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<td height="80"><img height="80" width="80" src="images/edition.gif" alt="Summer 2000"></td>
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<p><font size="2" face="Arial,Helvetica,sans-serif"><br>
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<br>
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<img height="33" width="178" src="images/issue.gif" alt="In this issue"><br>
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<br>
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<b>Human Genome<br>
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Map Viewer</b></font></p>
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<p><b><font size="2" face="Arial,Helvetica,sans-serif"><a href="profile.html">Investigator
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Profile:<br>
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Eugene V. Koonin</a></font></b></p>
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<p><b><font size="2" face="Arial,Helvetica,sans-serif"><a href="mouse.html">Mouse
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Genome<br>
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Resources</a></font></b></p>
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<p><b><font size="2" face="Arial,Helvetica,sans-serif"><a href="unists.html">UniSTS<br>
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Integrates Markers</a></font></b></p>
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<p><b><font size="2" face="Arial,Helvetica,sans-serif"><a href="genbank.html">GenBank<br>
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Mirror Sites</a></font></b></p>
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<p><b><font size="2" face="Arial,Helvetica,sans-serif"><a href="blastlab.html">BLAST
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Lab</a> </font></b></p>
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<p><b><font size="2" face="Arial,Helvetica,sans-serif"><a href="features.html">New
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BLAST<br>
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Features</a></font> </b></p>
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<p><b><font face="Arial, Helvetica, sans-serif" size="2" color="003399"><a href="masthead.html"><span class="subheads"><span class="subheads">Ma<span class="heads">sthead</span></span></span></a>
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</font></b><font face="Arial, Helvetica, sans-serif" size="2" color="003399"></font>
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</td>
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<td width="10" valign="left"> </td>
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<td width="420" bordercolor="003399">
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<div valign="left">
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<p><br>
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<br>
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<font face="Arial, Helvetica, sans-serif" size="3" color="003399"><b>Tour
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the Human Genome with Map Viewer</b></font></p>
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<p><font face="Times New Roman, Times, serif" size="3" color="#000000"><br>
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NCBI is committed to an ongoing program of incorporating new data and
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annotation into its human genome resources and producing updated assemblies
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on a regular basis. The data used to generate NCBI's assembly of the
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human genome include draft and finished sequence deposited in GenBank
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by the Human Genome Project sequencing centers, as well as by individual
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contributors. New and updated sequence data continues to be submitted
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from both sources.<br>
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<br>
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The Human Genome Map Viewer provides integrated access to the genome
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data through a collection of genetic, physical, and sequence maps. Views
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of the data range from specific genes to whole genomic regions of interest.<br>
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<br>
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A total of 7 maps may be chosen for simultaneous display from a set
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of 21, including clone and FISH-mapped clone maps, several radiation
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hybrid maps, an EST map, and the Genethon and Marshfield genetic maps.
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The Map Viewer can display a particular region of the genome centered
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on a gene or marker of interest, or a region defined by an arbitrary
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base range. <br>
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<br>
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<a href="#" onClick="CSAction(new Array(/*CMP*/'B74548FE0'));return CSClickReturn();MM_openBrWindow('genome1.html','Figure1','scrollbars=yes,resizable=yes,width=640,height=480')" csclick="B74548FE0"><img src="images/intro_im.gif" width="421" height="379" border="1"></a>
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<font size="1" face="Arial, Helvetica, sans-serif"><b><font color="003399" size="2"><br>
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Figure 1:</font></b></font><font size="2" color="003399"> Map Viewer
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display of six parallel maps for human BRCA1</font><br>
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<br>
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<br>
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Figure 1 shows six selected maps, with the display centered on the 100Kb
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area surrounding the BRCA2 gene. The rightmost is called the Master
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Map, which shows the greatest detail and provides additional links.
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The other maps provide summary information only. <br>
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<br>
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In this example, the initial search was for the term “brca2”.
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Two BRCA2 records were found on chromosome 13; one for the disease associated
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with the gene and one for the gene itself. Following the gene link,
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the default display showed two maps—a sequence map labeled “Genes_seq”
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and a cytogenetic map labeled “Genes_ cyto”. To view the alternative
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set of maps shown in Figure 1, the Display Options and Zoom features
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were used. Each of the maps is discussed below.<br>
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<br>
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The Master Map is designated by the user through the Display Options
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function and, in this example, it is the sequence map labelled “Genes_
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seq”. The exon structure of the BRCA2 gene is shown as a set of
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thick lines superimposed upon the thin line that represents the entire
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gene.<br>
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<br>
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First on the left, the Contig map shows the location of BRCA2 on a particular
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contig created by the NCBI genome assembly process. The entire contig
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may be downloaded from the map page, or viewed directly as a GenBank
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contig record. This contig record contains links to all features found
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on the contig, such as STSs, SNPs, FISH-mapped clones, annotated genes
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and CDSs.<br>
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<br>
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Second from the left in Figure 1 is the STS map, which indicates the
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positions of sequence-tagged sites in the region of BRCA2. Four STS
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markers are shown within the range of the BRCA2 gene given on the Genes_seq
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map. Next, the Variation map shows many SNPs within the BRCA2 gene,
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with a particularly dense clustering in the region of the largest exon
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of BRCA2.<br>
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<br>
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Figure 1 also includes two recent additions to the palette of maps available
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in the human Map Viewer. The EST map shows where ESTs align well to
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the genomic sequence, with histograms indicating the mapping density.
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Including links to UniGene, the EST map can be used to identify undocumented
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exons or to identify the prominent splice variants of genes. The GScan
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map shows <i>ab initio</i> gene models derived from GenomeScan, a program
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related to the popular GenScan gene prediction tool. This map includes
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links to the protein similarities, discovered via a blastx search of
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the protein databases, that were used to support the gene predictions.<br>
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<br>
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Returning to the Genes_seq map, the Master Map in this example, two
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links to additional information are provided. The BRCA2 link leads to
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the corresponding Locus Link record, which provides a complete summary
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of information relating to the gene plus links to related resources.
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The “sv” link leads to the NCBI Sequence Viewer, which provides
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the most detailed sequence-level view of the human genome.<br>
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<br>
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<a href="#" onClick="CSAction(new Array(/*CMP*/'B74549611'));return CSClickReturn();MM_openBrWindow('genome1.html','Figure1','scrollbars=yes,resizable=yes,width=640,height=480')" csclick="B74549611"><img src="images/intro_image2.gif" width="421" height="664" border="1" alt="Figure 1"></a><br>
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<font color="003399" size="2" face="Arial, Helvetica, sans-serif"><b><br>
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Figure 2:</b></font><font color="003399" size="2"> Sequence-level
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view of the human BRCA2 gene.</font><br>
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<br>
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<br>
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The Sequence Viewer display, a small portion of which is shown in Figure
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2, shows the location of exons, CDSs, and STS markers along the BRCA2
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gene. This example includes the DNA sequence for the initial region
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of the gene, showing the first two exons and intervening intron. One
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can see that the start codon is located within the second exon and that
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translation of this CDS indicates an initial amino acid sequence of
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“MPIGS...” for the BRCA2 gene product. Directly following
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is the STS marker sts-X95152, which is also visible on the STS map shown
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in Figure 1. The ends of the BRCA2 gene are marked by sts-X95152 and
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H48122. Note that the BRCA2 gene is encoded on the reverse complement
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of contig NT_009984, such that sts-X95152, which is near the beginning
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of the gene, is found at the bottom of the Map Viewer display. The Sequence
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Viewer also pin-points the location of three SNPs, two in the first
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intron and one in the second exon. All three SNPs are found in noncoding
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regions.<br>
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<br>
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Any portion of the sequence shown in a Map Viewer view may be downloaded
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for further analysis using the Download/View feature. A tabular report
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for the displayed region can also be generated, including the coordinates
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of all Map Viewer features shown on the displayed maps, with links to
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each feature.<br>
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<br>
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An advanced search feature is also offered. Search terms can be restricted
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to particular maps; specific features such STSs, clones, or contigs;
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certain subsets of SNPs (such as SNPs in coding vs. non-coding regions,
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or SNPs with various degrees of heterozygosity); or particular chromosomes.
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It is also possible to search for several items together so as to generate
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a Map View containing several features, or to search a particular region
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defined by a set of markers. A syntax such as “H48122 OR sts-X95157
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OR brca2” will generate three hits on chromosome 13, which can
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be viewed together.<br>
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<br>
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The latest NCBI human genome assembly can be downloaded from the Genome
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side of the FTP site at <a href="ftp://ftp.ncbi.nih.gov/genomes/H_sapiens">ftp.ncbi.nih.gov/genomes/H_sapiens</a>.<br>
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<br>
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The FTP site includes sequence data for each chromosome, as well as
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the mRNA and protein sequences generated by the NCBI annotation project.
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The data used by the Map Viewer to display the various integrated maps
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is contained within the “maps” sub-directory. A README file
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contains more details. <i><font face="Arial, Helvetica, sans-serif" size="2">—VP,
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DW</font></i><br>
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<br>
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<br>
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</font></p>
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<p> <font face="Times New Roman, Times, serif" size="3" color="#000000">
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</font> </p>
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<p align="right"><a href="profile.html"><img height="27" width="69" src="images/continue.gif" border="0" alt="Continue"></a><br>
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<div align="right"><font color="#003399"> </font></div>
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</font>
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<div align="right"><img height="32" width="158" src="images/foot.gif" border="0" alt="NCBI News | Spring 2000" usemap="#NCBI News foot">
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<br>
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<br>
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<br>
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<p class="body_text"> </p>
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