=
        if (portNodes.length > 0) { // if the page has ANY reference =
portlets=0A=
            // remember that there is something to do=0A=
            var portsInPage =3D true;=0A=
            var firstPortN =3D $j(portNodes[0]);=0A=
=0A=
            // Max shown per page is already decided by xslt that =
generates portlet server-side,=0A=
            // and should be the number of <li>s per portlet=0A=
            var MAXREFS =3D 5;=0A=
=0A=
            // get dimensions of elements inside sample portlet, account =
for padding by using outerHeight=0A=
            var lis =3D firstPortN.find('li.ovfl');=0A=
            var firstRefH =3D $j(lis[0]).outerHeight(true);=0A=
            var firstSeeAllH =3D =
firstPortN.find('a.all-articles').outerHeight(true);=0A=
            var firstUl =3D firstPortN.find('ul');=0A=
            // the ul might have padding or margins applied=0A=
            var ulPaddingMargin =3D parseInt(firstUl.css('padding-top')) =
+=0A=
                                  =
parseInt(firstUl.css('padding-bottom')) +=0A=
                                  parseInt(firstUl.css('margin-top')) +=0A=
                                  parseInt(firstUl.css('margin-bottom'));=0A=
            // same goes for the actual portlet div=0A=
            var portNPadding =3D parseInt(firstPortN.css('padding-top')) =
+=0A=
                               =
parseInt(firstPortN.css('padding-bottom'));=0A=
=0A=
            // The horizontal position of all cited ref blocks should =
line up with recent history=0A=
            // portlet, which should be above any reference portlets=0A=
            var leftPos =3D $j('#recent-activity').position().left;=0A=
            //console.info('Got leftPos of all portlets: ' + leftPos);=0A=
=0A=
            // Get positions of any existing portlets in side column, so =
we can later hide any=0A=
            // reference portlets that take up same space=0A=
            var sideBarCell =3D $j('td.sidebar-cell')[0];=0A=
            var portRanges =3D {};=0A=
            var ports =3D jQuery('div.port', sideBarCell);=0A=
            for (var i =3D 0; i < ports.length; i++) {=0A=
                var p =3D jQuery(ports[i]);=0A=
                var pos =3D p.position();=0A=
                var t =3D pos.top;=0A=
                portRanges[i] =3D {=0A=
                    't': t,=0A=
                    'b': t + p.height() // bottom is top + height of =
portlet=0A=
                };=0A=
            }=0A=
=0A=
        } // end if portNodes in doc=0A=
=0A=
        // Now, for each paragraph, get associated portlet and position =
appropriately, we still need=0A=
        // to iterate through each paragraph even if there are no =
reference links in entire document.=0A=
        // We are doing some weird stuff here.  We have to do iterate =
through each paragraph, but=0A=
        // for performance reasons, on large pages we need to pause a ms =
between iterations. So:=0A=
        // 1) we get all "paragraph" elements=0A=
        // 2) we execute the "loopdloop" function, which every ms passes =
all the paras to paraLoop=0A=
        // 3) paraLoop does all the positioning of the reference portlets=0A=
        // 4) When loopdloop is done, it calls hideInterfering, which =
hides any portlets =0A=
        //    that overlap existing ones=0A=
=0A=
        // First make a hash of all of the CRBs indexed by their @rid =
attributes.=0A=
        var crbs =3D $j('div.cited-ref');=0A=
        var numCrbs =3D crbs.length;=0A=
        //console.info("Number of crbs is " + numCrbs);=0A=
=0A=
        var crbsByRid =3D {};=0A=
        for (var i =3D 0; i < numCrbs; ++i) {=0A=
            var crb =3D crbs[i];=0A=
            //console.info("crb is " + crb.toString());=0A=
            var jcrb =3D $j(crb);=0A=
            //console.info("jcrb is " + jcrb.toString());=0A=
            var rid =3D jcrb.attr('rid');=0A=
            //console.info("@rid is '" + rid + "'");=0A=
            crbsByRid[rid] =3D jcrb;=0A=
        }=0A=
=0A=
        //var paraLoop =3D function(crb) {=0A=
        //    var jcrb =3D $j(crb);=0A=
        //    var paraRid =3D jcrb.attr('rid');=0A=
        //    var p =3D $j('#' + paraRid);=0A=
        var paraLoop =3D function(para) {=0A=
            //console.group('para');=0A=
            var p =3D $j(para);=0A=
            //console.info(p[0]);=0A=
=0A=
            // Get the @id attribute, and from that, look up the CRB.=0A=
            var paraId =3D p.attr('id');=0A=
            //console.info("paragraph @id is " + paraId);=0A=
            var jcrb =3D crbsByRid[paraId];=0A=
=0A=
            if (jcrb) {=0A=
                //console.info("jcrb is " + jcrb.toString());=0A=
=0A=
                // if a 'paragraph' has an associated portlet, it will =
have a 'cite' attribute on it=0A=
                // CFM:  taking this check out, the @cite attribute is =
going away, see PMC-5595:=0A=
                //var citeAttr =3D p.attr('cite');=0A=
                //if (citeAttr) {=0A=
=0A=
                // Get the number of unique references per paragraph.  =
This could be more than the=0A=
                // max shown in portlet.=0A=
                // CFM:  Now, getting this info from the crb, not the =
paragraph, because the @pmids=0A=
                // attribute will be going away from the paragraph, see =
PMC-5595.=0A=
//              var numRefs =3D p.attr('pmids').split(' ').length;=0A=
                var numRefs =3D jcrb.attr('pmids').split(' ').length;=0A=
                //console.info("numRefs is " + numRefs);=0A=
=0A=
                // get paragraph dims. We need these to position portlet =
to paragraph=0A=
                var pPos =3D p.position();=0A=
                var pPosX =3D pPos.left;=0A=
=0A=
                 // needs to be a number because we will add/subtract =
margin=0A=
                var pPosY =3D parseInt(pPos.top);=0A=
                var pPosH =3D p.height();=0A=
=0A=
                // Get paragraph top and bottom margins.  We need to =
account for these when calculating =0A=
                // reference portlet placement. Margin is not accounted =
for when getting an element's =0A=
                // height, but it does affect appearance of element's =
dimensions when there is no border.=0A=
                var pMarT =3D parseInt(p.css('marginTop'));=0A=
                var pMarB =3D parseInt(p.css('marginBottom'));=0A=
=0A=
                // Get associated portlet from 'cited' attribute, we can =
now safely overwrite portN =0A=
                // variable from beginning of script.=0A=
                // CFM:  change from using 'portN' to using the variable =
'jcrb', from above.=0A=
                //var portN =3D $j('#' + citeAttr);=0A=
                //var refNodes =3D portN.find('li');=0A=
                var refNodes =3D jcrb.find('li');=0A=
                var numRefsInP =3D refNodes.length;=0A=
                //console.info("numRefsInP is " + numRefsInP);=0A=
=0A=
                // Set styles on portlet node to align to paragraph=0A=
                // We set portlet node to position: absolute in the css =
file, because that is more=0A=
                // efficient than setting it in JavaScript, and that =
property does not change.=0A=
//              portN.css( {=0A=
                jcrb.css( {=0A=
                    'top': pPosY + pMarT + 2 + 'px', // Add an xtra 2px, =
otherwise it appears too low=0A=
                    'left': leftPos + 'px'=0A=
                });=0A=
=0A=
                // Calculate how many refs will fit per paragraph and if =
we need the =0A=
                // 'See more articles cited in this paragraph' link. =0A=
                var refsFit =3D null;=0A=
                var needAllLink =3D false;=0A=
                if (numRefs > MAXREFS || numRefs * firstRefH >=3D pPosH =
- pMarB) {=0A=
                    //console.info('more links than allowed, OR links =
allowed are higher than paragraph height');=0A=
                    refsFit =3D Math.floor( pPosH / (firstRefH + =
firstSeeAllH) );=0A=
                    needAllLink =3D true;=0A=
                    if (refsFit > MAXREFS) {=0A=
                        refsFit =3D MAXREFS;=0A=
                    }=0A=
                    //console.info('refsFit: ' + refsFit);=0A=
                } else {=0A=
                    //console.info('all refs in para fit');=0A=
                    refsFit =3D numRefs;=0A=
                    //console.info('refsFit: ' + refsFit);=0A=
                }=0A=
=0A=
                var aSeeArticles =3D jcrb.find('a.all-articles');=0A=
                if (!needAllLink) {=0A=
                    aSeeArticles.hide();=0A=
                }=0A=
                else if (refsFit =3D=3D 0) {=0A=
                    // If the visible number of links is zero, then =
change the text from=0A=
                    // "See more articles ..." to just "See articles =
...".=0A=
                    // See PMC-6076.=0A=
                    var seeMoreT =3D aSeeArticles.text();=0A=
                    aSeeArticles.text( seeMoreT.replace(/more /, "") );=0A=
                    // After all, we decided that we'd rather just not =
see it:=0A=
                    jcrb.hide();=0A=
                }=0A=
=0A=
                //console.info('need to take off refs:');=0A=
                // how many references (lis) from the portlet do we need =
to hide?=0A=
                var takeOff =3D numRefsInP - refsFit;=0A=
                //console.info(takeOff);=0A=
=0A=
                if ( takeOff > 0 ) {=0A=
                    // we need to take off some nodes, loop through li =
nodes in reverse order and hide them=0A=
                    for (var i =3D numRefsInP - 1; i >=3D refsFit; i--) {=0A=
                        $j(refNodes[i]).hide();=0A=
                    }=0A=
                } // end if we need to take off nodes=0A=
=0A=
                // we now need to add mouseovers on reference links that =
are not hidden. We get the text=0A=
                // from the title attribute of the link=0A=
                //var elems2 =3D portN.find('a.popnode:visible');=0A=
                var elems2 =3D jcrb.find('a.popnode:visible');=0A=
                //console.info(elems2);=0A=
=0A=
                if (elems2.length > 0) {=0A=
                    addPopper2(elems2, 0);=0A=
                }=0A=
=0A=
            } // end if jcrb=0A=
=0A=
            // Now, we are back touching on each paragraph, regardless =
whether there =0A=
            // are links with pmids or not we need to get all the =
reference links per =0A=
            // paragraph and do the mouseover which links to reference =
section at the=0A=
            // bottom of the page.  This is a little Eric trick for =
performance. We get =0A=
            // the links in the paragraph and create our own custom loop =
and setTimeout =0A=
            // for each link.  This allows "multithreading" and doesn't =
lock up the =0A=
            // browser.=0A=
            var elems =3D p.find('a.cite-reflink');=0A=
            if (elems.length > 0) {=0A=
                addPopper(elems, 0);=0A=
            }=0A=
=0A=
            //console.groupEnd('para');=0A=
        }; // end paraloop function=0A=
=0A=
        var hideInterfering =3D function(){=0A=
            // At this point all reference divs are positioned in =
document. We now check that =0A=
            // the first two reference portlets (which were already =
queried for in beginning =0A=
            // of the script don't interfere with any other portlets =
that may be at the top of =0A=
            // column.  Loop thru them and compare them against what =
exists in portRanges=0A=
            if (portsInPage =3D=3D=3D true) {=0A=
                portNodes.each( function() {=0A=
                    var citedRefJ =3D $j(this);=0A=
                    // We refer to portRanges, which is an obj in which =
we stored dims of existing=0A=
                    // portlets before positioning reference portlets=0A=
                    for (var i in portRanges){=0A=
                        var range =3D portRanges[i];=0A=
=0A=
                        var existingT =3D range.t;=0A=
                        var existingB =3D range.b;=0A=
=0A=
                        var citedRefT =3D citedRefJ.position().top;=0A=
=0A=
                        // This is the parameter to the rectIntersect =
helper func defined in the beginning=0A=
                        // of the script.  It contains top and bottom =
dims for two rectanges.  The=0A=
                        // rectIntersect returns true if they intersect.=0A=
                        // PMC-6175:  add a little buffer of ten pixels.=0A=
                        var dims =3D {=0A=
                            'L1t': existingT, // we are comparing =
against the existing portlet=0A=
                            'L1b': existingB + 10,  // little buffer to =
be sure.=0A=
                            'L2t': citedRefT,=0A=
                            'L2b': citedRefT + citedRefJ.height()=0A=
                        }=0A=
                        //console.info('L1t: ' + existingT);=0A=
                        //console.info('L1b: ' + existingB);=0A=
                        //console.info('L2t: ' + citedRefT);=0A=
                        //console.info('L2b: ' + (citedRefT + =
citedRefJ.height()));=0A=
=0A=
                        if ( rectIntersect(dims) =3D=3D=3D true) {=0A=
                            //console.info('interferes');=0A=
                            citedRefJ.css('display', 'none');=0A=
                        }=0A=
                    }=0A=
                }); // end iterating through first two existing portlets=0A=
            }=0A=
        }=0A=
=0A=
        // Get the list of all paragraphs in the document.=0A=
        var allParas =3D $j('div.p');=0A=
        var numParas =3D allParas.length;=0A=
=0A=
        var loopdloop =3D function(curr){=0A=
          paraLoop(allParas[curr++]);=0A=
          if (curr >=3D numParas) {=0A=
            hideInterfering();=0A=
          } else {=0A=
            setTimeout( function(){ loopdloop(curr); }, 1);=0A=
          }=0A=
        }=0A=
        //document.title =3D new Date().getTime() - start.toString() + =
'ms';=0A=
        loopdloop(0);=0A=
    };=0A=
=0A=
=0A=
    // We use window.load for Safari, not ready, because in Safari, we =
cannot be =0A=
    // sure all CSS has loaded, and we cannot be sure=0A=
    // dims of images are accounted for when getting top positions of =
paragraphs=0A=
    if ( $j.browser.safari) {=0A=
        $j(window).load(main);=0A=
    } else {=0A=
        $j(main);=0A=
    }=0A=
=0A=
})();=0A=
=0A=

------=_NextPart_000_0000_01CA72A3.109DE760
Content-Type: application/octet-stream
Content-Transfer-Encoding: quoted-printable
Content-Location: http://www.ncbi.nlm.nih.gov/corehtml/jsutils/tileshop_pmc.1/tileshop_pmc.1.js

// =
/web/private/htdocs/staff/sponomar/TEST/corehtml/jsutils/tileshop_pmc.1/t=
ileshop_pmc.1.js.orig=0A=
=0A=
utils.jsLoader.load(["firebugx.js","tile.1.js","tileshop_pmc.1/scale_pmc.=
1.js"]);function TileShop(){this.oTexts=3D{sTitle:"Drag image to =
reposition. Double click to magnify further.",sTitleUp:"Drag image to =
reposition.",sTitleDown:"Click on image to =
magnify.",sTitleWait:"Wait...",sPanoramaTitle:"Click to change focus to =
this area of image.",sPanTitle:"Drag to focus on a different part of =
image.",sCloseButton:"Return to standard image view."};}=0A=
TileShop.prototype.Init=3Dfunction(e){var =
oTargetImg=3Dutils.getTargetObj(e);var oThis=3Dthis;this.oNotifier=3Dnew =
Notifier();var oDim=3Dutils.getXY(oTargetImg);var =
oScroll=3Dutils.getScrolls();var =
x=3DparseInt((oScroll.x+e.clientX-oDim.x)/oDim.w*100);var =
y=3DparseInt((oScroll.y+e.clientY-oDim.y)/oDim.h*100);var =
rel=3DoTargetImg.getAttribute("rel");if(rel&&rel!=3D""){oTargetImg.setAtt=
ribute("rel",rel+"&x=3D"+x+"&y=3D"+y);}else{var =
src=3DoTargetImg.getAttribute("src");oTargetImg.setAttribute("src",src+"&=
x=3D"+x+"&y=3D"+y);}=0A=
var oDt=3Dutils.getParent(oTargetImg);var oDl=3Dutils.getParent(oDt);var =
oDiv=3Dutils.getParent(oDl);var =
oTitlePanel=3Dutils.getFirstChild(oDiv);var =
oTitleBar=3Dutils.getFirstChild(oTitlePanel);var =
oCloseButton=3Dutils.getNextSibling(oTitleBar);oCloseButton.title=3Dthis.=
oTexts.sCloseButton;var oScalePanel=3Dutils.getFirstChild(oDl);var =
oTilePanel=3Dutils.getNextSibling(oScalePanel);var oScalePanelW=3D48;var =
iTitleBarH=3DoTitlePanel.offsetHeight;oDt.style.position=3D"relative";var=
 =
sTitleBar=3DoTitleBar.innerHTML;oTitleBar.innerHTML=3Dthis.oTexts.sTitleW=
ait;var oScaleCtrl,oPanoramaSwitcher,oPanorama,oTileData;var =
bClosing=3Dfalse;oThis.oNotifier.setListener(this,"close",function(){bClo=
sing=3Dtrue;if(!oThis.oTile)return;utils.removeChildren(oThis.oTile.oCanv=
as);oTilePanel.removeChild(oThis.oTile.oCanvas);utils.removeChildren(oPan=
oramaSwitcher.oCanvas);oDt.removeChild(oPanoramaSwitcher.oCanvas);oPanora=
maSwitcher.oCanvas=3Dnull;utils.removeChildren(oPanorama.oCanvas);oDt.rem=
oveChild(oPanorama.oCanvas);utils.removeChildren(oScaleCtrl.oCanvas);oSca=
lePanel.removeChild(oScaleCtrl.oCanvas);oThis.oTile.oCanvas=3Dnull;oPanor=
ama.oCanvas=3Dnull;oScaleCtrl.oCanvas=3Dnull;oThis.oTile=3Dnull;oPanorama=
=3Dnull;oPanoramaSwitcher=3Dnull;oScaleCtrl=3Dnull;oTargetImg.style.displ=
ay=3D"block";oCloseButton.className=3D"";oTitlePanel.className=3D"";oScal=
ePanel.className=3D"";oScalePanel.style.width=3D"0px";oTilePanel.style.wi=
dth=3D"auto";oTilePanel.style.height=3D"auto";oDl.style.height=3D"auto";o=
ScalePanel.style.height=3D"auto";oDiv.style.width=3DoTargetImg.offsetWidt=
h+"px";oDiv.style.height=3D"auto";oTitleBar.innerHTML=3DsTitleBar;},null)=
;this.oNotifier.setListener(this,"resize-canvas",function(xx,bFlag){if(bC=
losing)return;var kW=3D0.9;var kH=3D0.7;var minW=3D400;var =
minH=3D300;var oDimW=3Dutils.getWindowDim();var =
W=3DparseInt(kW*oDimW.w);var =
H=3DparseInt(kH*oDimW.h);if(W<minW)W=3DminW;if(H<minH)H=3DminH;var =
oTilePanelW=3DW-oScalePanelW;var =
oTilePanelH=3DH-iTitleBarH;oDiv.style.width=3DW+"px";oDiv.style.height=3D=
H+"px";oTilePanel.style.width=3DoTilePanelW+"px";oTilePanel.style.height=3D=
oTilePanelH+"px";oTilePanel.style.overflow=3D"hidden";oScalePanel.style.w=
idth=3DoScalePanelW+"px";oScalePanel.style.height=3DoTilePanelH+"px";if(b=
Flag){oThis.oNotifier.Notify(oThis,"resize",{w:oTilePanelW,h:oTilePanelH}=
);}},null);this.oNotifier.setListener(oThis,"picture-is-drawn",function()=
{oTitlePanel.className=3D"active";oCloseButton.className=3D"active";oScal=
ePanel.className=3D"active";utils.addEvent(oCloseButton,"click",function(=
e){oThis.oNotifier.Notify(this,"close","");});});oThis.oNotifier.setListe=
ner(oThis,"disable",function(xx,oComment){if(oComment=3D=3D"scale-up"){oT=
itleBar.innerHTML=3DoThis.oTexts.sTitleUp;}else =
if(oComment=3D=3D"scale-down"){oTitleBar.innerHTML=3DoThis.oTexts.sTitleD=
own;}else{oTitleBar.innerHTML=3DoThis.oTexts.sTitle;}});oThis.oNotifier.N=
otify(this,"resize-canvas",false);var =
oImgForTiler=3DoTargetImg.cloneNode(false);oImgForTiler.width=3DoTargetIm=
g.offsetWidth;oImgForTiler.height=3DoTargetImg.offsetHeight;oImgForTiler.=
setAttribute("title",this.oTexts.sPanoramaTitle);oTargetImg.style.display=
=3D"none";setTimeout(function(){oTileData=3Dnew =
TileDataDb(oImgForTiler,oThis.oNotifier);oTileData.oViewport.w=3DparseInt=
(oTilePanel.style.width);oTileData.oViewport.h=3DparseInt(oTilePanel.styl=
e.height);oTileData.oViewport.x=3D0;oTileData.oViewport.y=3D0;oThis.oTile=
=3Dnew =
Tile(oTileData,oThis.oNotifier);oTilePanel.appendChild(oThis.oTile.oCanva=
s);oPanorama=3Dnew =
Panorama(oTileData,oThis.oNotifier);oPanorama.oCanvas.style.zIndex=3D100;=
oPanorama.oPan.oCanvas.setAttribute("title",oThis.oTexts.sPanTitle);oTile=
Panel.appendChild(oPanorama.oCanvas);oPanoramaSwitcher=3Dnew =
PanoramaSwitcher(oTileData,oThis.oNotifier);oPanoramaSwitcher.oCanvas.sty=
le.zIndex=3DoPanorama.oCanvas.style.zIndex+1;oTilePanel.appendChild(oPano=
ramaSwitcher.oCanvas);oScaleCtrl=3Dnew =
ScaleCtrl(oTileData,oThis.oNotifier);oScalePanel.appendChild(oScaleCtrl.o=
Canvas);},100);}=0A=
TileShop.Load=3Dfunction(sClassName){utils.addEvent(window,"load",functio=
n(){oTileshop=3D$C(sClassName);for(var i in =
oTileshop){utils.addEvent(oTileshop[i],"click",function(e){oTileshop[i].o=
App=3Dnew TileShop();oTileshop[i].oApp.Init(e);});}=0A=
utils.addEvent(window,"resize",function(e){for(var i in =
oTileshop){if(oTileshop[i].oApp&&oTileshop[i].oApp.oTile){oTileshop[i].oA=
pp.oNotifier.Notify(oTileshop[i],"resize-canvas",true);}}});});}=0A=
TileShop.Load("tileshop");
------=_NextPart_000_0000_01CA72A3.109DE760
Content-Type: application/octet-stream
Content-Transfer-Encoding: quoted-printable
Content-Location: http://www.ncbi.nlm.nih.gov/corecgi/tileshop/tileshop_data_db.1.js

// $Id: tileshop_data_db.1.js 114734 2007-11-28 17:58:54Z sponomar $=0A=
utils.jsLoader.load(["remote_data_provider.1.js"]);=0A=
function TileDataDb(oImg,oNotifier) {=0A=
this.NAME =3D "TileDataDb";=0A=
var oThis=3Dthis;=0A=
this.sProjectId =3D "";=0A=
this.sPictureId =3D "";=0A=
this.sSatId =3D "";=0A=
this.oMetadata =3D "";=0A=
this.Init(oImg,oNotifier);=0A=
var oDataProvider=3Dnew RemoteDataProvider();=0A=
oDataProvider.sUrl =3D this.sUrl + "?manifest=3D1&p=3D" + this.sProjectId=0A=
+ "&id=3D" + this.sPictureId + "&w=3D" + this.oViewport.w + "&h=3D" + =
this.oViewport.h;=0A=
oDataProvider.onSuccess=3Dfunction (obj) {=0A=
eval("oThis.oMetadata=3D" + obj.responseText);=0A=
oNotifier.Notify(oThis, "metadata", oThis.oMetadata);=0A=
};=0A=
oDataProvider.onError=3Dfunction(obj) {=0A=
alert("Error occured: can not get metadata. Check Project name and/or =
Image name");=0A=
};=0A=
function x_Update(oMetadata,i) {=0A=
oThis.fScale=3DoMetadata.aView[i].W/oMetadata.aView[0].W;=0A=
oThis.bIsStaticImage=3DoMetadata.aView[i].W=3D=3DoMetadata.aView[i].w=0A=
&& oMetadata.aView[i].H=3D=3DoMetadata.aView[i].h;=0A=
oThis.oPicture.w=3DoMetadata.aView[i].W;=0A=
oThis.oPicture.h=3DoMetadata.aView[i].H;=0A=
oThis.sSat=3DoMetadata.Sat;=0A=
oThis.sTileDbId=3DoMetadata.aView[i].sId;=0A=
oThis.sPrefix =3D "id_" + oThis.sSat + "_" + oThis.sTileDbId;=0A=
oThis.oTile.w=3DoMetadata.aView[i].w;=0A=
oThis.oTile.h=3DoMetadata.aView[i].h;=0A=
oThis.Calculate();=0A=
}=0A=
oNotifier.setListener(this, "metadata", function(oListener, oMetadata) {=0A=
oThis.oMetadata=3DoMetadata;=0A=
if (oMetadata.aView.length<1) {=0A=
return true;=0A=
}=0A=
oThis.iScaleIndex=3D0;=0A=
if (oThis.fScale=3D=3D-1) {=0A=
oThis.iScaleIndex=3DoMetadata.aView.length-2;=0A=
if (oThis.iScaleIndex<0) oThis.iScaleIndex=3D0;=0A=
} else if (oThis.fScale=3D=3D0) {=0A=
oThis.iScaleIndex=3DoMetadata.aView.length-1;=0A=
} else if (oThis.fScale<=3D1&& oThis.fScale>0) {=0A=
var W=3DoMetadata.aView[0].W * oThis.fScale;=0A=
for =
(oThis.iScaleIndex=3D0;oThis.iScaleIndex<oMetadata.aView.length-1;oThis.i=
ScaleIndex++) {=0A=
var s=3DoMetadata.aView[oThis.iScaleIndex].W/W;=0A=
if (s<=3D0.5|| s<1.36) break;=0A=
}=0A=
} else=0A=
oThis.iScaleIndex=3D0;=0A=
var W=3DoMetadata.aView[0].W;=0A=
for (var i=3D0;i<oMetadata.aView.length;i++) {=0A=
var v=3DoMetadata.aView[i].W/W;=0A=
oThis.oScales[i]=3D{=0A=
n:oMetadata.aView[i].sName,=0A=
v:v,=0A=
w:oMetadata.aView[i].W,=0A=
h:oMetadata.aView[i].H,=0A=
enable:true=0A=
};=0A=
if (oMetadata.aView[i].W=3D=3DoMetadata.aView[i].w=0A=
&& oMetadata.aView[i].H=3D=3DoMetadata.aView[i].h) {=0A=
oThis.oScales[i]=3D{n:oMetadata.aView[i].sName,v:v};=0A=
break;=0A=
}=0A=
}=0A=
x_Update(oMetadata,oThis.iScaleIndex);=0A=
},null);=0A=
oNotifier.setListener(this, "scale", function(oListener, oComment) {=0A=
oThis.iScaleIndexPrevious=3DoThis.iScaleIndex;=0A=
switch (oComment) {=0A=
case "up":=0A=
if (oThis.iScaleIndex<1) return;=0A=
oThis.iScaleIndex--;=0A=
while (!oThis.oScales[oThis.iScaleIndex]) {=0A=
oThis.iScaleIndex--;=0A=
if (oThis.iScaleIndex<1) break;=0A=
}=0A=
break;=0A=
case "down":=0A=
if (oThis.oScales.length-1<=3DoThis.iScaleIndex) return;=0A=
oThis.iScaleIndex++;=0A=
while (oThis.oScales[oThis.iScaleIndex]=3D=3Dnull) {=0A=
oThis.iScaleIndex++;=0A=
if (oThis.oScales.length-1<=3DoThis.iScaleIndex) break;=0A=
}=0A=
break;=0A=
default:=0A=
oThis.iScaleIndex=3DoComment;=0A=
break;=0A=
}=0A=
x_Update(oThis.oMetadata,oThis.iScaleIndex);=0A=
});=0A=
setTimeout(function() {=0A=
oDataProvider.Request();=0A=
},5);=0A=
}=0A=
TileDataDb.prototype=3Dnew TileData();=0A=
TileDataDb.prototype.Parse=3Dfunction(arr) {=0A=
var tmp;=0A=
if (arr.indexOf("p=3D") =3D=3D 0) {=0A=
tmp =3D arr.split("=3D");=0A=
this.sProjectId=3Dtmp[1];=0A=
} else if (arr.indexOf("id=3D") =3D=3D 0) {=0A=
tmp =3D arr.split("=3D");=0A=
this.sPictureId=3Dtmp[1];=0A=
}=0A=
}=0A=
TileDataDb.prototype.GetTileUrl=3Dfunction(row,col) {=0A=
return this.sUrl + "?p=3D" + this.sProjectId=0A=
+ "&id=3D" + this.sTileDbId + "&s=3D" + this.sSat=0A=
+ "&r=3D" + (row + 1) + "&c=3D" + (col + 1);=0A=
}=0A=
TileDataDb.prototype.GetFitUrl=3Dfunction() {=0A=
return this.sUrl + "?p=3D" + this.sProjectId=0A=
+ "&id=3D" + this.oMetadata.aView[this.oMetadata.aView.length - 1].sId=0A=
+ "&s=3D" + this.sSat + "&r=3D1&c=3D1";=0A=
}=0A=

------=_NextPart_000_0000_01CA72A3.109DE760
Content-Type: application/octet-stream
Content-Transfer-Encoding: quoted-printable
Content-Location: http://www.ncbi.nlm.nih.gov/portal/portalrc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js

var s_account =3D "nihncbiprod";=0A=
=0A=
(function(){=0A=
        =0A=
    if (document.cookie.length>0){=0A=
        var c_start=3Ddocument.cookie.indexOf("NCBISTATLOC=3D");=0A=
        if(c_start!=3D-1){ =0A=
            c_start =3D c_start + 12; =0A=
            var c_end =3D document.cookie.indexOf(";",c_start);=0A=
            if (c_end=3D=3D-1) c_end =3D document.cookie.length;=0A=
            var ckVal =3D document.cookie.substring(c_start,c_end);=0A=
            if(ckVal.length>0){=0A=
                s_account=3DckVal;=0A=
            }=0A=
        } =0A=
    }=0A=
    =0A=
})();=0A=
=0A=
=0A=
=0A=
/* SiteCatalyst code version: H.19.3.
Copyright 1997-2009 Omniture, Inc. More info available at
http://www.omniture.com */
/************************ ADDITIONAL FEATURES ************************
     Plugins
*/


var s=3Ds_gi(s_account)
/************************** CONFIG SECTION **************************/
/* You may add or alter any code config here. */
/* Specify the life time of the cookie in seconds, or */
/* set to "Session" to turn off persistent cookies.   */
s.cookieLifetime=3D"Session"
/* Conversion Config */
s.currencyCode=3D"USD"
/* Link Tracking Config */
s.trackDownloadLinks=3Dtrue
s.trackExternalLinks=3Dtrue
s.trackInlineStats=3Dtrue
s.linkDownloadFileTypes=3D"exe,zip,wav,mp3,mov,mpg,avi,wmv,pdf,doc,docx,x=
ls,xlsx,ppt,pptx"
s.linkInternalFilters=3D"javascript:,ncbi.nlm.nih.gov"
s.linkLeaveQueryString=3Dfalse
s.linkTrackVars=3D"None"
s.linkTrackEvents=3D"None"
/* Plugin Config */
s.usePlugins=3Dtrue

/* Page Name Plugin Config */
s.siteID=3D""            // leftmost value in pagename
s.defaultPage=3D""       // filename to add when none exists
s.queryVarsList=3D""     // query parameters to keep
s.pathExcludeDelim=3D";" // portion of the path to exclude
s.pathConcatDelim=3D""   // page name component separator
s.pathExcludeList=3D""   // elements to exclude from the path

function s_doPlugins(s) {
	/* Add calls to plugins here */
=09
	/*Populate Page Name*/
	if(!s.pageName && !s.pageType)
		s.pageName=3Ds.getPageName();
=09
	/*Track External Campaign*/
	if(!s.campaign)
		s.campaign=3Ds.getQueryParam('psrc');
		s.campaign=3Ds.getValOnce(s.campaign,'s_campaign',0);
=09
	/*Page View*/
	s.events=3Ds.apl(s.events,'event2',',',2)
=09
	/****************Internal Search****************/
	/*Copy Internal Search Term*/
	if(s.prop3) s.prop3=3Ds.prop3.toLowerCase()
	if(s.prop3){
	    s.eVar3=3Ds.prop3

	/* Set de-duped onsite search event */
	var t_search=3Ds.getValOnce(s.eVar3,'ev3',0)
	if(t_search)
		s.events=3Ds.apl(s.events,'event1',',',1)
	}
=09
	/*Copy Search Type*/
	if(s.prop4 && !s.eVar4) s.eVar4 =3D s.prop4 //Search Type
=09
	/***************Entrez Limit**********************/
	/*Copy Limit Criteria Set (Entrez limit) */
	if(s.prop17) s.prop17=3Ds.prop17.toLowerCase()
	if(s.prop17){
	    s.eVar17=3Ds.prop17

	/* Set de-duped onsite search event */
	var t_search=3Ds.getValOnce(s.eVar17,'ev17',0)
	if(t_search)
		s.events=3Ds.apl(s.events,'event7',',',1)
	}
=09
	/*Copy Limit Criteria Set Values */
	if(s.prop19) s.prop19=3Ds.prop19.toLowerCase()
	if(s.prop19){
	    s.eVar19=3Ds.prop19

	/* Set de-duped onsite search event */
	var t_search=3Ds.getValOnce(s.eVar19,'ev19',0)
	if(t_search)
		s.events=3Ds.apl(s.events,'event7',',',1)
	}
=09
	/******************Advanced Search***************/
	/*Copy Advanced Search Criteria*/
	if(s.prop18) s.prop18=3Ds.prop18.toLowerCase()
	if(s.prop18){
	    s.eVar18=3Ds.prop18

	/* Set de-duped onsite search event */
	var t_search=3Ds.getValOnce(s.eVar18,'ev18',0)
	if(t_search)
		s.events=3Ds.apl(s.events,'event8',',',1)
	}
=09
	/*Copy Advanced Search Criteria Values*/
	if(s.prop20) s.prop20=3Ds.prop20.toLowerCase()
	if(s.prop20){
	    s.eVar20=3Ds.prop20

	/* Set de-duped onsite search event */
	var t_search=3Ds.getValOnce(s.eVar20,'ev20',0)
	if(t_search)
		s.events=3Ds.apl(s.events,'event8',',',1)
	}
=09
	/***************Entrez Filter Applied**************/
	/*Copy Entrez Filter Applies*/
	if(s.prop38) s.prop38=3Ds.prop38.toLowerCase()
	if(s.prop38){
	    s.eVar38=3Ds.prop38

	/* Set de-duped onsite search event */
	var t_search=3Ds.getValOnce(s.eVar38,'ev38',0)
	if(t_search)
		s.events=3Ds.apl(s.events,'event9',',',1)
	}
=09
	/*Time Parting*/
	s.prop34=3Ds.getTimeParting('h','-5','2009'); // Set hour
	s.prop35=3Ds.getTimeParting('d','-5','2009'); // Set day
	s.prop36=3Ds.getTimeParting('w','-5','2009'); // Set Weekend / Weekday
	s.eVar34=3Ds.prop34;
	s.eVar35=3Ds.prop35;
	s.eVar36=3Ds.prop36;
=09
	/*Google Scholars tracking*/
	if(document.referrer.indexOf('scholar.google.com') > -1){
		s.eVar32=3D'scholar.google.com';
		s.prop32=3Ds.getAndPersistValue(s.eVar32,'s_dr_persist',0);
		s.prop33=3Ds.prop32+':'+s.pageName;
	}
=09
	/*Copy props to eVars*/
	if(s.prop1 && !s.eVar1) s.eVar1 =3D s.prop1; //Page Hit ID
	if(s.prop2 && !s.eVar2) s.eVar2 =3D s.prop2; //Database
	if(s.prop5 && !s.eVar5) s.eVar5 =3D s.prop5; //Search Display(Report =
Name)
	if(s.prop6 && !s.eVar6) s.eVar6 =3D s.prop6; //SEarch Show (Page Size)
	if(s.prop7 && !s.eVar7) s.eVar7 =3D s.prop7; //Search Sort By (Sort =
Order)
	if(s.prop8 && !s.eVar8) s.eVar8 =3D s.prop8; //Current Page (Search =
Page)
	if(s.prop11 && !s.eVar11) s.eVar11 =3D s.prop11; //Link Name
	if(s.prop12 && !s.eVar12) s.eVar12 =3D s.prop12; //Database Source
	if(s.prop13 && !s.eVar13) s.eVar13 =3D s.prop13; //Link Id (TI)
	if(s.prop14 && !s.eVar14) s.eVar14 =3D s.prop14; //Link Name (TN)
	if(s.prop15 && !s.eVar15) s.eVar15 =3D s.prop15; //Link Pos (TS)
	if(s.prop16 && !s.eVar16) s.eVar16 =3D s.prop16; //Entrez Operation
	if(s.prop21 && !s.eVar21) s.eVar21 =3D s.prop21; //Page Design ID
	if(s.prop22 && !s.eVar22) s.eVar22 =3D s.prop22; //Session ID
	if(s.prop23 && !s.eVar23) s.eVar23 =3D s.prop23; //Site Section 2
	if(s.prop24 && !s.eVar24) s.eVar24 =3D s.prop24; //Sub Section 3
	if(s.prop25 && !s.eVar25) s.eVar25 =3D s.prop25; //Sub Section 3
	if(s.prop26 && !s.eVar26) s.eVar26 =3D s.prop26; //Content ID
	if(s.channel && !s.eVar27) s.eVar27 =3D s.channel; //Site Section
	if(s.pageName && !s.eVar41) s.eVar41 =3D s.pageName; //Page Name

}
s.doPlugins=3Ds_doPlugins
/************************** PLUGINS SECTION *************************/
/* You may insert any plugins you wish to use here.                 */


/* WARNING: Changing any of the below variables will cause drastic
changes to how your visitor data is collected.  Changes should only be
made when instructed to do so by your account manager.*/
s.visitorNamespace=3D"nih"
s.trackingServer=3D"a.ncbi.nlm.nih.gov"
s.dc=3D122

/*
 * Plugin: getAndPersistValue 0.3 - get a value on every page
 */
s.getAndPersistValue=3Dnew Function("v","c","e",""
+"var s=3Dthis,a=3Dnew =
Date;e=3De?e:0;a.setTime(a.getTime()+e*86400000);if("
+"v)s.c_w(c,v,e?a:0);return s.c_r(c);");

/*
 * Plugin: getPageName v2.1 - parse URL and return
 */
s.getPageName=3Dnew Function("u",""
+"var =
s=3Dthis,v=3Du?u:''+s.wd.location,x=3Dv.indexOf(':'),y=3Dv.indexOf('/',"
+"x+4),z=3Dv.indexOf('?'),c=3Ds.pathConcatDelim,e=3Ds.pathExcludeDelim,g=3D=
s."
+"queryVarsList,d=3Ds.siteID,n=3Dd?d:'',q=3Dz<0?'':v.substring(z+1),p=3Dv=
.sub"
+"string(y+1,q?z:v.length);z=3Dp.indexOf('#');p=3Dz<0?p:s.fl(p,z);x=3De?p=
.i"
+"ndexOf(e):-1;p=3Dx<0?p:s.fl(p,x);p+=3D!p||p.charAt(p.length-1)=3D=3D'/'=
?s.d"
+"efaultPage:'';y=3Dc?c:'/';while(p){x=3Dp.indexOf('/');x=3Dx<0?p.length:=
x;"
+"z=3Ds.fl(p,x);if(!s.pt(s.pathExcludeList,',','p_c',z))n+=3Dn?y+z:z;p=3D=
p."
+"substring(x+1)}y=3Dc?c:'?';while(g){x=3Dg.indexOf(',');x=3Dx<0?g.length=
:x"
+";z=3Ds.fl(g,x);z=3Ds.pt(q,'&','p_c',z);if(z){n+=3Dn?y+z:z;y=3Dc?c:'&'}g=
=3Dg.s"
+"ubstring(x+1)}return n");

/*
 * Utility Function: p_c
 */
s.p_c=3Dnew Function("v","c",""
+"var x=3Dv.indexOf('=3D');return =
c.toLowerCase()=3D=3Dv.substring(0,x<0?v.le"
+"ngth:x).toLowerCase()?v:0");


/*
 * Utility Function: split v1.5 - split a string (JS 1.0 compatible)
 */
s.split=3Dnew Function("l","d",""
+"var i,x=3D0,a=3Dnew =
Array;while(l){i=3Dl.indexOf(d);i=3Di>-1?i:l.length;a[x"
+"++]=3Dl.substring(0,i);l=3Dl.substring(i+d.length);}return a");

/*
 * Plugin: getQueryParam 2.3
 */
s.getQueryParam=3Dnew Function("p","d","u",""
+"var =
s=3Dthis,v=3D'',i,t;d=3Dd?d:'';u=3Du?u:(s.pageURL?s.pageURL:s.wd.locati"
+"on);if(u=3D=3D'f')u=3Ds.gtfs().location;while(p){i=3Dp.indexOf(',');i=3D=
i<0?p"
+".length:i;t=3Ds.p_gpv(p.substring(0,i),u+'');if(t){t=3Dt.indexOf('#')>-=
"
+"1?t.substring(0,t.indexOf('#')):t;}if(t)v+=3Dv?d+t:t;p=3Dp.substring(i=3D=
"
+"=3Dp.length?i:i+1)}return v");
s.p_gpv=3Dnew Function("k","u",""
+"var =
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/*
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/*
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/*
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