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"9288106\tClustering of missense mutations in the <category=\"Modifier\">ataxia-telangiectasia</category> gene in a <category=\"SpecificDisease\">sporadic T-cell leukaemia</category>.\t<category=\"SpecificDisease\">Ataxia-telangiectasia</category> ( <category=\"SpecificDisease\">A-T</category> ) is a <category=\"DiseaseClass\">recessive multi-system disorder</category> caused by mutations in the ATM gene at 11q22-q23 ( ref . 3 ) . The risk of <category=\"DiseaseClass\">cancer</category> , especially <category=\"DiseaseClass\">lymphoid neoplasias</category> , is substantially elevated in <category=\"Modifier\">A-T</category> patients and has long been associated with chromosomal instability . By analysing <category=\"Modifier\">tumour</category> DNA from patients with <category=\"SpecificDisease\">sporadic T-cell prolymphocytic leukaemia</category> ( <category=\"SpecificDisease\">T-PLL</category> ) , a rare <category=\"DiseaseClass\">clonal malignancy</category> with similarities to a <category=\"SpecificDisease\">mature T-cell leukaemia</category> seen in <category=\"SpecificDisease\">A-T</category> , we demonstrate a high frequency of ATM mutations in <category=\"SpecificDisease\">T-PLL</category> . In marked contrast to the ATM mutation pattern in <category=\"SpecificDisease\">A-T</category> , the most frequent nucleotide changes in this <category=\"DiseaseClass\">leukaemia</category> were missense mutations . These clustered in the region corresponding to the kinase domain , which is highly conserved in ATM-related proteins in mouse , yeast and Drosophila . The resulting amino-acid substitutions are predicted to interfere with ATP binding or substrate recognition . Two of seventeen mutated <category=\"SpecificDisease\">T-PLL</category> samples had a previously reported <category=\"Modifier\">A-T</category> allele . In contrast , no mutations were detected in the p53 gene , suggesting that this <category=\"Modifier\">tumour</category> suppressor is not frequently altered in this <category=\"DiseaseClass\">leukaemia</category> . Occasional missense mutations in ATM were also found in <category=\"Modifier\">tumour</category> DNA from patients with <category=\"SpecificDisease\">B-cell non-Hodgkins lymphomas</category> ( <category=\"SpecificDisease\">B-NHL</category> ) and a <category=\"Modifier\">B-NHL</category> cell line . The evidence of a significant proportion of loss-of-function mutations and a complete absence of the normal copy of ATM in the majority of mutated <category=\"DiseaseClass\">tumours</category> establishes somatic inactivation of this gene in the pathogenesis of <category=\"SpecificDisease\">sporadic T-PLL</category> and suggests that ATM acts as a <category=\"Modifier\">tumour</category> suppressor . As constitutional DNA was not available , a putative hereditary predisposition to <category=\"SpecificDisease\">T-PLL</category> will require further investigation . . \n"
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"outputs": [],
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"source": [
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"# If you want to see more examples, you can explore the text of the corpus using the file browser to the left, or open files directly, for example typing a command like the following in a code-cell:\n",
"Identification of APC2 , a homologue of the adenomatous polyposis coli tumour suppressor . \n",
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"The adenomatous polyposis coli ( APC ) tumour - suppressor protein controls the Wnt signalling pathway by forming a complex with glycogen synthase kinase 3beta ( GSK - 3beta ) , axin / conductin and betacatenin . \n",
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"Complex formation induces the rapid degradation of betacatenin . \n",
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"In colon carcinoma cells , loss of APC leads to the accumulation of betacatenin in the nucleus , where it binds to and activates the Tcf - 4 transcription factor ( reviewed in [ 1 ] [ 2 ] ) . \n",
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"Here , we report the identification and genomic structure of APC homologues . \n",
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"Mammalian APC2 , which closely resembles APC in overall domain structure , was functionally analyzed and shown to contain two SAMP domains , both of which are required for binding to conductin . \n",
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"Like APC , APC2 regulates the formation of active betacatenin - Tcf complexes , as demonstrated using transient transcriptional activation assays in APC - / - colon carcinoma cells . \n",
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"Human APC2 maps to chromosome 19p13 . \n",
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"3 . \n",
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"APC and APC2 may therefore have comparable functions in development and cancer . \n"
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"outputs": [],
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"source": [
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"!head $NER_DATA_DIR/text_train.txt"
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"cell_type": "code",
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"execution_count": 30,
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"execution_count": null,
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"id": "spectacular-strain",
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"metadata": {},
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"outputs": [
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"O O O O O O O O B-Disease I-Disease I-Disease I-Disease O O \n",
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"O B-Disease I-Disease I-Disease I-Disease I-Disease I-Disease I-Disease O O O O O O O O O O O O O O O O O O O O O O O O O O O O O \n",
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"O O O O O O O O O \n",
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"O B-Disease I-Disease O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O \n",
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"O O O O O O O O O O O O O \n",
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"O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O \n",
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"O O O O O O O O O O O O O O O O O O O O O O O O O O B-Disease I-Disease O O \n",
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