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Built site for AMR: 1.8.2.9049@496c08d
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@@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9047</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9049</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -82,6 +82,11 @@
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Get properties of an antibiotic
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</a>
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<a class="dropdown-item" href="../reference/av_property.html">
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<span class="fa fa-capsules"></span>
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Get properties of an antiviral agent
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</a>
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</div>
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</li>
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<li class="nav-item">
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@@ -249,13 +254,13 @@
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># all properties:</span></span></span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Amoxicillin"</span></span></span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin"</span>
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<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "J01CA04" (ATC code from the WHO)</span></span></span>
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<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA04"</span>
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<span class="r-in"><span><span class="fu">ab_cid</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># 33613 (Compound ID from PubChem)</span></span></span>
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<span class="r-in"><span><span class="fu">ab_cid</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 33613</span>
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<span class="r-in"><span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># a list with brand names of amoxicillin</span></span></span>
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<span class="r-in"><span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "actimoxi" "amoclen" "amolin" </span>
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<span class="r-out co"><span class="r-pr">#></span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
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<span class="r-out co"><span class="r-pr">#></span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
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@@ -275,7 +280,7 @@
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<span class="r-out co"><span class="r-pr">#></span> [49] "robamox" "sawamox pm" "tolodina" </span>
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<span class="r-out co"><span class="r-pr">#></span> [52] "topramoxin" "unicillin" "utimox" </span>
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<span class="r-out co"><span class="r-pr">#></span> [55] "vetramox" </span>
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<span class="r-in"><span><span class="fu">ab_tradenames</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># same</span></span></span>
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<span class="r-in"><span><span class="fu">ab_tradenames</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "actimoxi" "amoclen" "amolin" </span>
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<span class="r-out co"><span class="r-pr">#></span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
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<span class="r-out co"><span class="r-pr">#></span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
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@@ -295,33 +300,30 @@
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<span class="r-out co"><span class="r-pr">#></span> [49] "robamox" "sawamox pm" "tolodina" </span>
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<span class="r-out co"><span class="r-pr">#></span> [52] "topramoxin" "unicillin" "utimox" </span>
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<span class="r-out co"><span class="r-pr">#></span> [55] "vetramox" </span>
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<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Beta-lactams/penicillins"</span></span></span>
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<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
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<span class="r-in"><span><span class="fu">ab_atc_group1</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Beta-lactam antibacterials, penicillins"</span></span></span>
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<span class="r-in"><span><span class="fu">ab_atc_group1</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactam antibacterials, penicillins"</span>
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<span class="r-in"><span><span class="fu">ab_atc_group2</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Penicillins with extended spectrum"</span></span></span>
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<span class="r-in"><span><span class="fu">ab_atc_group2</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Penicillins with extended spectrum"</span>
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<span class="r-in"><span><span class="fu">ab_url</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># link to the official WHO page</span></span></span>
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<span class="r-in"><span><span class="fu">ab_url</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Amoxicillin </span>
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<span class="r-out co"><span class="r-pr">#></span> "https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no" </span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># smart lowercase tranformation</span></span></span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"PLB"</span><span class="op">)</span><span class="op">)</span> <span class="co"># "Amoxicillin/clavulanic acid" "Polymyxin B"</span></span></span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"PLB"</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin/clavulanic acid" "Polymyxin B" </span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span></span></span>
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<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"PLB"</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> tolower <span class="op">=</span> <span class="cn">TRUE</span></span></span>
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<span class="r-in"><span><span class="op">)</span> <span class="co"># "amoxicillin/clavulanic acid" "polymyxin B"</span></span></span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"PLB"</span><span class="op">)</span>, tolower <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "amoxicillin/clavulanic acid" "polymyxin B" </span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># defined daily doses (DDD)</span></span></span>
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<span class="r-in"><span><span class="fu">ab_ddd</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"oral"</span><span class="op">)</span> <span class="co"># 1.5</span></span></span>
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<span class="r-in"><span><span class="fu">ab_ddd</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"oral"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.5</span>
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<span class="r-in"><span><span class="fu">ab_ddd_units</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"oral"</span><span class="op">)</span> <span class="co"># "g"</span></span></span>
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<span class="r-in"><span><span class="fu">ab_ddd_units</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"oral"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
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<span class="r-in"><span><span class="fu">ab_ddd</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"iv"</span><span class="op">)</span> <span class="co"># 3</span></span></span>
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<span class="r-in"><span><span class="fu">ab_ddd</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 3</span>
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<span class="r-in"><span><span class="fu">ab_ddd_units</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"iv"</span><span class="op">)</span> <span class="co"># "g"</span></span></span>
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<span class="r-in"><span><span class="fu">ab_ddd_units</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">ab_info</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># all properties as a list</span></span></span>
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@@ -390,17 +392,17 @@
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':</span></span></span>
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<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMP"</span><span class="op">)</span> <span class="co"># ATC code of AMP (ampicillin)</span></span></span>
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<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMP"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA01" "S01AA19"</span>
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<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span> <span class="co"># Drug group of ampicillins ATC code</span></span></span>
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<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
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<span class="r-in"><span><span class="fu">ab_loinc</span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># LOINC codes of ampicillin</span></span></span>
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<span class="r-in"><span><span class="fu">ab_loinc</span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span> <span class="co"># "Ampicillin" (using LOINC)</span></span></span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="fl">6249</span><span class="op">)</span> <span class="co"># "Ampicillin" (using CID)</span></span></span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="fl">6249</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span> <span class="co"># "Ampicillin" (using ATC)</span></span></span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
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