tag:blogger.com,1999:blog-5952438689226645702024-03-05T05:23:32.335-08:00Datta AnalysisRuchira Dattahttp://www.blogger.com/profile/11225230326635564528noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-595243868922664570.post-25399583323963513702016-06-15T20:55:00.001-07:002016-06-15T20:55:46.131-07:00Spring Work<div dir="ltr" style="text-align: left;" trbidi="on">
<!--[if gte mso 9]><xml>
<o:DocumentProperties>
<o:Revision>0</o:Revision>
<o:TotalTime>0</o:TotalTime>
<o:Pages>1</o:Pages>
<o:Words>12</o:Words>
<o:Characters>74</o:Characters>
<o:Company>University of California at Berkeley</o:Company>
<o:Lines>1</o:Lines>
<o:Paragraphs>1</o:Paragraphs>
<o:CharactersWithSpaces>85</o:CharactersWithSpaces>
<o:Version>14.0</o:Version>
</o:DocumentProperties>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]-->
<!--[if gte mso 9]><xml>
<w:WordDocument>
<w:View>Normal</w:View>
<w:Zoom>0</w:Zoom>
<w:TrackMoves/>
<w:TrackFormatting/>
<w:PunctuationKerning/>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:DoNotPromoteQF/>
<w:LidThemeOther>EN-US</w:LidThemeOther>
<w:LidThemeAsian>JA</w:LidThemeAsian>
<w:LidThemeComplexScript>X-NONE</w:LidThemeComplexScript>
<w:Compatibility>
<w:BreakWrappedTables/>
<w:SnapToGridInCell/>
<w:WrapTextWithPunct/>
<w:UseAsianBreakRules/>
<w:DontGrowAutofit/>
<w:SplitPgBreakAndParaMark/>
<w:EnableOpenTypeKerning/>
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
<w:UseFELayout/>
</w:Compatibility>
<m:mathPr>
<m:mathFont m:val="Cambria Math"/>
<m:brkBin m:val="before"/>
<m:brkBinSub m:val="--"/>
<m:smallFrac m:val="off"/>
<m:dispDef/>
<m:lMargin m:val="0"/>
<m:rMargin m:val="0"/>
<m:defJc m:val="centerGroup"/>
<m:wrapIndent m:val="1440"/>
<m:intLim m:val="subSup"/>
<m:naryLim m:val="undOvr"/>
</m:mathPr></w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" DefUnhideWhenUsed="true"
DefSemiHidden="true" DefQFormat="false" DefPriority="99"
LatentStyleCount="276">
<w:LsdException Locked="false" Priority="0" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Normal"/>
<w:LsdException Locked="false" Priority="9" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="heading 1"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 2"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 3"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 4"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 5"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 6"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 7"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 8"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 9"/>
<w:LsdException Locked="false" Priority="39" Name="toc 1"/>
<w:LsdException Locked="false" Priority="39" Name="toc 2"/>
<w:LsdException Locked="false" Priority="39" Name="toc 3"/>
<w:LsdException Locked="false" Priority="39" Name="toc 4"/>
<w:LsdException Locked="false" Priority="39" Name="toc 5"/>
<w:LsdException Locked="false" Priority="39" Name="toc 6"/>
<w:LsdException Locked="false" Priority="39" Name="toc 7"/>
<w:LsdException Locked="false" Priority="39" Name="toc 8"/>
<w:LsdException Locked="false" Priority="39" Name="toc 9"/>
<w:LsdException Locked="false" Priority="35" QFormat="true" Name="caption"/>
<w:LsdException Locked="false" Priority="10" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Title"/>
<w:LsdException Locked="false" Priority="1" Name="Default Paragraph Font"/>
<w:LsdException Locked="false" Priority="11" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtitle"/>
<w:LsdException Locked="false" Priority="22" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" Priority="59" SemiHidden="false"
UnhideWhenUsed="false" Name="Table Grid"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Placeholder Text"/>
<w:LsdException Locked="false" Priority="1" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="No Spacing"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Revision"/>
<w:LsdException Locked="false" Priority="34" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="List Paragraph"/>
<w:LsdException Locked="false" Priority="29" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Quote"/>
<w:LsdException Locked="false" Priority="30" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Quote"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 1"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 1"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 1"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 1"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 1"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 1"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 1"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 2"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 2"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 2"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 2"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 2"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 2"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 2"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 2"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 2"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 2"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 2"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 3"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 3"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 3"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 3"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 3"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 3"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 3"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 3"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 3"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 3"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 3"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 3"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 3"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 4"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 4"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 4"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 4"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 4"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 4"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 4"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 4"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 4"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 4"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 4"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 4"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 4"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 4"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 5"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 5"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 5"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 5"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 5"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 5"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 5"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 5"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 5"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 5"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 5"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 5"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 5"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 5"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 6"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 6"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 6"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 6"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 6"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/>
<w:LsdException Locked="false" Priority="19" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/>
<w:LsdException Locked="false" Priority="21" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/>
<w:LsdException Locked="false" Priority="31" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/>
<w:LsdException Locked="false" Priority="32" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/>
<w:LsdException Locked="false" Priority="33" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Book Title"/>
<w:LsdException Locked="false" Priority="37" Name="Bibliography"/>
<w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/>
</w:LatentStyles>
</xml><![endif]-->
<!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:"Table Normal";
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-priority:99;
mso-style-parent:"";
mso-padding-alt:0in 5.4pt 0in 5.4pt;
mso-para-margin:0in;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:11.0pt;
font-family:Arial;
mso-fareast-language:JA;}
</style>
<![endif]-->
<!--StartFragment-->
<!--EndFragment--><br />
<div align="center" class="MsoNormal" style="text-align: center;">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Gentium Book Basic";">Quantitative Modeling of
Signaling Interactions in the Breast Tumor Microenvironment</span><br /></b></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Gentium Book Basic";">Specific Aims<o:p></o:p></span></b></div>
<div align="center" class="MsoNormal" style="text-align: center;">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Gentium Book Basic";"><o:p></o:p></span></b></div>
<div style="text-align: left;">
<!--[if gte mso 9]><xml>
<o:DocumentProperties>
<o:Revision>0</o:Revision>
<o:TotalTime>0</o:TotalTime>
<o:Pages>1</o:Pages>
<o:Words>351</o:Words>
<o:Characters>2002</o:Characters>
<o:Company>University of California at Berkeley</o:Company>
<o:Lines>16</o:Lines>
<o:Paragraphs>4</o:Paragraphs>
<o:CharactersWithSpaces>2349</o:CharactersWithSpaces>
<o:Version>14.0</o:Version>
</o:DocumentProperties>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]-->
<!--[if gte mso 9]><xml>
<w:WordDocument>
<w:View>Normal</w:View>
<w:Zoom>0</w:Zoom>
<w:TrackMoves/>
<w:TrackFormatting/>
<w:PunctuationKerning/>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:DoNotPromoteQF/>
<w:LidThemeOther>EN-US</w:LidThemeOther>
<w:LidThemeAsian>JA</w:LidThemeAsian>
<w:LidThemeComplexScript>X-NONE</w:LidThemeComplexScript>
<w:Compatibility>
<w:BreakWrappedTables/>
<w:SnapToGridInCell/>
<w:WrapTextWithPunct/>
<w:UseAsianBreakRules/>
<w:DontGrowAutofit/>
<w:SplitPgBreakAndParaMark/>
<w:EnableOpenTypeKerning/>
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
<w:UseFELayout/>
</w:Compatibility>
<m:mathPr>
<m:mathFont m:val="Cambria Math"/>
<m:brkBin m:val="before"/>
<m:brkBinSub m:val="--"/>
<m:smallFrac m:val="off"/>
<m:dispDef/>
<m:lMargin m:val="0"/>
<m:rMargin m:val="0"/>
<m:defJc m:val="centerGroup"/>
<m:wrapIndent m:val="1440"/>
<m:intLim m:val="subSup"/>
<m:naryLim m:val="undOvr"/>
</m:mathPr></w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" DefUnhideWhenUsed="true"
DefSemiHidden="true" DefQFormat="false" DefPriority="99"
LatentStyleCount="276">
<w:LsdException Locked="false" Priority="0" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Normal"/>
<w:LsdException Locked="false" Priority="9" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="heading 1"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 2"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 3"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 4"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 5"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 6"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 7"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 8"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 9"/>
<w:LsdException Locked="false" Priority="39" Name="toc 1"/>
<w:LsdException Locked="false" Priority="39" Name="toc 2"/>
<w:LsdException Locked="false" Priority="39" Name="toc 3"/>
<w:LsdException Locked="false" Priority="39" Name="toc 4"/>
<w:LsdException Locked="false" Priority="39" Name="toc 5"/>
<w:LsdException Locked="false" Priority="39" Name="toc 6"/>
<w:LsdException Locked="false" Priority="39" Name="toc 7"/>
<w:LsdException Locked="false" Priority="39" Name="toc 8"/>
<w:LsdException Locked="false" Priority="39" Name="toc 9"/>
<w:LsdException Locked="false" Priority="35" QFormat="true" Name="caption"/>
<w:LsdException Locked="false" Priority="10" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Title"/>
<w:LsdException Locked="false" Priority="1" Name="Default Paragraph Font"/>
<w:LsdException Locked="false" Priority="11" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtitle"/>
<w:LsdException Locked="false" Priority="22" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" Priority="59" SemiHidden="false"
UnhideWhenUsed="false" Name="Table Grid"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Placeholder Text"/>
<w:LsdException Locked="false" Priority="1" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="No Spacing"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Revision"/>
<w:LsdException Locked="false" Priority="34" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="List Paragraph"/>
<w:LsdException Locked="false" Priority="29" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Quote"/>
<w:LsdException Locked="false" Priority="30" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Quote"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 1"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 1"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 1"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 1"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 1"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 1"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 1"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 2"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 2"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 2"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 2"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 2"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 2"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 2"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 2"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 2"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 2"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 2"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 3"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 3"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 3"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 3"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 3"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 3"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 3"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 3"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 3"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 3"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 3"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 3"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 3"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 4"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 4"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 4"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 4"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 4"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 4"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 4"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 4"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 4"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 4"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 4"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 4"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 4"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 4"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 5"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 5"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 5"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 5"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 5"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 5"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 5"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 5"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 5"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 5"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 5"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 5"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 5"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 5"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 6"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 6"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 6"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 6"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 6"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/>
<w:LsdException Locked="false" Priority="19" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/>
<w:LsdException Locked="false" Priority="21" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/>
<w:LsdException Locked="false" Priority="31" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/>
<w:LsdException Locked="false" Priority="32" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/>
<w:LsdException Locked="false" Priority="33" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Book Title"/>
<w:LsdException Locked="false" Priority="37" Name="Bibliography"/>
<w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/>
</w:LatentStyles>
</xml><![endif]-->
<!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:"Table Normal";
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-priority:99;
mso-style-parent:"";
mso-padding-alt:0in 5.4pt 0in 5.4pt;
mso-para-margin:0in;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:11.0pt;
font-family:Arial;
mso-fareast-language:JA;}
</style>
<![endif]-->
<!--StartFragment-->
<div class="MsoNormal">
<b><span style="font-family: "Gentium Book Basic";"><br />
<u>Aim 1</u>: Identify sets of stromal-epithelial interactions that suggest
candidate hypotheses for the causal mechanisms through which stroma expression
levels can affect tumor functions.<br />
<br />
<u>Aim 2</u>: Identify modules in the stromal-epithelial signaling network that
are conserved between mouse and human, supporting the assignment of degrees of
confidence to predictions regarding human disease made based on mouse models.<br />
<br />
<u>Aim 3</u>: Integrate candidate causal mechanisms through which stroma
expression levels can affect tumor functions into one or more stochastic models
and use these to develop statistical measures that can distinguish or reject
these alternative hypotheses based on experimental data that can be feasibly
obtained.<o:p></o:p></span></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b><span style="font-family: "Gentium Book Basic";">Data I was given<o:p></o:p></span></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">I was given mouse
mammary transcriptome data. Breast tissue had been collected from 8 week old
virgin Fvb/N mice, under four conditions: either wild type ErbB2 or mutant
ErbB2, combined with either normal PTEN or conditional knockout of PTEN in the
fibroblasts only. This tissue had been
separated into four cell types: epithelial cells, fibroblasts, macrophages, and
endothelial cells. Then microarrays were used to probe the expression levels of
17548 genes. Among different probes for the same gene, the one with the maximum
value had been chosen as the representative entry in the data that I have. If different probes reflected different
isoforms of the same gene, this information has been lost in the file I have.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">I was given
mouse mammary fibroblast secretome data.
Mouse mammary fibroblasts, with either normal PTEN or PTEN knockout,
were cultured. The medium was collected and proteomics were run to determine
which proteins were present. I was given the names of 67 genes whose protein
products were secreted in both the normal and PTEN knockout conditions, and 54
other genes whose protein products were detected only in the PTEN knockout
condition. <br />
<br />
These are the two datasets to be used for Aim 1.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">I was given
gene expression data from tumor epithelial cells and from matched adjacent
stromal cells from 123 human breast cancer patients. In this case the expression levels were
obtained by averaging the microarray probes in those cases where there were
multiple probes (as I interpret the note: “Technical replicates averaged. There
are multiple probes for some genes.”)<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";"><br /></span></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">I was given exome
data from 21 of the human breast cancer patients, of which 12 had matched tumor
and normal samples and 9 had only tumor samples.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">These are the
two datasets to be used in conjunction with the previous two, for Aim 2.<span style="mso-spacerun: yes;"> </span>The results of Aims 1 and 2 are to be
integrated for Aim 3.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">Most of the
transcripts in the mouse transcriptome data have protein products and some are
noncoding RNAs. The same is true of the patient transcriptome data.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: "Gentium Book Basic";">What I have done<o:p></o:p></span></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<!--[if gte mso 9]><xml>
<o:DocumentProperties>
<o:Revision>0</o:Revision>
<o:TotalTime>0</o:TotalTime>
<o:Pages>1</o:Pages>
<o:Words>215</o:Words>
<o:Characters>1231</o:Characters>
<o:Company>University of California at Berkeley</o:Company>
<o:Lines>10</o:Lines>
<o:Paragraphs>2</o:Paragraphs>
<o:CharactersWithSpaces>1444</o:CharactersWithSpaces>
<o:Version>14.0</o:Version>
</o:DocumentProperties>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]-->
<!--[if gte mso 9]><xml>
<w:WordDocument>
<w:View>Normal</w:View>
<w:Zoom>0</w:Zoom>
<w:TrackMoves/>
<w:TrackFormatting/>
<w:PunctuationKerning/>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:DoNotPromoteQF/>
<w:LidThemeOther>EN-US</w:LidThemeOther>
<w:LidThemeAsian>JA</w:LidThemeAsian>
<w:LidThemeComplexScript>X-NONE</w:LidThemeComplexScript>
<w:Compatibility>
<w:BreakWrappedTables/>
<w:SnapToGridInCell/>
<w:WrapTextWithPunct/>
<w:UseAsianBreakRules/>
<w:DontGrowAutofit/>
<w:SplitPgBreakAndParaMark/>
<w:EnableOpenTypeKerning/>
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
<w:UseFELayout/>
</w:Compatibility>
<m:mathPr>
<m:mathFont m:val="Cambria Math"/>
<m:brkBin m:val="before"/>
<m:brkBinSub m:val="--"/>
<m:smallFrac m:val="off"/>
<m:dispDef/>
<m:lMargin m:val="0"/>
<m:rMargin m:val="0"/>
<m:defJc m:val="centerGroup"/>
<m:wrapIndent m:val="1440"/>
<m:intLim m:val="subSup"/>
<m:naryLim m:val="undOvr"/>
</m:mathPr></w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" DefUnhideWhenUsed="true"
DefSemiHidden="true" DefQFormat="false" DefPriority="99"
LatentStyleCount="276">
<w:LsdException Locked="false" Priority="0" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Normal"/>
<w:LsdException Locked="false" Priority="9" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="heading 1"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 2"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 3"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 4"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 5"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 6"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 7"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 8"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 9"/>
<w:LsdException Locked="false" Priority="39" Name="toc 1"/>
<w:LsdException Locked="false" Priority="39" Name="toc 2"/>
<w:LsdException Locked="false" Priority="39" Name="toc 3"/>
<w:LsdException Locked="false" Priority="39" Name="toc 4"/>
<w:LsdException Locked="false" Priority="39" Name="toc 5"/>
<w:LsdException Locked="false" Priority="39" Name="toc 6"/>
<w:LsdException Locked="false" Priority="39" Name="toc 7"/>
<w:LsdException Locked="false" Priority="39" Name="toc 8"/>
<w:LsdException Locked="false" Priority="39" Name="toc 9"/>
<w:LsdException Locked="false" Priority="35" QFormat="true" Name="caption"/>
<w:LsdException Locked="false" Priority="10" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Title"/>
<w:LsdException Locked="false" Priority="1" Name="Default Paragraph Font"/>
<w:LsdException Locked="false" Priority="11" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtitle"/>
<w:LsdException Locked="false" Priority="22" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" Priority="59" SemiHidden="false"
UnhideWhenUsed="false" Name="Table Grid"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Placeholder Text"/>
<w:LsdException Locked="false" Priority="1" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="No Spacing"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Revision"/>
<w:LsdException Locked="false" Priority="34" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="List Paragraph"/>
<w:LsdException Locked="false" Priority="29" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Quote"/>
<w:LsdException Locked="false" Priority="30" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Quote"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 1"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 1"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 1"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 1"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 1"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 1"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 1"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 2"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 2"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 2"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 2"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 2"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 2"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 2"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 2"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 2"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 2"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 2"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 3"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 3"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 3"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 3"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 3"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 3"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 3"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 3"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 3"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 3"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 3"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 3"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 3"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 4"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 4"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 4"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 4"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 4"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 4"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 4"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 4"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 4"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 4"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 4"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 4"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 4"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 4"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 5"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 5"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 5"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 5"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 5"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 5"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 5"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 5"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 5"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 5"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 5"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 5"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 5"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 5"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 6"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 6"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 6"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 6"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 6"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/>
<w:LsdException Locked="false" Priority="19" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/>
<w:LsdException Locked="false" Priority="21" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/>
<w:LsdException Locked="false" Priority="31" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/>
<w:LsdException Locked="false" Priority="32" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/>
<w:LsdException Locked="false" Priority="33" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Book Title"/>
<w:LsdException Locked="false" Priority="37" Name="Bibliography"/>
<w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/>
</w:LatentStyles>
</xml><![endif]-->
<!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:"Table Normal";
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-priority:99;
mso-style-parent:"";
mso-padding-alt:0in 5.4pt 0in 5.4pt;
mso-para-margin:0in;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:11.0pt;
font-family:Arial;
mso-fareast-language:JA;}
</style>
<![endif]-->
<!--StartFragment-->
<span style="font-family: "Gentium Book Basic"; font-size: 11.0pt; mso-ansi-language: EN-US; mso-bidi-font-family: Arial; mso-bidi-language: AR-SA; mso-fareast-font-family: "MS 明朝"; mso-fareast-language: JA; mso-fareast-theme-font: minor-fareast;">I have
mapped the gene names used in the mouse transcriptome data to currently used
gene names. I resolved most of these by
querying MGI. I resolved some by following up on deprecated Ensembl transcript
ids, resolving genes with two possible current symbols using the chromosomal
location in the data file, following the
history of changed Entrez gene ids, looking on Vesiclepedia, and using the
Ensembl transcript ids. I mapped most of the genes to Ensembl gene ids and
Uniprot accessions. The gene Hist2h2aa1 appeared twice in the transcriptome
data files, on the + and – strands of chr3.
I edited my copy of the data files to reflect that Hist2h2aa1 is on the
+ strand and Hist2h2aa2 is on the – strand. <br />
<br />
I need to similarly update the nomenclature for the human genes in the McGill
transcriptome data. <br />
<br />
I extracted the human orthologs of the mouse genes from the Ensembl ortholog
files, as Ensembl protein ids for proteins and Ensembl transcript ids for
genes.<br />
<!--[if !supportLineBreakNewLine]--><br />
<!--[endif]--></span><!--EndFragment--></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">I ran the
first step of the exome analysis pipeline I was given, FastQC, on the exome
data. I looked at the results of FastQC (although this did not seem to be part
of the protocol) and found that some sort of unidentified adapters had been
left in the data.<span style="mso-spacerun: yes;"> </span>Upon reviewing the
literature I chose PEAT (Paired End Adapter Trimming) for trimming adapters as
it requires no a priori adapter sequence.<span style="mso-spacerun: yes;">
</span>FastQC also indicated quality dropoff at the ends of the reads.<span style="mso-spacerun: yes;"> </span>I used Sickle to trim the low-quality bases.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">I looked over
the steps in the exome analysis pipeline I was given and noticed that some of
them seemed to use outdated methods.<span style="mso-spacerun: yes;"> </span>For
instance, bwa aln was included in the pipeline, whereas bwa mem has been
recommended for read lengths longer than 70 base pairs for several years.<span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>Furthermore,
disk space was at a premium on the OSC cluster. Modern next-generation
sequencing pipelines pipe intermediate results in memory from one process to
the next for several steps, saving on intermediate steps.<span style="mso-spacerun: yes;"> </span>I switched to the Blue Collar Bioinformatics
suite, developed at the Harvard School of Public Health and now widely used for
many bioinformatics tasks and began running it. This suite includes a standard
pipeline for variant calling of matched tumor-normal samples. As given, this
requires running one job for each sample that pools all lanes of the tumor
sequence and all lanes of the normal sequence.<span style="mso-spacerun: yes;">
</span>This seems to require tinkering with the resource allocation when
submitting the job to OSC, such that the job is not killed in the middle of
alignment, yet the resource allocation is not so large that the scheduler never
schedules it. Another alternative is to downsample each tumor and normal exome
sample. I asked Xing Tang for help with all this when she has time.<span style="mso-spacerun: yes;"> </span>The Blue Collar Bioinformatics blog also
describes a suggested analysis for tumor-only samples.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">Tuncbag et al
developed a method “Simultaneous Reconstruction of Signaling Pathways Using
Prize-Collecting Steiner Forests” that, given a set of proteins thought to be
involved in a signaling process within a cell, uses biological network data to
hypothesize what other proteins might be involved in this process.<span style="mso-spacerun: yes;"> </span>They use a message-passing algorithm from
Bayesian networks.<span style="mso-spacerun: yes;"> </span>I developed a novel
plate model (plate models are used in probabilistic graphical models) to extend
this from cell-autonomous processes to intercellular processes, in order to span
intercellularly between cells of different types (e.g., epithelial cells and
fibroblasts) as well as in the extracellular space.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<!--[if gte mso 9]><xml>
<o:DocumentProperties>
<o:Revision>0</o:Revision>
<o:TotalTime>0</o:TotalTime>
<o:Pages>1</o:Pages>
<o:Words>481</o:Words>
<o:Characters>2745</o:Characters>
<o:Company>University of California at Berkeley</o:Company>
<o:Lines>22</o:Lines>
<o:Paragraphs>6</o:Paragraphs>
<o:CharactersWithSpaces>3220</o:CharactersWithSpaces>
<o:Version>14.0</o:Version>
</o:DocumentProperties>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]-->
<!--[if gte mso 9]><xml>
<w:WordDocument>
<w:View>Normal</w:View>
<w:Zoom>0</w:Zoom>
<w:TrackMoves/>
<w:TrackFormatting/>
<w:PunctuationKerning/>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:DoNotPromoteQF/>
<w:LidThemeOther>EN-US</w:LidThemeOther>
<w:LidThemeAsian>JA</w:LidThemeAsian>
<w:LidThemeComplexScript>X-NONE</w:LidThemeComplexScript>
<w:Compatibility>
<w:BreakWrappedTables/>
<w:SnapToGridInCell/>
<w:WrapTextWithPunct/>
<w:UseAsianBreakRules/>
<w:DontGrowAutofit/>
<w:SplitPgBreakAndParaMark/>
<w:EnableOpenTypeKerning/>
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
<w:UseFELayout/>
</w:Compatibility>
<m:mathPr>
<m:mathFont m:val="Cambria Math"/>
<m:brkBin m:val="before"/>
<m:brkBinSub m:val="--"/>
<m:smallFrac m:val="off"/>
<m:dispDef/>
<m:lMargin m:val="0"/>
<m:rMargin m:val="0"/>
<m:defJc m:val="centerGroup"/>
<m:wrapIndent m:val="1440"/>
<m:intLim m:val="subSup"/>
<m:naryLim m:val="undOvr"/>
</m:mathPr></w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" DefUnhideWhenUsed="true"
DefSemiHidden="true" DefQFormat="false" DefPriority="99"
LatentStyleCount="276">
<w:LsdException Locked="false" Priority="0" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Normal"/>
<w:LsdException Locked="false" Priority="9" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="heading 1"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 2"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 3"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 4"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 5"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 6"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 7"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 8"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 9"/>
<w:LsdException Locked="false" Priority="39" Name="toc 1"/>
<w:LsdException Locked="false" Priority="39" Name="toc 2"/>
<w:LsdException Locked="false" Priority="39" Name="toc 3"/>
<w:LsdException Locked="false" Priority="39" Name="toc 4"/>
<w:LsdException Locked="false" Priority="39" Name="toc 5"/>
<w:LsdException Locked="false" Priority="39" Name="toc 6"/>
<w:LsdException Locked="false" Priority="39" Name="toc 7"/>
<w:LsdException Locked="false" Priority="39" Name="toc 8"/>
<w:LsdException Locked="false" Priority="39" Name="toc 9"/>
<w:LsdException Locked="false" Priority="35" QFormat="true" Name="caption"/>
<w:LsdException Locked="false" Priority="10" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Title"/>
<w:LsdException Locked="false" Priority="1" Name="Default Paragraph Font"/>
<w:LsdException Locked="false" Priority="11" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtitle"/>
<w:LsdException Locked="false" Priority="22" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" Priority="59" SemiHidden="false"
UnhideWhenUsed="false" Name="Table Grid"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Placeholder Text"/>
<w:LsdException Locked="false" Priority="1" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="No Spacing"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Revision"/>
<w:LsdException Locked="false" Priority="34" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="List Paragraph"/>
<w:LsdException Locked="false" Priority="29" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Quote"/>
<w:LsdException Locked="false" Priority="30" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Quote"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 1"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 1"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 1"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 1"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 1"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 1"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 1"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 2"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 2"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 2"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 2"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 2"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 2"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 2"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 2"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 2"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 2"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 2"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 3"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 3"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 3"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 3"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 3"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 3"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 3"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 3"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 3"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 3"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 3"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 3"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 3"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 4"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 4"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 4"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 4"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 4"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 4"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 4"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 4"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 4"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 4"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 4"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 4"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 4"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 4"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 5"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 5"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 5"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 5"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 5"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 5"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 5"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 5"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 5"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 5"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 5"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 5"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 5"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 5"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 6"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 6"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 6"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 6"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 6"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/>
<w:LsdException Locked="false" Priority="19" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/>
<w:LsdException Locked="false" Priority="21" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/>
<w:LsdException Locked="false" Priority="31" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/>
<w:LsdException Locked="false" Priority="32" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/>
<w:LsdException Locked="false" Priority="33" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Book Title"/>
<w:LsdException Locked="false" Priority="37" Name="Bibliography"/>
<w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/>
</w:LatentStyles>
</xml><![endif]-->
<!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:"Table Normal";
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-priority:99;
mso-style-parent:"";
mso-padding-alt:0in 5.4pt 0in 5.4pt;
mso-para-margin:0in;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:11.0pt;
font-family:Arial;
mso-fareast-language:JA;}
</style>
<![endif]-->
<!--StartFragment-->
<span style="font-family: "Gentium Book Basic"; font-size: 11.0pt; mso-ansi-language: EN-US; mso-bidi-font-family: Arial; mso-bidi-language: AR-SA; mso-fareast-font-family: "MS 明朝"; mso-fareast-language: JA; mso-fareast-theme-font: minor-fareast;">I have
downloaded the msgsteiner and OmicsIntegrator software from the Tuncbag et al
paper. I am modifying it to work intercellularly using my plate model. Also, it comes with generic protein-protein
interaction data. I will incorporate the ligand-receptor database used by Fuhai
Li in his CCCExplorer, and also the dbPTM database of post-translational
modifications of proteins, such as phosphorylation. Their method uses epigenome data to constrain
the possible transcription factors that might be hypothesized. I have found epigenome
data from mouse mammary luminal cells of virgin Fvb/N mice, and mouse dermal
fibroblast cells of Balb/c mice.<br />
<br />
<!--[if !supportLineBreakNewLine]--></span>
<!--[if gte mso 9]><xml>
<o:DocumentProperties>
<o:Revision>0</o:Revision>
<o:TotalTime>0</o:TotalTime>
<o:Pages>1</o:Pages>
<o:Words>388</o:Words>
<o:Characters>2214</o:Characters>
<o:Company>University of California at Berkeley</o:Company>
<o:Lines>18</o:Lines>
<o:Paragraphs>5</o:Paragraphs>
<o:CharactersWithSpaces>2597</o:CharactersWithSpaces>
<o:Version>14.0</o:Version>
</o:DocumentProperties>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]-->
<!--[if gte mso 9]><xml>
<w:WordDocument>
<w:View>Normal</w:View>
<w:Zoom>0</w:Zoom>
<w:TrackMoves/>
<w:TrackFormatting/>
<w:PunctuationKerning/>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:DoNotPromoteQF/>
<w:LidThemeOther>EN-US</w:LidThemeOther>
<w:LidThemeAsian>JA</w:LidThemeAsian>
<w:LidThemeComplexScript>X-NONE</w:LidThemeComplexScript>
<w:Compatibility>
<w:BreakWrappedTables/>
<w:SnapToGridInCell/>
<w:WrapTextWithPunct/>
<w:UseAsianBreakRules/>
<w:DontGrowAutofit/>
<w:SplitPgBreakAndParaMark/>
<w:EnableOpenTypeKerning/>
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
<w:UseFELayout/>
</w:Compatibility>
<m:mathPr>
<m:mathFont m:val="Cambria Math"/>
<m:brkBin m:val="before"/>
<m:brkBinSub m:val="--"/>
<m:smallFrac m:val="off"/>
<m:dispDef/>
<m:lMargin m:val="0"/>
<m:rMargin m:val="0"/>
<m:defJc m:val="centerGroup"/>
<m:wrapIndent m:val="1440"/>
<m:intLim m:val="subSup"/>
<m:naryLim m:val="undOvr"/>
</m:mathPr></w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" DefUnhideWhenUsed="true"
DefSemiHidden="true" DefQFormat="false" DefPriority="99"
LatentStyleCount="276">
<w:LsdException Locked="false" Priority="0" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Normal"/>
<w:LsdException Locked="false" Priority="9" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="heading 1"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 2"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 3"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 4"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 5"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 6"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 7"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 8"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 9"/>
<w:LsdException Locked="false" Priority="39" Name="toc 1"/>
<w:LsdException Locked="false" Priority="39" Name="toc 2"/>
<w:LsdException Locked="false" Priority="39" Name="toc 3"/>
<w:LsdException Locked="false" Priority="39" Name="toc 4"/>
<w:LsdException Locked="false" Priority="39" Name="toc 5"/>
<w:LsdException Locked="false" Priority="39" Name="toc 6"/>
<w:LsdException Locked="false" Priority="39" Name="toc 7"/>
<w:LsdException Locked="false" Priority="39" Name="toc 8"/>
<w:LsdException Locked="false" Priority="39" Name="toc 9"/>
<w:LsdException Locked="false" Priority="35" QFormat="true" Name="caption"/>
<w:LsdException Locked="false" Priority="10" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Title"/>
<w:LsdException Locked="false" Priority="1" Name="Default Paragraph Font"/>
<w:LsdException Locked="false" Priority="11" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtitle"/>
<w:LsdException Locked="false" Priority="22" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" Priority="59" SemiHidden="false"
UnhideWhenUsed="false" Name="Table Grid"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Placeholder Text"/>
<w:LsdException Locked="false" Priority="1" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="No Spacing"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Revision"/>
<w:LsdException Locked="false" Priority="34" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="List Paragraph"/>
<w:LsdException Locked="false" Priority="29" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Quote"/>
<w:LsdException Locked="false" Priority="30" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Quote"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 1"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 1"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 1"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 1"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 1"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 1"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 1"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 2"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 2"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 2"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 2"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 2"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 2"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 2"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 2"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 2"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 2"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 2"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 3"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 3"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 3"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 3"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 3"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 3"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 3"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 3"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 3"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 3"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 3"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 3"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 3"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 4"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 4"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 4"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 4"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 4"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 4"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 4"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 4"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 4"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 4"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 4"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 4"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 4"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 4"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 5"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 5"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 5"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 5"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 5"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 5"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 5"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 5"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 5"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 5"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 5"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 5"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 5"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 5"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 6"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 6"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 6"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 6"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 6"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/>
<w:LsdException Locked="false" Priority="19" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/>
<w:LsdException Locked="false" Priority="21" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/>
<w:LsdException Locked="false" Priority="31" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/>
<w:LsdException Locked="false" Priority="32" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/>
<w:LsdException Locked="false" Priority="33" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Book Title"/>
<w:LsdException Locked="false" Priority="37" Name="Bibliography"/>
<w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/>
</w:LatentStyles>
</xml><![endif]-->
<!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:"Table Normal";
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-priority:99;
mso-style-parent:"";
mso-padding-alt:0in 5.4pt 0in 5.4pt;
mso-para-margin:0in;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:11.0pt;
font-family:Arial;
mso-fareast-language:JA;}
</style>
<![endif]-->
<!--StartFragment-->
</div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">Once I have
incorporated the dbPTM database and the Li ligand-receptor database, I will try
the OmicsIntegrator method without the plate model on the fibroblast secretome
data alone. <o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">I attended as
a guest several sessions of the Pathology of Inflammation class taught by Traci
Wilgus. One key thing I learned is that
during wound healing, neutrophils that traffick to the wound don’t necessarily
all apoptose there as had previously been thought. In zebrafish, they have been
visualized trafficking back and forth repeatedly, to the wound and back out to
the blood vessel. Neutrophils have also
been imaged tethering one to another, i.e., a neutrophil grabs onto another
neutrophil. The class described the
several steps required for inflammatory cells to traffick from a blood vessel
to the wounded tissue: rolling with weak binding to the vessel wall via
selectins, activation with stronger binding to the vessel wall by integrins;
firm adhesion and crawling along the vessel wall, and transmigration through
the tissue along a chemokine gradient.
These steps require multiple specializations. I formulated a hypothesis,
which Wilgus thought novel, that the reverse trafficking of neutrophils back
out from the wound to the blood vessel may be in order to go fetch stem cells
from elsewhere. In this way the stem
cells would not require all the specializations that neutrophils have in order
to extravasate themselves; the neutrophils could carry them. If this were correct, and if macrophages do
the same thing, then the Tumor Microenvironment of Metastasis (TMEM) might be a
co-option of a similar process in
macrophages. In this case, understanding the gradients that lead the inflammatory
cells back to the wound carrying the stem cells could help illuminate the
reasons why metastasis occurs to particular sites, and what local and systemic
factors might affect when it occurs. <br />
<br />
I presented a poster at the T2C Wound Healing conference at OSU, constituting a
literature review of wound healing processes that might be related to
metastatic and post-metastatic cancer. I
found one novel connection.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: "Gentium Book Basic";">I learned
from Lisa Christian that the Experience Sampling Method is used in many studies
to track measurements of cytokine levels in the bloodstream of individual
patients, longitudinally or under different conditions, with clinical
variables. Data from such studies might be integrated into the model to be
developed in Aim 3, for instance to select the most useful molecules or
biomarkers to include in order to incorporate systemic factors affecting the
tumor microenvironment.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<!--EndFragment--><!--EndFragment--></div>
<div class="MsoNormal">
<br /></div>
<!--EndFragment--></div>
</div>
Ruchira Dattahttp://www.blogger.com/profile/11225230326635564528noreply@blogger.com0tag:blogger.com,1999:blog-595243868922664570.post-43336397230554598822014-07-08T04:54:00.001-07:002020-05-31T16:59:59.494-07:00A Nutritious Breakfast: Less Than 5 Minutes, No More Than $4<div dir="ltr" style="text-align: left;" trbidi="on">
Inspired by Lizzie Widdicombe's article <a href="http://www.newyorker.com/reporting/2014/05/12/140512fa_fact_widdicombe?currentPage=all">The End of Food</a> in the May 12, 2014 issue of the New Yorker, I recently set out on a quest to find a nutritious breakfast made up of foods I would normally eat.<br />
<br />
<h2 style="text-align: left;">
The Breakfasts</h2>
<br />
Let me start with the punchline. A breakfast of:<br />
<ul style="text-align: left;">
<li>1/2 cup instant dry Cream of Wheat prepared with 1 1/3 cups skim milk</li>
<li>1/4 cup (4 tbsp) sunflower seeds</li>
<li>3 tbsp pumpkin seeds</li>
<li>2 tbsp chia seeds (measured, then ground)</li>
<li>1 <a href="http://www.amazon.com/gp/product/B004LL7AXE/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B004LL7AXE&linkCode=as2&tag=httpwwwruchir-20&linkId=4K5LL5BZL227Z5F5" target="_blank">Ovega</a> capsule (to be sure of getting the recommended dietary omega-3 fatty acids EPA and DHA)</li>
<li>1 600 IU Vitamin D capsule</li>
<li>1 500μg Vitamin B12 tablet</li>
</ul>
is 884 calories and satisfies all the nutritional requirements in the USDA Daily Reference Intake except for Vitamin C, fiber, and calories. This breakfast's omega-6 to omega-3 ratio is below 4:1, and it provides 14.5g of total dietary fiber (whereas 25g is my recommended daily intake). I can get the remaining nutrients by eating fruits and vegetables throughout the day.<br />
<br />
I'm pleased that this breakfast is simple, quick, and tasty, and all the ingredients are easy to obtain. I've experimented with eating the seeds separately, or mixed in the Cream of Wheat; either way is fine.<br />
<br />
Pricing this out on Amazon:<br />
<ul style="text-align: left;">
<li>A <a href="http://www.amazon.com/gp/product/B0005YMKKE/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B0005YMKKE&linkCode=as2&tag=httpwwwruchir-20&linkId=GXLIDNQIVXIKLBBJ" target="_blank">12 oz. box of instant Cream of Wheat</a> currently costs $7.89. Twelve ounces is 336g. I'm using 89g (1/2 cup) in the above breakfast.</li>
<ul>
<li>The cost of the Cream of Wheat is $2.09.</li>
</ul>
<li>A half gallon of organic skim milk at <a href="http://www.naturalgrocery.com/retailer/store_templates/shell_id_1.asp?storeID=HEU5FKAQ17S92ND700AKHLBD34WUD8VB">my local natural grocery</a> currently costs $4.19. This is eight cups. I'm using 1 1/3 cups in the above breakfast.</li>
<ul>
<li>The cost of the skim milk is $0.70.</li>
</ul>
<li>A <a href="http://www.amazon.com/gp/product/B000ED9L6C/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B000ED9L6C&linkCode=as2&tag=httpwwwruchir-20&linkId=7MXJ2LLN4RZC6FDU" target="_blank">pack of four 20 oz. bags of Bob's Red Mill raw sunflower seeds</a> currently costs $12.60. Eighty ounces is 2240g. I'm using 35g (1/4 cup) in the above breakfast.</li>
<ul>
<li>The cost of the sunflower seeds is $0.20.</li>
</ul>
<li>A <a href="http://www.amazon.com/gp/product/B007NIXLEO/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B007NIXLEO&linkCode=as2&tag=httpwwwruchir-20&linkId=LYWXVCI5P55VOJTR" target="_blank">5 lb bag of Sincerely Nuts raw pumpkin seed kernels</a> currently costs $27.99. Eighty ounces is 2240g. I'm using 25.875g (9 tsp) in the above breakfast.</li>
<ul>
<li>The cost of the pumpkin seeds is $0.32.</li>
</ul>
<li>A <a href="http://www.amazon.com/gp/product/B00FJ4MLMW/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B00FJ4MLMW&linkCode=as2&tag=httpwwwruchir-20&linkId=EKEX3TOOAQRZTRVU" target="_blank">pair of 3 lb bags of Get Chia brand chia seeds</a> is currently $35.99. So 96 ounces is 2688g. I'm using 20.34g (6 tsp) in the above breakfast.</li>
<ul>
<li>The cost of the chia seeds is $0.27.</li>
</ul>
<li><a href="http://www.amazon.com/gp/product/B004LL7AXE/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B004LL7AXE&linkCode=as2&tag=httpwwwruchir-20&linkId=4K5LL5BZL227Z5F5" target="_blank">60 Ovega capsules</a> currently cost $15.73. I'm taking 1 capsule in the above breakfast.</li>
<ul>
<li>The cost of the Ovega capsule is $0.26.</li>
</ul>
<li><a href="http://www.amazon.com/gp/product/B00DG2YR8U/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B00DG2YR8U&linkCode=as2&tag=httpwwwruchir-20&linkId=RMYF3Z3BNU7WLUG4" target="_blank">120 Solgar 600 IU Vitamin D3 capsules</a> currently cost $10.63. I'm taking 1 capsule in the above breakfast.</li>
<ul>
<li>The cost of the Vitamin D capsule is $0.09.</li>
</ul>
<li><a href="http://www.amazon.com/gp/product/B00014E0YM/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B00014E0YM&linkCode=as2&tag=httpwwwruchir-20&linkId=NHA6DPET73WC3FRG" target="_blank">250 Solgar 500μg Vitamin B12 tablets</a> currently cost $18.38. I'm taking 1 tablet in the above breakfast.</li>
<ul>
<li>The cost of the Vitamin B12 tablet is $0.07.</li>
</ul>
<ul>
</ul>
</ul>
The total cost of this breakfast is $4.00.<br />
<br />
A vegan version of this breakfast:<br />
<ul style="text-align: left;">
<li>1/2 cup instant dry Cream of Wheat</li>
<li>1/4 cup (4 tbsp) sunflower seeds</li>
<li>8 tsp poppy seeds</li>
<li>6 tsp pumpkin seeds</li>
<li>8 tsp chia seeds (measured, then ground)</li>
<li>1 <a href="http://www.amazon.com/gp/product/B004LL7AXE/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B004LL7AXE&linkCode=as2&tag=httpwwwruchir-20&linkId=4K5LL5BZL227Z5F5" target="_blank">Ovega</a> capsule (to be sure of getting the recommended dietary omega-3 fatty acids EPA and DHA) </li>
<li>1 600 IU Vitamin D capsule</li>
<li>1 500μg Vitamin B12 tablet</li>
</ul>
is 884 calories and again satisfies all the nutritional requirements in the USDA Daily Reference Intake except for Vitamin C, fiber, possibly protein, a little carbohydrate, and calories. This breakfast's omega-6 to omega-3 ratio is below 4:1, and it provides 21g of total dietary fiber. (A word to the wise: rumor has it that consuming poppy seeds may cause you to fail a drug test. So if you need to undergo drug screening, you might want to keep this in mind.) Again, I can get the remaining nutrients by eating fruits and vegetables throughout the day.<br />
<br />
Pricing this out on Amazon:<br />
<ul style="text-align: left;">
<li>A <a href="http://www.amazon.com/gp/product/B000RHXK4Y/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B000RHXK4Y&linkCode=as2&tag=httpwwwruchir-20&linkId=DY2ODGOVW5YZQ6PP" target="_blank">10 lb bag of Angelina's Gourmet poppy seeds</a> is currently $31.99. So, 160 ounces is 4480g. I'm using 24g (8 tsp) of poppy seeds in the vegan breakfast.</li>
<ul>
<li>The cost of the poppy seeds is $0.17.</li>
</ul>
<li>Now I'm using 17.25g (6tsp) of pumpkin seeds, rather than 25.875g (9tsp).</li>
<ul>
<li>The cost of the pumpkin seeds is $0.22.</li>
</ul>
<li>Now I'm using 27.13g (8 tsp) of chia seeds, rather than 20.34g (6 tsp).</li>
<ul>
<li>The cost of the chia seeds is $0.36.</li>
</ul>
</ul>
The total cost of this vegan breakfast (including the other unchanged items from above) is $3.46.<br />
<br />
<h2 style="text-align: left;">
Synthesizing Breakfasts from Data</h2>
<br />
Now I'll explain a bit about how I came up with these breakfasts.<br />
<br />
<h3 style="text-align: left;">
Loading the Nutrition Data</h3>
<br />
First I downloaded the <a href="http://www.ars.usda.gov/Services/docs.htm?docid=23634">USDA nutritional database files</a>. Then I loaded the files into a <a href="http://www.postgresql.org/">PostgreSQL</a> database, using the <a href="https://github.com/echlebek/nutes">nutes</a> project that Eric Chlebek posted on Github. (A couple of minor details: I hand edited the paths to the USDA files which were hardcoded in <code>import.sql</code>, and I did the import as a superuser so the <code>COPY</code> commands in <code>import.sql</code> would work.)<br />
<br />
I also downloaded the <a href="http://www.iom.edu/Activities/Nutrition/SummaryDRIs/~/media/Files/Activity%20Files/Nutrition/DRIs/5_Summary%20Table%20Tables%201-4.pdf">Dietary Reference Intakes for Individuals</a> from the USDA. (It's beyond me why they provide these in a PDF rather than a spreadsheet.) I created a new table in my PostgreSQL database for this information:<br />
<br />
<pre>nutrition=> \d dietary_reference_intake
Table "public.dietary_reference_intake"
Column | Type | Modifiers
------------+------+-----------
kind | text |
life_stage | text |
nutr_no | text |
amount | real |
Foreign-key constraints:
"dietary_reference_intake_nutr_no_fkey" FOREIGN KEY (nutr_no) REFERENCES nutrients(nutr_no)</pre>
<br />
Here <code>nutr_no</code> is the primary key of the <code>nutrients</code> table. If I were doing the import again, I would edit <code>schema.sql</code> beforehand to make <code>nutr_no</code> an integer field instead of a text field.<br />
<br />
I populated the <code>dietary_reference_intake</code> table by hand using the information in the PDF. I only entered the information that's currently relevant to me:<br />
<br />
<pre>nutrition=> SELECT * FROM dietary_reference_intake;
life_stage | nutr_no | amount
------------+---------+--------
31-50 y | 301 | 800
31-50 y | 205 | 100
31-50 y | 320 | 500
31-50 y | 401 | 60
31-50 y | 328 | 10
31-50 y | 323 | 12
31-50 y | 404 | 0.9
31-50 y | 405 | 0.9
31-50 y | 406 | 11
31-50 y | 415 | 1.1
31-50 y | 417 | 320
31-50 y | 418 | 2
31-50 y | 303 | 8.1
31-50 y | 312 | 0.7
31-50 y | 304 | 265
31-50 y | 305 | 580
31-50 y | 317 | 45
31-50 y | 309 | 6.8
(18 rows)
</pre>
<br />
Here it is again joined with the <code>nutrients</code> table so you can verify that the <code>dietary_reference_intake</code> table matches what's in the PDF from the USDA:
<br />
<br />
<pre>nutrition=> SELECT i.nutr_no, i.amount, n.units, n.nutr_desc
nutrition-> FROM dietary_reference_intake as i, nutrients AS n
nutrition-> WHERE i.nutr_no = n.nutr_no;
nutr_no | amount | units | nutr_desc
---------+--------+-------+--------------------------------
301 | 800 | mg | Calcium, Ca
205 | 100 | g | Carbohydrate, by difference
320 | 500 | μg | Vitamin A, RAE
401 | 60 | mg | Vitamin C, total ascorbic acid
328 | 10 | μg | Vitamin D (D2 + D3)
323 | 12 | mg | Vitamin E (alpha-tocopherol)
404 | 0.9 | mg | Thiamin
405 | 0.9 | mg | Riboflavin
406 | 11 | mg | Niacin
415 | 1.1 | mg | Vitamin B-6
417 | 320 | μg | Folate, total
418 | 2 | μg | Vitamin B-12
303 | 8.1 | mg | Iron, Fe
312 | 0.7 | mg | Copper, Cu
304 | 265 | mg | Magnesium, Mg
305 | 580 | mg | Phosphorus, P
317 | 45 | μg | Selenium, Se
309 | 6.8 | mg | Zinc, Zn
(18 rows)
</pre>
<br />
NB: The units of copper in the Dietary Reference Intakes for Individuals PDF are μg, whereas the units of copper in the nutrient database are mg.<br />
<br />
I left out the protein requirement from this table as it depends on the mass of the individual. We'll check up on it below. Molybdenum and iodine are in the dietary reference intake, however they're not in the USDA nutrient database. Apparently molybdenum is in plenty of foods and the amount needed is minuscule; perhaps that's why they left it out. Iodine deficiency can be a real issue. Perhaps it was left out because its presence in foods is too variable? Iodized salt may take care of this requirement for many people.<br />
<br />
<h3 style="text-align: left;">
Finding Nutritional Information in the Database</h3>
<br />
<br />
Each food in the database is represented by an entry in the <code>foods</code> table, whose primary key is <code>ndb_no</code> (I guess that stands for Nutrient DataBase Number). To find out how much of a given nutrient is in 100g of a given food, we look at the corresponding <code>nutrition_value</code> entry in the <code>nutrient_data</code> table. For instance, how much niacin is in 100g of yeast extract spread?
<br />
<br />
<pre>nutrition=> SELECT d.ndb_no, d.nutr_no,
nutrition-> d.nutrition_value, n.units
nutrition-> FROM nutrient_data AS d,
nutrition-> foods AS f,
nutrition-> nutrients AS n
nutrition-> WHERE d.ndb_no = f.ndb_no
nutrition-> AND d.nutr_no = n.nutr_no
nutrition-> AND f.longdesc = 'Yeast extract spread'
nutrition-> AND n.nutr_desc = 'Niacin';
ndb_no | nutr_no | nutrition_value | units
--------+---------+-----------------+-------
43406 | 406 | 127.500 | mg
(1 row)</pre>
<br />
The <code>foods</code> table also lists the food group of each food, which is handy. Each entry in the <code>foods</code> table has a foreign key <code>foodgroup_code</code> referencing the <code>food_groups</code> table. Here is the <code>food_groups</code> table:<br />
<br />
<pre>nutrition=> SELECT * FROM food_groups;
foodgroup_code | foodgroup_desc
----------------+-------------------------------------
0100 | Dairy and Egg Products
0200 | Spices and Herbs
0300 | Baby Foods
0400 | Fats and Oils
0500 | Poultry Products
0600 | Soups, Sauces, and Gravies
0700 | Sausages and Luncheon Meats
0800 | Breakfast Cereals
0900 | Fruits and Fruit Juices
1000 | Pork Products
1100 | Vegetables and Vegetable Products
1200 | Nut and Seed Products
1300 | Beef Products
1400 | Beverages
1500 | Finfish and Shellfish Products
1600 | Legumes and Legume Products
1700 | Lamb, Veal, and Game Products
1800 | Baked Products
1900 | Sweets
2000 | Cereal Grains and Pasta
2100 | Fast Foods
2200 | Meals, Entrees, and Side Dishes
2500 | Snacks
3500 | American Indian/Alaska Native Foods
3600 | Restaurant Foods
(25 rows)
</pre>
<br />
<h3 style="text-align: left;">
Nutrient-dense Foods</h3>
<br />
<br />
Now, what are some possible dietary sources of, say, iron?<br />
<br />
<pre>nutrition=> SELECT round(
nutrition(> (i.amount / d.nutrition_value * 100)::numeric,
nutrition(> 1) AS amt,
nutrition-> f.longdesc
nutrition-> FROM dietary_reference_intake AS i,
nutrition-> nutrient_data AS d,
nutrition-> foods AS f,
nutrition-> nutrients AS n
nutrition-> WHERE i.nutr_no = d.nutr_no
nutrition-> AND d.ndb_no = f.ndb_no
nutrition-> AND d.nutr_no = n.nutr_no
nutrition-> AND n.nutr_desc = 'Iron, Fe'
nutrition-> AND d.nutrition_value > 0
nutrition-> AND f.foodgroup_code NOT IN
nutrition-> ('0400', '0500', '0700',
nutrition(> '1000', '1300', '1500',
nutrition(> '1700', '2500', '3500')
nutrition-> ORDER BY amt
nutrition-> LIMIT 10;
amt | longdesc
------+-------------------------------------------------------------------------
6.6 | Spices, thyme, dried
9.0 | Spices, basil, dried
9.3 | Spearmint, dried
9.8 | Spices, marjoram, dried
12.0 | Cereals ready-to-eat, Ralston Enriched Bran flakes
12.0 | Babyfood, cereal, oatmeal, with honey, dry
12.2 | Seaweed, Canadian Cultivated EMI-TSUNOMATA, dry
12.2 | Spices, cumin seed
13.0 | Cereals ready-to-eat, KELLOGG, KELLOGG'S ALL-BRAN COMPLETE Wheat Flakes
13.5 | Cereals ready-to-eat, GENERAL MILLS, Whole Grain TOTAL
(10 rows)
</pre>
<br />
This says that, for example, it would take 9g of dried basil to satisfy my entire dietary iron requirement for the day. We got this number as follows:
<br />
<br />
(amount of nutrient needed) <br />
÷ (amount of nutrient supplied per database serving of food)
<br />
= (database servings of food needed)
<br />
<br />
and
<br />
<br />
(database servings of food needed) * (100 g / database serving) = (g of food needed)
<br />
<br />
The amount of nutrient needed is <code>i.amount</code>, and the amount of nutrient supplied per database serving of food is <code>d.nutrition_value</code>, so the number of grams of food needed to supply the daily nutrient requirement is <code>i.amount/d.nutrition_value * 100</code>.
<br />
<br />
On the other hand, it would take only 6.6g of dried thyme to satisfy the same requirement, so thyme has more iron per gram than basil does.<br />
<br />
As we might expect, cereals with names like "Enriched", "Complete", and "Total" feature prominently. These cereals were designed with the nutrition-conscious marketing niche in mind. For various reasons, though, I would prefer hot cereal to cold cereal, so in other queries I excluded these by including <code>AND f.longdesc NOT LIKE 'Cereals ready-to-eat%'</code> in the <code>WHERE</code> clause.<br />
<br />
<h3 style="text-align: left;">
Selected Foods for Breakfast</h3>
<br />
<br />
By exploring each of the nutrients in the dietary reference intake with queries like this, I zeroed in on:<br />
<ul style="text-align: left;">
<li>Cream of Wheat (<code>ndb_no</code>: 08106) as a source of Vitamin A.</li>
<li>Sunflower seed kernels (<code>ndb_no</code>: 12036) as a source of Vitamin E.</li>
<li>Skim milk (<code>ndb_no</code>: 01151) as a source of calcium.</li>
<li>Poppy seeds (<code>ndb_no</code>: 02033) as a vegan source of calcium.</li>
<li>Pumpkin seed kernels (<code>ndb_no</code>: 12014) as a source of zinc.</li>
<li>Chia seeds (<code>ndb_no</code>: 12006) as a source of omega-3 fatty acids.</li>
</ul>
I had previously heard that milk might not be a good source of calcium, as protein would interfere with calcium absorption. However, when outcomes in terms of bone density/loss were looked at, this does not seem to have been borne out by the evidence, e.g., <a href="http://www.ncbi.nlm.nih.gov/pubmed/22127335">Calvez et al. 2011</a>, <a href="http://ajcn.nutrition.org/content/72/3/758.short">Heaney 2000</a>, <a href="http://press.endocrine.org/doi/abs/10.1210/jc.2004-0179">Kerstetter et al. 2005</a>.<br />
<br />
Once I had focused on a particular food, I then looked at the amount of it (in grams) needed to satisfy daily nutrient requirements with queries like this one for Cream of Wheat (<code>ndb_no</code>: 08106):<br />
<br />
<pre>nutrition=> SELECT round(
nutrition(> (i.amount / d.nutrition_value * 100)::numeric,
nutrition(> 1) AS amt,
nutrition-> n.nutr_desc
nutrition-> FROM dietary_reference_intake AS i,
nutrition-> nutrient_data AS d,
nutrition-> foods AS f,
nutrition-> nutrients AS n
nutrition-> WHERE i.nutr_no = d.nutr_no
nutrition-> AND d.ndb_no = f.ndb_no
nutrition-> AND d.nutr_no = n.nutr_no
nutrition-> AND d.nutrition_value > 0
nutrition-> AND f.ndb_no = '08106'
nutrition-> ORDER BY amt;
amt | nutr_desc
---------+------------------------------
28.3 | Iron, Fe
37.3 | Vitamin A, RAE
61.6 | Vitamin B-6
61.6 | Niacin
67.2 | Thiamin
74.1 | Riboflavin
89.6 | Folate, total
132.5 | Carbohydrate, by difference
224.1 | Calcium, Ca
225.0 | Selenium, Se
324.1 | Copper, Cu
563.1 | Phosphorus, P
693.9 | Zinc, Zn
779.4 | Magnesium, Mg
10909.1 | Vitamin E (alpha-tocopherol)
(15 rows)
</pre>
<br />
This says, for instance, that it would take 28.3g of Cream of Wheat to satisfy my daily iron requirement through Cream of Wheat alone. It's easier for me to measure foods by volume rather than weight. To convert between weights and volumes of foods, I went to <a href="http://nutritiondata.self.com/">SELFNutritionData</a>. It incorporates the USDA nutrient database, and also has a drop-down with various choices of serving size for each food. (If this information is in the USDA nutrient database I haven't been able to find it.) This tells me, for instance, that 1 cup of <a href="http://nutritiondata.self.com/facts/breakfast-cereals/1583/2">instant dry Cream of Wheat</a> is 178g.<br />
<br />
Now, for example, 1/2 cup of Cream of Wheat is easy to measure out, and this is 89g. It satisfies my daily requirements for iron, Vitamin A, Vitamin B-6, niacin, thiamin, and riboflavin, and almost satisfies the daily requirement for total folate. How much of my daily calcium requirement does this satisfy?<br />
<br />
(89g of Cream of Wheat in serving)<br />
÷ (224.1g of Cream of Wheat per daily calcium requirement)<br />
= (0.4 of daily calcium requirement)<br />
= 40% of daily calcium requirement<br />
<br />
Similarly, it provides<br />
<br />
<ul style="text-align: left;">
<li>39.6% of daily selenium requirement</li>
<li>27% of daily copper requirement</li>
<li>16% of daily phosphorus requirement</li>
<li>12.8% of daily zinc requirement</li>
<li>11% of daily magnesium requirement</li>
</ul>
<br />
It doesn't do anything significant for my daily Vitamin E requirement.<br />
<br />
By looking at the nutrient profiles of crude wheat bran (<code>ndb_no: 20077</code>) and crude wheat germ (<code>ndb_no: 20078</code>), we find that the Cream of Wheat was probably fortified with Vitamin A since it's not present in either wheat bran or wheat germ. <a href="http://onlinelibrary.wiley.com/doi/10.1111/nyas.12297/abstract">Fortification with Vitamin A leads to high bioavailability.</a>
<br />
<br />
Similarly, here's the amount (in grams) of sunflower seed kernels (<code>ndb_no</code>: 12036) needed to satisfy daily nutrient requirements:
<br />
<pre> amt | nutr_desc
---------+--------------------------------
34.1 | Vitamin E (alpha-tocopherol)
38.9 | Copper, Cu
60.8 | Thiamin
81.5 | Magnesium, Mg
81.8 | Vitamin B-6
84.9 | Selenium, Se
87.9 | Phosphorus, P
132.0 | Niacin
136.0 | Zinc, Zn
141.0 | Folate, total
154.3 | Iron, Fe
253.5 | Riboflavin
500.0 | Carbohydrate, by difference
1025.6 | Calcium, Ca
4285.7 | Vitamin C, total ascorbic acid
16666.7 | Vitamin A, RAE
(16 rows)
</pre>
<br />
We find that 1 cup of <a href="http://nutritiondata.self.com/facts/nut-and-seed-products/3076/2">dried sunflower seed kernels</a> is 140g.
<br />
<br />
Here's the amount (in grams) of skim milk (<code>ndb_no</code>: 01151) needed to satisfy daily nutrient requirements:
<br />
<pre> amt | nutr_desc
----------+------------------------------
400.0 | Vitamin B-12
494.5 | Riboflavin
574.3 | Phosphorus, P
655.7 | Calcium, Ca
1451.6 | Selenium, Se
1619.0 | Zinc, Zn
2000.0 | Thiamin
2016.1 | Carbohydrate, by difference
2409.1 | Magnesium, Mg
2973.0 | Vitamin B-6
5384.6 | Copper, Cu
6400.0 | Folate, total
11702.1 | Niacin
25000.0 | Vitamin A, RAE
27000.0 | Iron, Fe
120000.0 | Vitamin E (alpha-tocopherol)
(16 rows)
</pre>
<br />
We find that 1 cup of <a href="http://nutritiondata.self.com/facts/dairy-and-egg-products/139/2">nonfat milk</a> is 245g.
<br />
<br />
Here's the amount (in grams) of poppy seeds (<code>ndb_no</code>: 02033) needed to satisfy daily nutrient requirements:<br />
<pre> amt | nutr_desc
--------+--------------------------------
43.0 | Copper, Cu
55.6 | Calcium, Ca
66.7 | Phosphorus, P
76.4 | Magnesium, Mg
83.0 | Iron, Fe
86.1 | Zinc, Zn
105.4 | Thiamin
333.3 | Selenium, Se
355.5 | Carbohydrate, by difference
390.2 | Folate, total
445.3 | Vitamin B-6
678.0 | Vitamin E (alpha-tocopherol)
900.0 | Riboflavin
1227.7 | Niacin
6000.0 | Vitamin C, total ascorbic acid
(15 rows)
</pre>
<br />
We find that 1 tbsp of <a href="http://nutritiondata.self.com/facts/spices-and-herbs/203/2">poppy seeds</a> is 9g.
<br />
<br />
Here's the amount (in grams) of pumpkin seeds (<code>ndb_no</code>: 12014) needed to satisfy daily nutrient requirements:<br />
<pre> amt | nutr_desc
---------+--------------------------------
44.8 | Magnesium, Mg
47.0 | Phosphorus, P
52.1 | Copper, Cu
87.1 | Zinc, Zn
91.8 | Iron, Fe
220.6 | Niacin
329.7 | Thiamin
478.7 | Selenium, Se
550.5 | Vitamin E (alpha-tocopherol)
551.7 | Folate, total
588.2 | Riboflavin
769.2 | Vitamin B-6
933.7 | Carbohydrate, by difference
1739.1 | Calcium, Ca
3157.9 | Vitamin C, total ascorbic acid
50000.0 | Vitamin A, RAE
(16 rows)
</pre>
<br />
We find that 1 cup of <a href="http://nutritiondata.self.com/facts/nut-and-seed-products/3066/2">pumpkin seed kernels</a> is 138g. With 48 tsp to a cup, we have 2.875 g per teaspoon of pumpkin seeds.
<br />
<br />
Here's the amount (in grams) of chia seeds (<code>ndb_no</code>: 12006) needed to satisfy daily nutrient requirements:<br />
<pre> amt | nutr_desc
--------+--------------------------------
67.4 | Phosphorus, P
75.8 | Copper, Cu
79.1 | Magnesium, Mg
81.5 | Selenium, Se
104.9 | Iron, Fe
124.6 | Niacin
126.8 | Calcium, Ca
145.2 | Thiamin
148.5 | Zinc, Zn
237.4 | Carbohydrate, by difference
529.4 | Riboflavin
653.1 | Folate, total
2400.0 | Vitamin E (alpha-tocopherol)
3750.0 | Vitamin C, total ascorbic acid
(14 rows)
</pre>
<br />
For some reason, <a href="http://nutritiondata.self.com/">SELFNutritionData</a> did not have a volume measurement for chia seeds. I found through <a href="http://convert-to.com/527/chia-amounts-conversion-black-or-white-chia-seed.html">Chia amounts conversion</a> that 1 tsp of chia seeds is 3.39g.
<br />
<br />
<h3 style="text-align: left;">
Amounts of Each Food</h3>
<br />
<br />
Now, I came up with the amounts of these foods for the above breakfasts by considering what amounts would be easy to measure out and to eat, and putting them together to make up the dietary nutrient requirements.<br />
<br />
<h4 style="text-align: left;">
Omega Fatty Acids</h4>
<div style="text-align: left;">
<br /></div>
<div style="text-align: left;">
In an influential 2002 paper, A.P. Simopoulos described <a href="http://www.sciencedirect.com/science/article/pii/S0753332202002536">the importance of the ratio of omega-6/omega-3 essential fatty acids</a>. Omega-6 fatty acids are pro-inflammatory, whereas omega-3 fatty acids are anti-inflammatory. From the paper, I decided to make the ratio of omega-6 fatty acids to omega-3 fatty acids in the breakfasts no more than 4:1. Omega-3 fatty acids are thought to have <a href="http://umm.edu/health/medical/altmed/supplement/omega3-fatty-acids">a variety of health benefits</a>. Various scientific bodies have issued <a href="http://www.nutri-facts.org/eng/essential-fatty-acids/essential-fatty-acids/intake-recommendations/">guidelines recommending minimum daily amounts of omega fatty acids</a>. I include the <a href="http://www.amazon.com/gp/product/B004LL7AXE/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=B004LL7AXE&linkCode=as2&tag=httpwwwruchir-20&linkId=4K5LL5BZL227Z5F5" target="_blank">Ovega</a> capsule to get the recommended EPA and DHA.</div>
<div style="text-align: left;">
<br /></div>
<div style="text-align: left;">
To find the information about omega fatty acids, I needed to know the nomenclature used. The USDA answers the <a href="http://www.ars.usda.gov/main/docs.htm?docid=6233#omgea">Frequently Asked Question: What are omega-3 and omega-6 fatty acids?</a> as follows:</div>
<blockquote class="tr_bq">
<span style="background-color: white;"><span style="font-family: inherit;">These are types of polyunsaturated fatty acids. Linolenic acid, the shortest chain omega-3 fatty acid, and linoleic acid, the shortest chain omega-6 fatty acid, are essential fatty acids. This means they cannot be synthesized by the body from other fatty acids and must be obtained from food. The most common fatty acids of each class are linolenic (18:3), EPA (20:5), DHA (22:6) for omega-3 and linoleic (18:2) and arachidonic (20:4) for omega-6.</span></span></blockquote>
<h4 style="text-align: left;">
Putting It All Together</h4>
<br />
So, as mentioned above, I chose 89g or 1/2 cup of Cream of Wheat. Let's look at what this amount of Cream of Wheat gives me in terms of omega fatty acids:<br />
<br />
<pre>nutrition=> SELECT 0.89 * d.nutrition_value
nutrition-> AS amount_in_diet,
nutrition-> n.units, n.nutr_desc
nutrition-> FROM nutrient_data AS d,
nutrition-> nutrients n
nutrition-> WHERE d.nutr_no = n.nutr_no
nutrition-> AND n.nutr_no IN (
nutrition(> '618', '619', '620', '621', '629',
nutrition(> '665', '666', '669', '670', '675',
nutrition(> '685', '851', '855', '856'
nutrition(> ) AND d.nutrition_value > 0
nutrition-> AND d.ndb_no = '08106';
amount_in_diet | units | nutr_desc
----------------+-------+-----------------------------
amount_in_diet | units | nutr_desc
----------------+-------+-----------------------
0.61588 | g | 18:2 undifferentiated
0.07298 | g | 18:3 undifferentiated
(2 rows)
</pre>
<br />
Note that we have 0.62g of linoleic (18:2), an omega-6 fatty acid, and 0.07g of linolenic (18:3), an omega-3 fatty acid.
<br />
<br />
Next let's consider sunflower seeds. Among the above foods, the sunflower seed kernels are the only significant source of Vitamin E, so I chose 35g or 1/4 cup to satisfy the Vitamin E requirement. This 35g of sunflower seeds satisfies:<br />
<br />
<br />
<ul style="text-align: left;">
<li>103% of daily Vitamin E requirement</li>
<li>90% of daily copper requirement</li>
<li>43% of daily magnesium requirement</li>
<li>41.2% of daily selenium requirement</li>
<li>40% of daily phosphorus requirement</li>
<li>25.7% of daily zinc requirement</li>
<li>25% of daily total folate requirement</li>
<li>3% of daily calcium requirement</li>
</ul>
<br />
So, together with the Cream of Wheat, so far we've satisfied my daily requirements for iron, Vitamin A, Vitamin B-6, niacin, thiamin, riboflavin, folate, Vitamin E, and copper. We've also satisfied:<br />
<br />
<ul style="text-align: left;">
<li>80.8% of daily selenium requirement</li>
<li>56% of daily phosphorus requirement</li>
<li>54% of daily magnesium requirement</li>
<li>43% of daily calcium requirement</li>
<li>38.5% of daily zinc requirement</li>
</ul>
<br />
Let's look at what this amount of sunflower seeds gives me in terms of omega fatty acids:<br />
<pre>nutrition=> SELECT 0.35 * d.nutrition_value
nutrition-> AS amount_in_diet,
nutrition-> n.units, n.nutr_desc
nutrition-> FROM nutrient_data AS d,
nutrition-> nutrients n
nutrition-> WHERE d.nutr_no = n.nutr_no
nutrition-> AND n.nutr_no IN (
nutrition(> '618', '619', '620', '621', '629',
nutrition(> '665', '666', '669', '670', '675',
nutrition(> '685', '851', '855', '856'
nutrition(> ) AND d.nutrition_value > 0
nutrition-> AND d.ndb_no = '12036';
amount_in_diet | units | nutr_desc
----------------+-------+-----------------------------
8.06750 | g | 18:2 undifferentiated
0.02100 | g | 18:3 undifferentiated
0.00490 | g | 20:5 n-3 (EPA)
(3 rows)
</pre>
<br />
Here 20:5 n-3 (EPA) is another omega-3 fatty acid. Notice that, together with the Cream of Wheat, we have a total of 0.62g + 8.07g = 8.69g of omega-6 fatty acid, and only 0.073g + 0.026g = 0.099g of omega-3 fatty acid. If we take into account the Ovega capsule, that still gives us only 0.599g of omega-3 fatty acid.
<br />
<br />
We will fix this with some chia seeds. Let's look at what 100g of chia seeds gives me in terms of omega fatty acids:
<br />
<br />
<pre>nutrition=> SELECT d.nutrition_value
nutrition-> AS amount_in_diet,
nutrition-> n.units, n.nutr_desc
nutrition-> FROM nutrient_data AS d,
nutrition-> nutrients n
nutrition-> WHERE d.nutr_no = n.nutr_no
nutrition-> AND n.nutr_no IN (
nutrition(> '618', '619', '620', '621', '629',
nutrition(> '665', '666', '669', '670', '675',
nutrition(> '685', '851', '855', '856'
nutrition(> ) AND d.nutrition_value > 0
nutrition-> AND d.ndb_no = '12006';
amount_in_diet | units | nutr_desc
----------------+-------+-----------------------------
5.835 | g | 18:2 undifferentiated
17.830 | g | 18:3 undifferentiated
5.835 | g | 18:2 n-6 c,c
17.830 | g | 18:3 n-3 c,c,c (ALA)
(4 rows)
</pre>
<br />
We want to come up with an amount of chia seeds that brings the ratio of omega-6 fatty acids to omega-3 fatty acids back down to 4:1. Suppose we start with <em>a</em> grams of omega-3 fatty acids and <em>b</em> grams of omega-6 fatty acids from other foods, and we want to find an amount <em>c</em> of chia seeds to add so that the total ratio of omega-6 fatty acids to omega-3 fatty acids is 4:1. Then
<br />
<br />
<i>b</i> + 5.835 * <i>c</i> / 100 = 4 * (<i>a</i> + 17.83 * <i>c</i> / 100)
<br />
<br />
100 * <i>b</i> + 5.835 * <i>c</i> = 4 * (100 * <i>a</i> + 17.83 * <i>c</i>)
<br />
<br />
100 * (<i>b</i> - 4 * <i>a</i>) = (4 * 17.83 - 5.835) * <i>c</i> = 65.485 * <i>c</i><br />
<br />
<i>c</i> = (<i>b</i> - 4 * <i>a</i>) * 100 / 65.485<br />
<br />
So finally:<br />
<br />
<i>c</i> = (<i>b</i> - 4 * <i>a</i>) * 1.527
<br />
<br />
In particular, so far we have <i>a</i> = 0.599g and <i>b</i> = 8.69g, so we will add (8.69g - 4 * 0.599g) * 1.527 = 9.61g of chia seeds. The 9.61g of chia seeds satisfies:<br />
<ul style="text-align: left;">
<li>11.8% of daily selenium requirement</li>
<li>14% of daily phosphorus requirement</li>
<li>12% of daily magnesium requirement</li>
<li>7.6% of daily calcium requirement</li>
<li>6.5% of daily zinc requirement</li>
</ul>
Thus all together we have satisfied
<br />
<div>
<ul style="text-align: left;">
<li>92.6% of daily selenium rquirement</li>
<li>70% of daily phosphorus requirement</li>
<li>66% of daily magnesium requirement</li>
<li>50.6% of daily calcium requirement</li>
<li>45% of daily zinc requirement</li>
</ul>
</div>
<br />
Next, let's look at my daily calcium requirement. I need a total of 800mg of calcium, and 49.4% of this, or 395mg, still needs to be supplied.<br />
<br />
Suppose I get this from poppy seeds. Let's look at what 100g of poppy seeds gives me in terms of omega fatty acids:
<br />
<pre> amount_in_diet | units | nutr_desc
----------------+-------+-----------------------------
28.295 | g | 18:2 undifferentiated
0.273 | g | 18:3 undifferentiated
0.273 | g | 18:3 n-3 c,c,c (ALA)
(3 rows)
</pre>
<br />
In particular, 100g of poppy seeds has <em>a</em>=0.273g of omega-3 fatty acids and <em>b</em>=28.295g of omega-6 fatty acids. So for each 100g of poppy seeds, we would also need to add (28.295g - 4 * 0.273g) * 1.572 = 41.5g of chia seeds. How much calcium would this supply?
<br />
<pre>nutrition=> SELECT d1.nutrition_value
nutrition-> + 0.415 * d2.nutrition_value
nutrition-> AS total_calcium_supplied,
nutrition-> n.units
nutrition-> FROM nutrient_data AS d1,
nutrition-> nutrient_data AS d2,
nutrition-> nutrients AS n
nutrition-> WHERE d1.ndb_no = '02033'
nutrition-> AND d2.ndb_no = '12006'
nutrition-> AND d1.nutr_no = d2.nutr_no
nutrition-> AND d1.nutr_no = n.nutr_no
nutrition-> AND n.nutr_desc = 'Calcium, Ca';
total_calcium_supplied | units
------------------------+-------
1699.865 | mg
</pre>
<br />
We only need 395mg, so we only need (395mg/1700mg) * 100g = 23.2g poppy seeds. Let's make it 24g poppy seeds, that is, 8 tsp. Then we also add another 0.415 * 24g = 9.96g of chia seeds.
<br />
<br />
The 24g of poppy seeds satisfies:<br />
<br />
<ul style="text-align: left;">
<li>7.2% of daily selenium requirement</li>
<li>36% of daily phosphorus requirement</li>
<li>31.4% of daily magnesium requirement</li>
<li>43.2% of daily calcium requirement</li>
<li>27.9% of daily zinc requirement</li>
</ul>
<br />
The additional 9.96g of chia seeds satisfies:<br />
<br />
<ul style="text-align: left;">
<li>12.2% of daily selenium requirement</li>
<li>15% of daily phosphorus requirement</li>
<li>12.6% of daily magnesium requirement</li>
<li>7.9% of daily calcium requirement</li>
<li>6.7% of daily zinc requirement</li>
</ul>
<br />
So if we use poppy seeds for calcium, with some additional chia seeds, all together we have satisfied:<br />
<br />
<ul style="text-align: left;">
<li>112% of daily selenium requirement</li>
<li>121% of daily phosphorus requirement</li>
<li>110% of daily magnesium requirement</li>
<li>101.7% of daily calcium requirement</li>
<li>79.6% of daily zinc requirement</li>
</ul>
<br />
Alternatively, suppose we use skim milk for calcium. Let's look at what 100g of skim milk gives me in terms of omega fatty acids:<br />
<pre> amount_in_diet | units | nutr_desc
----------------+-------+-----------------------------
0.002 | g | 18:2 undifferentiated
0.001 | g | 18:3 undifferentiated
(2 rows)
</pre>
<br />
The omega-6 to omega-3 ratio of skim milk is already only 2:1, so we don't need additional chia seeds to go with it. 655.7g of skim milk would satisfy my entire daily calcium requirement. We only need to satisfy 49.4% of it, so we only need 0.494 * 655.7g = 323.9g of skim milk. Since 1 cup is 245g, this would be 1.32 cups. Let's make it 1 1/3 cups or 326.67g since this is easy to measure. It also makes the Cream of Wheat a reasonable consistency. 326.67g of skim milk satisfies:<br />
<ul style="text-align: left;">
<li>22.5% of the daily selenium requirement</li>
<li>57% of the daily phosphorus requirement</li>
<li>13.6% of the daily magnesium requirement</li>
<li>49.8% of the daily calcium requirement</li>
<li>20.2% of the daily zinc requirement</li>
</ul>
<div>
Thus all together we have satisfied:<br />
<br />
<ul style="text-align: left;">
<li>115% of the daily selenium requirement</li>
<li>127% of the daily phosphorus requirement</li>
<li>79.6% of the daily magnesium requirement</li>
<li>100.4% of the daily calcium requirement</li>
<li>65.2% of the daily zinc requirement</li>
</ul>
</div>
Finally, let's look at my daily zinc requirement. This is 6.8mg. If I've used poppy seeds, then 79.6% of this has already been satisfied, so I only need another 20.4% of 6.8mg or 1.39mg. If I've used skim milk, then 65.2% of this has already been satisfied, so I only need another 34.8% of 6.8mg or 2.37mg.<br />
<br />
Let's look at what 100g of pumpkin seeds gives me in terms of omega fatty acids:<br />
<pre> amount_in_diet | units | nutr_desc
----------------+-------+----------------------------
20.710 | g | 18:2 undifferentiated
0.120 | g | 18:3 undifferentiated
0.131 | g | 20:4 undifferentiated
0.039 | g | 18:2 t not further defined
0.004 | g | 18:2 CLAs
20.667 | g | 18:2 n-6 c,c
0.120 | g | 18:3 n-3 c,c,c (ALA)
(7 rows)
</pre>
<br />
Here 20:4 is arachidonic, another omega-6 fatty acid. We have <em>a</em>=0.120g of omega-3 fatty acids and <em>b</em>=20.841g of omega-6 fatty acids. So for each 100g of pumpkin seeds, we would also need to add (20.841g - 4 * 0.12g) * 1.572 = 32g of chia seeds. How much zinc would this supply?
<br />
<pre>nutrition=> SELECT d1.nutrition_value
nutrition-> + 0.32 * d2.nutrition_value
nutrition-> AS total_zinc_supplied,
nutrition-> n.units
nutrition-> FROM nutrient_data AS d1,
nutrition-> nutrient_data AS d2,
nutrition-> nutrients AS n
nutrition-> WHERE d1.nutr_no = d2.nutr_no
nutrition-> AND d2.nutr_no = n.nutr_no
nutrition-> AND d1.ndb_no = '12014'
nutrition-> AND d2.ndb_no = '12006'
nutrition-> AND n.nutr_desc = 'Zinc, Zn';
total_zinc_supplied | units
---------------------+-------
9.2756 | mg
(1 row)
</pre>
<br />
If I've used poppy seeds, I only need (1.39mg/9.2756mg) * 100g = 15g of pumpkin seeds. Since there are 2.875g per teaspoon, this is 5.2 tsp. Let's make it an even 6 tsp or 2 tbsp. This is 17.25g. Then we also add another 0.32 * 17.25g = 5.52g of chia seeds.
<br />
<br />
The 17.25g of pumpkin seeds satisfy:<br />
<br />
<ul style="text-align: left;">
<li>19.8% of the daily zinc requirement</li>
</ul>
<br />
The additional 5.52g of chia seeds satisfy:
<br />
<br />
<ul style="text-align: left;">
<li>3.7% of the daily zinc requirement</li>
</ul>
<br />
So all together we've satisfied:
<br />
<br />
<ul style="text-align: left;">
<li>103% of the daily zinc requirement</li>
</ul>
<div>
On the other hand, if I've used skim milk, I only need (2.37mg/9.2756mg) * 100g = 25.6g of pumpkin seeds. Since there are 2.875g per teaspoon, this is 8.9 teaspoons. Let's make it an even 9 tsp or 3 tbsp. This is 25.875g. Then we also add 0.32 * 25.875g = 8.28g of chia seeds.</div>
<div>
<br /></div>
<div>
The 25.875g of pumpkin seeds satisfy:</div>
<div>
<ul style="text-align: left;">
<li>57.8% of the daily magnesium requirement</li>
<li>29.7% of the daily zinc requirement</li>
</ul>
The additional 8.28g of chia seeds satisfy:</div>
<div>
<ul style="text-align: left;">
<li>10.5% of the daily magnesium requirement</li>
<li>5.6% of the daily zinc requirement</li>
</ul>
</div>
<br />
So all together we've satisfied:<br />
<ul style="text-align: left;">
<li>148% of the daily magnesium requirement</li>
<li>100.5% of the daily zinc requirement</li>
</ul>
<br />
If I've used poppy seeds, the total amount of chia seeds is 9.61g + 9.96g + 5.52g = 25.09g. This is 7.4 tsp. Let's make it an even 8 tsp. This is 27.14g.<br />
<br />
If I've used skim milk, the total amount of chia seeds is 9.61g + 8.28g = 17.89g. This is 5.27 tsp. Let's make it an even 6 tsp or 2 tbsp. This is 20.34g.<br />
<br />
I use a 500μg Vitamin B-12 tablet to satisfy the Vitamin B-12 requirement, even though it is only 2μg, because various conditions can lead to decreased absorption efficiency. The 600 IU Vitamin D capsule is based on <a href="http://ods.od.nih.gov/factsheets/VitaminD-HealthProfessional/">this recommendation</a>.<br />
<br />
<h2 style="text-align: left;">
Macronutrients</h2>
<br />
Let's see what these breakfasts provide in terms of macronutrients.<br />
<br />
The breakfast with skim milk provides:
<br />
<pre>nutrition=> SELECT 0.89 * d1.nutrition_value
nutrition-> + 0.35 * d2.nutrition_value
nutrition-> + 3.26667 * d3.nutrition_value
nutrition-> + 0.25875 * d4.nutrition_value
nutrition-> + 0.2034 * d5.nutrition_value
nutrition-> AS amount_in_diet,
nutrition-> n.units, n.nutr_desc
nutrition-> FROM nutrient_data AS d1,
nutrition-> nutrient_data AS d2,
nutrition-> nutrient_data AS d3,
nutrition-> nutrient_data AS d4,
nutrition-> nutrient_data AS d5,
nutrition-> nutrients AS n
nutrition-> WHERE d1.nutr_no = n.nutr_no
nutrition-> AND d2.nutr_no = n.nutr_no
nutrition-> AND d3.nutr_no = n.nutr_no
nutrition-> AND d4.nutr_no = n.nutr_no
nutrition-> AND d5.nutr_no = n.nutr_no
nutrition-> AND d1.ndb_no = '08106'
nutrition-> AND d2.ndb_no = '12036'
nutrition-> AND d3.ndb_no = '01151'
nutrition-> AND d4.ndb_no = '12014'
nutrition-> AND d5.ndb_no = '12006'
nutrition-> AND n.nutr_no IN (
nutrition(> '203', '204', '205', '208', '209',
nutrition(> '210', '211', '212', '213', '214',
nutrition(> '287', '269', '291');
amount_in_diet | units | nutr_desc
----------------+-------+-----------------------------
38.9019264 | g | Protein
38.4625371 | g | Total lipid (fat)
101.7361037 | g | Carbohydrate, by difference
884.70043 | kcal | Energy
14.496460 | g | Fiber, total dietary
(5 rows)
</pre>
<br />
The vegan breakfast provides:
<br />
<pre>nutrition=> SELECT 0.89 * d1.nutrition_value
nutrition-> + 0.35 * d2.nutrition_value
nutrition-> + 0.24 * d3.nutrition_value
nutrition-> + 0.1725 * d4.nutrition_value
nutrition-> + 0.2714 * d5.nutrition_value
nutrition-> AS amount_in_diet,
nutrition-> n.units, n.nutr_desc
nutrition-> FROM nutrient_data AS d1,
nutrition-> nutrient_data AS d2,
nutrition-> nutrient_data AS d3,
nutrition-> nutrient_data AS d4,
nutrition-> nutrient_data AS d5,
nutrition-> nutrients AS n
nutrition-> WHERE d1.nutr_no = n.nutr_no
nutrition-> AND d2.nutr_no = n.nutr_no
nutrition-> AND d3.nutr_no = n.nutr_no
nutrition-> AND d4.nutr_no = n.nutr_no
nutrition-> AND d5.nutr_no = n.nutr_no
nutrition-> AND d1.ndb_no = '08106'
nutrition-> AND d2.ndb_no = '12036'
nutrition-> AND d3.ndb_no = '02033'
nutrition-> AND d4.ndb_no = '12014'
nutrition-> AND d5.ndb_no = '12006'
nutrition-> AND n.nutr_no IN (
nutrition(> '203', '204', '205', '208', '209',
nutrition(> '210', '211', '212', '213', '214',
nutrition(> '287', '269', '291');
amount_in_diet | units | nutr_desc
----------------+-------+-----------------------------
30.728231 | g | Protein
46.035361 | g | Total lipid (fat)
94.225043 | g | Carbohydrate, by difference
884.4679 | kcal | Energy
20.99816 | g | Fiber, total dietary
</pre>
<br />
The Dietary Reference Intake's protein requirement is 0.66g per kg of body weight. So, the breakfast including skim milk provides enough protein in itself for a 58.9kg or 130lb person, and the vegan breakfast provides enough protein in itself for a 46.6kg or 103lb person.
<br />
<div style="text-align: left;">
<br /></div>
<h3 style="text-align: left;">
Essential Amino Acids</h3>
<div style="text-align: left;">
<br /></div>
<div style="text-align: left;">
The World Health Organization recommends daily amounts of <a href="http://en.wikipedia.org/wiki/Essential_amino_acid">essential amino acids</a> in mg per kg of body mass. Here we present these along with the resulting requirement for a 60kg individual:<br />
<br />
<table border="1">
<tbody>
<tr>
<th><b>Amino acid(s)</b></th>
<th><b>mg per kg body mass</b></th>
<th><b>g for a 60kg individual</b></th>
</tr>
<tr>
<td><b>H</b> Histidine</td>
<td>10</td>
<td>0.6</td>
</tr>
<tr>
<td><b>I</b> Isoleucine</td>
<td>20</td>
<td>1.2</td>
</tr>
<tr>
<td><b>L</b> Leucine</td>
<td>39</td>
<td>2.34</td>
</tr>
<tr>
<td><b>K</b> Lysine</td>
<td>30</td>
<td>1.8</td>
</tr>
<tr>
<td><b>M</b> Methionine <br />
+ <b>C</b> Cysteine</td>
<td>10.4 + 4.1 (15 total)</td>
<td>0.624 + 0.246 (0.9 total)</td>
</tr>
<tr>
<td><b>F</b> Phenylalanine <br />
+ <b>Y</b> Tyrosine</td>
<td>25 (total)</td>
<td>1.5 (total)</td>
</tr>
<tr>
<td><b>T</b> Threonine</td>
<td>15</td>
<td>0.9</td>
</tr>
<tr>
<td><b>W</b> Tryptophan</td>
<td>4</td>
<td>0.24</td>
</tr>
<tr>
<td><b>V</b> Valine</td>
<td>26</td>
<td>1.56</td>
</tr>
</tbody></table>
</div>
<br />
Here are the amounts of each of these amino acids in the breakfast with skim milk:
<br />
<pre>nutrition=> SELECT 0.89 * d1.nutrition_value
nutrition-> + 0.35 * d2.nutrition_value
nutrition-> + 3.2666667 * d3.nutrition_value
nutrition-> + 0.25875 * d4.nutrition_value
nutrition-> + 0.2034 * d5.nutrition_value
nutrition-> AS amount_in_diet,
nutrition-> n.units, n.nutr_desc
nutrition-> FROM nutrient_data AS d1,
nutrition-> nutrient_data AS d2,
nutrition-> nutrient_data AS d3,
nutrition-> nutrient_data AS d4,
nutrition-> nutrient_data AS d5,
nutrition-> nutrients AS n
nutrition-> WHERE d1.nutr_no = n.nutr_no
nutrition-> AND d2.nutr_no = n.nutr_no
nutrition-> AND d3.nutr_no = n.nutr_no
nutrition-> AND d4.nutr_no = n.nutr_no
nutrition-> AND d5.nutr_no = n.nutr_no
nutrition-> AND d1.ndb_no = '08106'
nutrition-> AND d2.ndb_no = '12036'
nutrition-> AND d3.ndb_no = '01151'
nutrition-> AND d4.ndb_no = '12014'
nutrition-> AND d5.ndb_no = '12006'
nutrition-> AND n.nutr_no IN (
nutrition(> '501', '502', '503', '504', '505',
nutrition(> '506', '507', '508', '509', '510',
nutrition(> '512');
amount_in_diet | units | nutr_desc
----------------+-------+---------------
0.6290390681 | g | Tryptophan
1.4931231048 | g | Threonine
1.8708321558 | g | Isoleucine
3.2394943273 | g | Leucine
2.0083430094 | g | Lysine
0.9104321196 | g | Methionine
0.6069588007 | g | Cystine
2.1440748225 | g | Phenylalanine
1.4839112890 | g | Tyrosine
2.2405495907 | g | Valine
1.0796104034 | g | Histidine
</pre>
<br />
This breakfast meets or exceeds the recommended amounts of each of the essential amino acids for a 60kg individual.
<br />
Here are the amounts of each of these amino acids in the vegan breakfast:
<br />
<pre>nutrition=> SELECT 0.89 * d1.nutrition_value
nutrition-> + 0.35 * d2.nutrition_value
nutrition-> + 0.24 * d3.nutrition_value
nutrition-> + 0.1725 * d4.nutrition_value
nutrition-> + 0.2714 * d5.nutrition_value
nutrition-> AS amount_in_diet,
nutrition-> n.units, n.nutr_desc
nutrition-> FROM nutrient_data AS d1,
nutrition-> nutrient_data AS d2,
nutrition-> nutrient_data AS d3,
nutrition-> nutrient_data AS d4,
nutrition-> nutrient_data AS d5,
nutrition-> nutrients AS n
nutrition-> WHERE d1.nutr_no = n.nutr_no
nutrition-> AND d2.nutr_no = n.nutr_no
nutrition-> AND d3.nutr_no = n.nutr_no
nutrition-> AND d4.nutr_no = n.nutr_no
nutrition-> AND d5.nutr_no = n.nutr_no
nutrition-> AND d1.ndb_no = '08106'
nutrition-> AND d2.ndb_no = '12036'
nutrition-> AND d3.ndb_no = '02033'
nutrition-> AND d4.ndb_no = '12014'
nutrition-> AND d5.ndb_no = '12006'
nutrition-> AND n.nutr_no IN (
nutrition(> '501', '502', '503', '504', '505',
nutrition(> '506', '507', '508', '509', '510',
nutrition(> '512');
amount_in_diet | units | nutr_desc
----------------+-------+---------------
0.5127004 | g | Tryptophan
1.1494976 | g | Threonine
1.4429739 | g | Isoleucine
2.3990569 | g | Leucine
1.2749780 | g | Lysine
0.7314207 | g | Methionine
0.6086798 | g | Cystine
1.6739449 | g | Phenylalanine
1.0470707 | g | Tyrosine
1.7098275 | g | Valine
0.8282834 | g | Histidine
(11 rows)
</pre>
<br />
This exceeds all but one of the recommended amounts of essential amino acids for a 60kg individual. The amount of lysine, 1.27g, would only be sufficient for an individual with a body mass of (1270mg)/(30mg per kg of body mass) = 42.3kg or 93.2lb. Many kinds of beans are rich in lysine. For instance, to get 1.8g - 1.27g = 0.53g more of lysine, one could eat kidney beans (<code>ndb_no</code>: 16032):
<br />
<pre>nutrition=> SELECT 0.53 / d.nutrition_value AS amount_needed
nutrition-> FROM nutrient_data AS d
nutrition-> WHERE d.ndb_no = '16032'
nutrition-> AND d.nutr_no = '505';
amount_needed
------------------------
0.34259857789269553975
(1 row)
</pre>
<br />
Since 1 tbsp of <a href="http://nutritiondata.self.com/facts/legumes-and-legume-products/4301/2">kidney beans</a> is 12g, this would be a little less than 3 tbsp. This would also supply another 7.7g of protein, 20.8g of carbohydrate, 115 calories, and 5.2g of fiber. There are many other possibilities.
</div>
Ruchira Dattahttp://www.blogger.com/profile/11225230326635564528noreply@blogger.com0tag:blogger.com,1999:blog-595243868922664570.post-76321378596759180132014-03-18T22:09:00.004-07:002014-03-18T22:38:27.852-07:00Towards Computing A Genetic Risk of Obesity Score<div dir="ltr" style="text-align: left;" trbidi="on">
<div dir="ltr" style="text-align: left;" trbidi="on">
<a href="http://www.medscape.com/viewarticle/822180">Genetic Makeup Can Exacerbate Effects of Fried Food Diet</a>, published today, summarizes the findings in <a href="http://press.psprings.co.uk/bmj/march/friedfoods.pdf">Fried food consumption, genetic risk, and body mass index: gene-diet interaction analysis in three US cohort studies</a>, an Open Access article in the British Medical Journal by Qi <i>et al</i>, a group of Harvard professors. In this article, the authors reused a genetic risk of obesity score that they had previously published in <a href="http://www.nejm.org/doi/full/10.1056/NEJMoa1203039">Sugar-Sweetened Beverages and Genetic Risk of Obesity</a> in the New England Journal of Medicine. Unfortunately, the latter article is not Open Access. So, I'll describe the Qi <i>et al</i> Genetic Risk of Obesity score (which I'll call QiGRO for short) in this post.<br />
<br />
The information needed to compute QiGRO is presented in Table 1 of the Supplementary Appendix to <a href="http://www.nejm.org/doi/full/10.1056/NEJMoa1203039">Sugar-Sweetened Beverages and Genetic Risk of Obesity</a>. This lists 32 SNPs (single-nucleotide polymorphisms) contributing to risk of increased BMI (body mass index), along with a β-coefficient describing the relative effect size for each. Here are the relevant columns from the table:<br />
<br />
<br />
<br />
<br />
<br /></div>
<table border="0" cellpadding="0" cellspacing="0" style="border-collapse: collapse; table-layout: fixed; width: 316px;">
<colgroup><col class="xl66" span="3" style="mso-width-alt: 3072; mso-width-source: userset; width: 72pt;" width="72"></col>
<col class="xl65" span="2" style="mso-width-alt: 1493; mso-width-source: userset; width: 35pt;" width="35"></col>
<col style="mso-width-alt: 1280; mso-width-source: userset; width: 30pt;" width="30"></col>
</colgroup><tbody>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt; width: 72pt;" width="72">SNP</td>
<td class="xl66" style="width: 72pt;" width="72">Nearest Gene</td>
<td class="xl66" style="width: 72pt;" width="72">Chromosome</td>
<td class="xl65" style="width: 35pt;" width="35">Effect</td>
<td class="xl65" style="width: 35pt;" width="35">Other</td>
<td style="width: 30pt;" width="30">Beta</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs543874</td>
<td class="xl66">SEC16B</td>
<td class="xl66">1</td>
<td class="xl65">G</td>
<td class="xl65">A</td>
<td align="right">0.22</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs1514175</td>
<td class="xl66">TNNI3K</td>
<td class="xl66">1</td>
<td class="xl65">A</td>
<td class="xl65">G</td>
<td align="right">0.07</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs1555543</td>
<td class="xl66">PTBP2</td>
<td class="xl66">1</td>
<td class="xl65">C</td>
<td class="xl65">A</td>
<td align="right">0.06</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs2815752</td>
<td class="xl66">NEGR1</td>
<td class="xl66">1</td>
<td class="xl65">A</td>
<td class="xl65">G</td>
<td align="right">0.13</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs2890652</td>
<td class="xl66">LRP1B</td>
<td class="xl66">2</td>
<td class="xl65">C</td>
<td class="xl65">T</td>
<td align="right">0.09</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs887912</td>
<td class="xl66">FANCL</td>
<td class="xl66">2</td>
<td class="xl65">T</td>
<td class="xl65">C</td>
<td align="right">0.1</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs713586</td>
<td class="xl66">RBJ</td>
<td class="xl66">2</td>
<td class="xl65">C</td>
<td class="xl65">T</td>
<td align="right">0.14</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs2867125</td>
<td class="xl66">TMEM18</td>
<td class="xl66">2</td>
<td class="xl65">C</td>
<td class="xl65">T</td>
<td align="right">0.31</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs13078807</td>
<td class="xl66">CADM2</td>
<td class="xl66">3</td>
<td class="xl65">G</td>
<td class="xl65">A</td>
<td align="right">0.1</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs9816226</td>
<td class="xl66">ETV5</td>
<td class="xl66">3</td>
<td class="xl65">T</td>
<td class="xl65">A</td>
<td align="right">0.14</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs13107325</td>
<td class="xl66">SLC39A8</td>
<td class="xl66">4</td>
<td class="xl65">T</td>
<td class="xl65">C</td>
<td align="right">0.19</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs10938397</td>
<td class="xl66">GNPDA2</td>
<td class="xl66">4</td>
<td class="xl65">G</td>
<td class="xl65">A</td>
<td align="right">0.18</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs4836133</td>
<td class="xl66">ZNF608</td>
<td class="xl66">5</td>
<td class="xl65">A</td>
<td class="xl65">C</td>
<td align="right">0.07</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs2112347</td>
<td class="xl66">FLJ35779</td>
<td class="xl66">5</td>
<td class="xl65">T</td>
<td class="xl65">G</td>
<td align="right">0.1</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs987237</td>
<td class="xl66">TFAP2B</td>
<td class="xl66">6</td>
<td class="xl65">G</td>
<td class="xl65">A</td>
<td align="right">0.13</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs206936</td>
<td class="xl66">NUDT3</td>
<td class="xl66">6</td>
<td class="xl65">G</td>
<td class="xl65">A</td>
<td align="right">0.06</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs10968576</td>
<td class="xl66">LRRN6C</td>
<td class="xl66">9</td>
<td class="xl65">G</td>
<td class="xl65">A</td>
<td align="right">0.11</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs3817334</td>
<td class="xl66">MTCH2</td>
<td class="xl66">11</td>
<td class="xl65">T</td>
<td class="xl65">C</td>
<td align="right">0.06</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs4929949</td>
<td class="xl66">RPL27A</td>
<td class="xl66">11</td>
<td class="xl65">C</td>
<td class="xl65">T</td>
<td align="right">0.06</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs10767664</td>
<td class="xl66">BDNF</td>
<td class="xl66">11</td>
<td class="xl65">A</td>
<td class="xl65">T</td>
<td align="right">0.19</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs7138803</td>
<td class="xl66">FAIM2</td>
<td class="xl66">12</td>
<td class="xl65">A</td>
<td class="xl65">G</td>
<td align="right">0.12</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs4771122</td>
<td class="xl66">MTIF3</td>
<td class="xl66">13</td>
<td class="xl65">G</td>
<td class="xl65">A</td>
<td align="right">0.09</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs11847697</td>
<td class="xl66">PRKD1</td>
<td class="xl66">14</td>
<td class="xl65">T</td>
<td class="xl65">C</td>
<td align="right">0.17</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs10150332</td>
<td class="xl66">NRXN3</td>
<td class="xl66">14</td>
<td class="xl65">C</td>
<td class="xl65">T</td>
<td align="right">0.13</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs2241423</td>
<td class="xl66">MAP2K5</td>
<td class="xl66">15</td>
<td class="xl65">G</td>
<td class="xl65">A</td>
<td align="right">0.13</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs7359397</td>
<td class="xl66">SH2B1</td>
<td class="xl66">16</td>
<td class="xl65">T</td>
<td class="xl65">C</td>
<td align="right">0.15</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs1558902</td>
<td class="xl66">FTO</td>
<td class="xl66">16</td>
<td class="xl65">A</td>
<td class="xl65">T</td>
<td align="right">0.39</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs12444979</td>
<td class="xl66">GPRC5B</td>
<td class="xl66">16</td>
<td class="xl65">C</td>
<td class="xl65">T</td>
<td align="right">0.17</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs571312</td>
<td class="xl66">MC4R</td>
<td class="xl66">18</td>
<td class="xl65">A</td>
<td class="xl65">C</td>
<td align="right">0.23</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs29941</td>
<td class="xl66">KCTD15</td>
<td class="xl66">19</td>
<td class="xl65">G</td>
<td class="xl65">A</td>
<td align="right">0.06</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs3810291</td>
<td class="xl66">TMEM160</td>
<td class="xl66">19</td>
<td class="xl65">A</td>
<td class="xl65">G</td>
<td align="right">0.09</td>
</tr>
<tr height="15" style="height: 15.0pt;">
<td class="xl66" height="15" style="height: 15.0pt;">rs2287019</td>
<td class="xl66">QPCTL</td>
<td class="xl66">19</td>
<td class="xl65">C</td>
<td class="xl65">T</td>
<td align="right">0.15</td>
</tr>
</tbody></table>
<br />
<div>
If you subscribe to <a href="http://23andme.com/">23andMe</a>, you can get some idea about your QiGRO score. Not all of the above SNPs are included in the 23andMe data at this time, so you can't compute it exactly. You can compute the contribution to your QiGRO score from the SNPs that 23andMe does include. We'll call this the modified QiGRO score for short. Here's how to compute it.<br />
<br />
Sign in to the service, click on the downward arrow next to your name in the upper right, and click "Browse Raw Data". This brings you to a page where you can "Jump to a gene" "or a SNP".<br />
<br />
Copy the first SNP from the table above, rs543874, into the "or a SNP" box (the righthand one) on the "Browse Raw Data" page and click Go. 23andMe will list a result with your genotype at this SNP: it might be AA, AG, or GG. Since the above table lists G as the Effect allele, count the number of Gs in your genotype. If your genotype is AA, AG, or GG, you will get 0, 1, or 2, respectively. Multiply the number you get by the Beta coefficient, 0.22, from the first row of the above table. So if your genotype is AA, AG, or GG, you will get 0.0, 0.22, or 0.44, respectively. Start a running tally for your score using this number. Also start another running tally of the Beta coefficients, 0.22. Keep track of the number of SNPs you've checked. This is now 1.<br />
<br />
In case you're curious, here's what this means. You got two copies of this locus (a site on a chromosome), one from your mother and one from your father. The above table says that there are two possible variants, or <i>alleles</i>, at this locus: A (the DNA nucleotide alanine) or G (the DNA nucleotide guanine). Here G is the <i>effect</i> allele, meaning that each G increases the risk of a higher BMI. The Beta coefficient describes how much it increases the risk.<br />
<br />
Continuing, copy the second SNP from the table above, rs1514175, into the "or a SNP" box and click Go. In this case again your genotype at this SNP might be AA, AG, or GG. However, this time A is the Effect allele, so count the number of As in your genotype. If your genotype is AA, AG, or GG, you will get 2, 1, or 0, respectively. Multiply this by the Beta coefficient, 0.07, from the second row of the above table. So if your genotype is AA, AG, or GG, you will get 0.14, 0.07, or 0.0, respectively. Add this to your running tally for your score. For instance, if your genotype at rs543874 was AG, and your genotype at rs1514175 was AA, your running tally for your score would be 0.22 + 0.14 = 0.36. Also add the Beta coefficient, 0.07 to your running tally of the Beta coefficients, yielding 0.22 + 0.07 = 0.39. The number of SNPs you've checked is now 2.<br />
<br />
Copy the third SNP from the table above, rs1555543, into the "or a SNP" box and click Go. Currently, 23andMe tells me: “No SNPs matching '<em>rs1555543</em>' found in the data from your chip.” I deliberately did not include this information in the table above since 23andMe updates their chips and reruns samples from time to time, so by the time you read this post the data may be present. Try it and see. If there is no data, skip adding anything either to the running tally for your score or the running tally using the Beta coefficients.<br />
<br />
Copy the fourth SNP from the table above, rs2815752, into the "or a SNP" box and click Go. In this case your genotype at this SNP might be AA, AG, or GG. Here A is the Effect allele, so count the number of A's in your genotype. If your genotype is AA, AG, or GG, you will get 2, 1, or 0, respectively. Multiply this by the Beta coefficient, 0.13, from the fourth row of the above table. So if your genotype is AA, AG, or GG, you will get 0.26, 0.13, or 0.0, respectively. Add this to your running tally for your score. For instance, if your running tally for your score was 0.36 as in the example above, and your genotype at rs2815752 is AA, your running tally for your score will now be 0.36 + 0.26 = 0.62. Add the Beta coefficient 0.13 to your running tally of the Beta coefficients, yielding 0.39 + 0.13 = 0.52. The number of SNPs you've checked is now 3.<br />
<br />
Currently, rs2890652, rs887912, and rs713586 are not included in the 23andMe data. Just to be completely clear, I'll write out one more step.<br />
<br />
Copy the eighth SNP from the table above, rs2867125, into the "or a SNP" box and click Go. In this case your genotype at this SNP might be CC, CT, or TT. Here C is the Effect allele, so count the number of C's in your genotype. If your genotype is CC, CT, or TT, you will get 2, 1, or 0, respectively. Multiply this by the Beta coefficient, 0.31, from the eighth row of the above table. So if your genotype is CC, CT, or TT, you will get 0.62, 0.31, or 0.0, respectively. Add this to your running tally for your score. For instance, if your running tally for your score was 0.62 as in the example above, and your genotype at rs2867125 is CT, your running tally for your score will now be 0.62 + 0.31 = 0.93. Add the Beta coefficient 0.31 to your running tally of the Beta coefficients, yielding 0.52 + 0.31 = 0.83. The number of SNPs you've checked is now 4.<br />
<br />
Continue in this way until you've checked all 32 SNPs in the table. Currently there's no data for rs9816226, rs4836133, rs2112347, rs3817334, rs4929949, rs10767664, rs4771122, rs11847697, rs10150332, or rs7359397. So the number of SNPs you've checked would end up at 18, and your running tally of the Beta coefficients would end up at 2.84, assuming the same set of SNPs are included. Your running tally for your score will be some number between 0 and twice the sum of the Beta coefficients, i.e., 5.68 currently.<br />
<br />
To get your modified QiGRO score, take your running tally for your score, divide it by your running tally of the Beta coefficients, and multiply it by the number of SNPs you've checked. You will get a number between 0 and twice the number of SNPs you've checked, i.e., between 0 and 36 currently.<br />
<br />
Your actual QiGRO score includes the contributions of the other (currently 14) SNPs you weren't able to check, so it lies between your modified QiGRO score and your modified QiGRO score plus twice the number of SNPs you weren't able to check, i.e., currently your modified QiGRO score plus 28. Unfortunately this range is too large to provide useful information. According to Figure S1 in the Supplementary Appendix to <a href="http://www.nejm.org/doi/full/10.1056/NEJMoa1203039">Sugar-Sweetened Beverages and Genetic Risk of Obesity</a>, almost the entire cohorts studied fall between a QiGRO score of 19 and a QiGRO score of 39, a range of only 20. In the absence of any other information, you might look at the middle of the range, i.e., your modified QiGRO score plus 14. To get a better estimate we would need to know the distribution of these SNPs in the population.<br />
<br />
In <a href="http://press.psprings.co.uk/bmj/march/friedfoods.pdf">Fried food consumption, genetic risk, and body mass index: gene-diet interaction analysis in three US cohort studies</a>, all study participants had a QiGRO score between 13 and 43. Qi <i>et al</i> divided their study participants into thirds by increments of 10 risk alleles, i.e., the lower third with scores between 13 and 23, the middle third with scores between 24 and 33, and the upper third with scores between 34 and 43. (They did not publish the exact cutoffs in their paper, so the intermediate boundaries may be off by one.) Qi <i>et al</i> found in these two studies that fried foods and sugar sweetened beverages increase BMI more among those with a higher QiGRO score. So, if it appears that your QiGRO score is on the high side, it may be more beneficial for you to cut back on sugar sweetened beverages and fried foods.<br />
<br />
You might also note your genotype at rs1558902 in particular (which is currently included in the 23andMe data). Qi <i>et al</i> found that the association between BMI and this variant alone was significant, and strengthened as more fried foods were consumed.</div>
</div>
Ruchira Dattahttp://www.blogger.com/profile/11225230326635564528noreply@blogger.com2tag:blogger.com,1999:blog-595243868922664570.post-77169527679465628552011-03-22T11:12:00.001-07:002011-03-22T11:36:21.522-07:00Patrimony and the Evolution of Risk-takingThis paper by <a href="http://www.grc.nia.nih.gov/branches/irp/mstern.htm">Michael D. Stern</a> provides an interesting insight into the evolutionary dynamics of risk-taking: it is evolutionarily favored when and only when parental resources can be passed to offspring. The paper deserves to be widely read and followed up by testing its robustness to changing assumptions, probing its applicability in biological and social contexts, and teasing out its implications for the generation of diversity by evolutionary processes. One question that immediately springs to mind is how this fits in with <a href="http://www.des.ucdavis.edu/faculty/Richerson/Richerson.htm">Peter Richerson</a>'s and <a href="http://www.sscnet.ucla.edu/anthro/faculty/boyd/">Robert Boyd</a>'s theory of cultural evolution—see <a href="http://www.amazon.com/gp/product/0226712842/ref=as_li_ss_tl?ie=UTF8&tag=httpwwwruchir-20&linkCode=as2&camp=1789&creative=390957&creativeASIN=0226712842"><span style="font-style:italic;">Not By Genes Alone: How Culture Transformed Human Evolution</span></a> (affiliate link). Another is to what extent this relates to <a href="http://psychology.ucdavis.edu/simonton/">Dean K. Simonton</a>'s historically-based viewpoint laid out in <a href="http://www.amazon.com/gp/product/0195128796/ref=as_li_ss_tl?ie=UTF8&tag=httpwwwruchir-20&linkCode=as2&camp=1789&creative=390957&creativeASIN=0195128796"><span style="font-style:italic;">Origins of Genius: Darwinian Perspectives on Creativity</span></a> (ditto). A third is the interplay between this dynamic and “relaxed selection.” I personally would be most interested in seeing to how this dynamic extends to cooperating groups, whether of kin or of nonrelated individuals—see <a href="http://www.amazon.com/gp/product/0262083264/ref=as_li_ss_tl?ie=UTF8&tag=httpwwwruchir-20&linkCode=as2&camp=1789&creative=390957&creativeASIN=0262083264"><span style="font-style:italic;">Genetic and Cultural Evolution of Cooperation</span></a> (ditto).<br /><br /><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011656">Patrimony and the Evolution of Risk-Taking</a><br /><br /><span style="font-weight:bold;">Abstract:</span> <span style="font-style:italic;">The propensity to make risky choices has a genetic component, and recent studies have identified several specific genes that contribute to this trait. Since risk-taking often appears irrational or maladaptive, the question arises how (or if) natural selection favors risk-taking. Here we show, using a stochastic simulation of selection between two hypothetical species, “R” (risk-seeking) and “A” (risk-averse) that, when expected reproductive fitness of the individual is unaffected by the making of the risky choice (winnings balanced by losses) natural selection (taken to the point of extinction) favors the risk-averse species. However, the situation is entirely reversed if offspring are permitted to inherit a small fraction of the parent's increased or decreased fitness acquired through risk-taking. This seemingly Lamarckian form of inheritance actually corresponds to the human situation when property or culture are transmitted in families. In the presence of this “cultural inheritance”, the long-shot risk-taking species was overwhelmingly favored, even when 90% of individuals were rendered sterile by a losing choice. Given this strong effect in a minimal model, it is important to consider the co-evolution of genes and culture when interpreting the genetics of risk-taking. This conclusion applies, in principle, to any species where parental resources can directly affect the fecundity of offspring. It might also be relevant to the effects of epigenetic inheritance, if the epigenetic state of zygotes can be affected by parental experiences.</span>Ruchira Dattahttp://www.blogger.com/profile/11225230326635564528noreply@blogger.com0tag:blogger.com,1999:blog-595243868922664570.post-65739158204771150032010-03-13T13:19:00.000-08:002010-03-13T14:35:53.832-08:00Protein Space Still Ripe For Exploration<div>Proteins are <i><a href="http://www.amazon.com/gp/product/019860694X?ie=UTF8&tag=httpwwwruchir-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=019860694X">Nature's Robots</a>: </i>they<i> </i>carry out most of the activities of life, as well as constituting some of its major structural building blocks. Many of them fold into structurally stable conformations, which can then form crystals. Crystallographers “solve” the 3-dimensional structure of a protein by computing the coordinates of each of its constituent atoms from the X-ray diffraction pattern of these crystals. Thousands of such structures have been deposited in the <a href="http://www.rcsb.org/pdb/home/home.do">Protein Data Bank (PDB)</a>. These beautiful macromolecules constitute <i><a href="http://www.amazon.com/gp/product/0387849246?ie=UTF8&tag=httpwwwruchir-20&linkCode=as2&camp=1789&creative=390957&creativeASIN=0387849246">The Machinery Of Life</a>; </i>author and illustrator <a href="http://mgl.scripps.edu/people/goodsell/">David S. Goodsell</a> highlights some of the fascinating stories of how they work in his <a href="http://www.rcsb.org/pdb/motm.do">Molecule of the Month column</a>.</div><div><br /></div><div>Clearly, only a finite number of proteins exist among all the living organisms on the Earth today. How far have we gotten in exploring the space of proteins? From a historical point of view, we can judge the extent to which a culture had explored the surface of the Earth over time by looking at the maps drawn by people of that culture. Had they encountered all the continents? How fine is the level of detail for each continent?</div><div><br /></div><div>Current maps of protein space can be found at <a href="http://scop.mrc-lmb.cam.ac.uk/scop/">SCOP: Structural Classification of Proteins</a> and <a href="http://www.cathdb.info/">CATH: Protein Structure Classification Database</a>. For simplicity I'll discuss SCOP, although CATH is similar. From the <a href="http://scop.mrc-lmb.cam.ac.uk/scop/intro.html">Introduction to SCOP</a>, “the different major levels in the hierarchy are: <b>Family:</b> <i>Clear evolutionary relationship;</i> <b>Superfamily: </b><i>Probable common evolutionary origin; </i>and <b>Fold: </b><i>Major structural similarity</i>.” Let's look at the growth of each of these categories in SCOP over time:</div><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHSdBNHpe4Vnm3qSFfZejqPjFoaW4xenjDSjknCkeXewMSOCqirUiarLUNq6A-6zHCKEUB9TrfpBOfviZbOa6fs69T2FVlg66m1bULtQU4ekgRLR6VvwSE-HOufaVCtD513nEE4xRuTRPm/s1600-h/image001.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 273px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHSdBNHpe4Vnm3qSFfZejqPjFoaW4xenjDSjknCkeXewMSOCqirUiarLUNq6A-6zHCKEUB9TrfpBOfviZbOa6fs69T2FVlg66m1bULtQU4ekgRLR6VvwSE-HOufaVCtD513nEE4xRuTRPm/s400/image001.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5448246056443895394" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg8HReIIyJe9kn3opWrwv97WcsLZxU4CiNADIFQjt5LLCXowXh5i0fO4_rCd81gzElsNrWcO4GfrxHJV2_kLFtVhEFit_GWvECW65MVttYZ3Ku4SRRck37NirBcIPkKQ2bRnZc1u7kuejcg/s1600-h/image002.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 273px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg8HReIIyJe9kn3opWrwv97WcsLZxU4CiNADIFQjt5LLCXowXh5i0fO4_rCd81gzElsNrWcO4GfrxHJV2_kLFtVhEFit_GWvECW65MVttYZ3Ku4SRRck37NirBcIPkKQ2bRnZc1u7kuejcg/s400/image002.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5448246444630615458" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5KQ5PfgNQ5oUdOrKDGzUQx4sA7fQhSN9cVPB-7afRbO1vx0frAKApsFIXsh1MTO_jfj7gxYsp0hdVi-o5lLq73886DavYMFK1WzEQg8DgFJXhKlb9ivfkbHGVEJJKdiCj4egUPXbOQOzC/s1600-h/image003.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 273px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5KQ5PfgNQ5oUdOrKDGzUQx4sA7fQhSN9cVPB-7afRbO1vx0frAKApsFIXsh1MTO_jfj7gxYsp0hdVi-o5lLq73886DavYMFK1WzEQg8DgFJXhKlb9ivfkbHGVEJJKdiCj4egUPXbOQOzC/s400/image003.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5448246692605337826" /></a><br />In each case I've set the height of the Y-axis at three times the value in July 2001 when SCOP version 1.55 was released. The rate of finding new folds (the “continents” of protein space) is neither taking off (as we might expect if there had been the same kinds of fundamental advances in protein structure determination as in sequencing) nor levelling off (as we might expect if we had explored most of the existing space). The conclusion is clear: there's plenty of unknown territory left for the pioneers of tomorrow.<br /><div><br /></div><div><br /></div>Ruchira Dattahttp://www.blogger.com/profile/11225230326635564528noreply@blogger.com1