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Clinical NLP Lab 23

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Abnormal hepatic copper accumulation is recognized as an inherited disorder in man , mouse , rat and dog . ### Output Text:

Abnormal <span class="disease">hepatic copper accumulation</span> is recognized as an <span class="disease">inherited disorder</span> in man , mouse , rat and dog .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: The major cause of hepatic copper accumulation in man is a dysfunctional ATP7B gene , causing Wilson disease ( WD ) . ### Output Text:

The major cause of <span class="disease">hepatic copper accumulation</span> in man is a dysfunctional ATP7B gene , causing <span class="disease">Wilson disease</span> ( <span class="disease">WD</span> ) .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Mutations in the ATP7B genes have also been demonstrated in mouse and rat . ### Output Text:

Mutations in the ATP7B genes have also been demonstrated in mouse and rat .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: The ATP7B gene has been excluded in the much rarer human copper overload disease non - Indian childhood cirrhosis , indicating genetic heterogeneity . ### Output Text:

The ATP7B gene has been excluded in the much rarer human <span class="disease">copper overload</span> disease <span class="disease">non - Indian childhood cirrhosis</span> , indicating genetic heterogeneity .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: By investigating the common autosomal recessive copper toxicosis ( CT ) in Bedlington terriers , we have identified a new locus involved in progressive liver disease . ### Output Text:

By investigating the common autosomal recessive <span class="disease">copper toxicosis</span> ( <span class="disease">CT</span> ) in Bedlington terriers , we have identified a new locus involved in progressive <span class="disease">liver disease</span> .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: We examined whether the WD gene ATP7B was also causative for CT by investigating the chromosomal co - localization of ATP7B and C04107 , using fluorescence in situ hybridization ( FISH ) . ### Output Text:

We examined whether the <span class="disease">WD</span> gene ATP7B was also causative for <span class="disease">CT</span> by investigating the chromosomal co - localization of ATP7B and C04107 , using fluorescence in situ hybridization ( FISH ) .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: C04107 is an anonymous microsatellite marker closely linked to CT . ### Output Text:

C04107 is an anonymous microsatellite marker closely linked to <span class="disease">CT</span> .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: However , BAC clones containing ATP7B and C04107 mapped to the canine chromosome regions CFA22q11 and CFA10q26 , respectively , demonstrating that WD cannot be homologous to CT . ### Output Text:

However , BAC clones containing ATP7B and C04107 mapped to the canine chromosome regions CFA22q11 and CFA10q26 , respectively , demonstrating that <span class="disease">WD</span> cannot be homologous to <span class="disease">CT</span> .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: The copper transport genes CTR1 and CTR2 were also excluded as candidate genes for CT since they both mapped to canine chromosome region CFA11q22 . ### Output Text:

The copper transport genes CTR1 and CTR2 were also excluded as candidate genes for <span class="disease">CT</span> since they both mapped to canine chromosome region CFA11q22 .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: 2 - 22 . ### Output Text:

2 - 22 .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: 5 . ### Output Text:

5 .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: A transcribed sequence identified from the C04107 - containing BAC was found to be homologous to a gene expressed from human chromosome 2p13 - p16 , a region devoid of any positional candidate genes . ### Output Text:

A transcribed sequence identified from the C04107 - containing BAC was found to be homologous to a gene expressed from human chromosome 2p13 - p16 , a region devoid of any positional candidate genes .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Molecular analysis of the APC gene in 205 families : extended genotype - phenotype correlations in FAP and evidence for the role of APC amino acid changes in colorectal cancer predisposition . ### Output Text:

Molecular analysis of the <span class="disease">APC</span> gene in 205 families : extended genotype - phenotype correlations in <span class="disease">FAP</span> and evidence for the role of <span class="disease">APC</span> amino acid changes in <span class="disease">colorectal cancer</span> predisposition .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: BACKGROUND / AIMS The development of colorectal cancer and a variable range of extracolonic manifestations in familial adenomatous polyposis ( FAP ) is the result of the dominant inheritance of adenomatous polyposis coli ( APC ) gene mutations . ### Output Text:

BACKGROUND / AIMS The development of <span class="disease">colorectal cancer</span> and a variable range of extracolonic manifestations in <span class="disease">familial adenomatous polyposis</span> ( <span class="disease">FAP</span> ) is the result of the dominant inheritance of <span class="disease">adenomatous polyposis coli</span> ( <span class="disease">APC</span> ) gene mutations .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: In this study , direct mutation analysis of the APC gene was performed to determine genotype - phenotype correlations for nine extracolonic manifestations and to investigate the incidence of APC mutations in non - FAP colorectal cancer . ### Output Text:

In this study , direct mutation analysis of the <span class="disease">APC</span> gene was performed to determine genotype - phenotype correlations for nine extracolonic manifestations and to investigate the incidence of <span class="disease">APC</span> mutations in non - FAP <span class="disease">colorectal cancer</span> .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: METHODS The APC gene was analysed in 190 unrelated FAP and 15 non - FAP colorectal cancer patients using denaturing gradient gel electrophoresis , the protein truncation test , and direct sequencing . ### Output Text:

METHODS The <span class="disease">APC</span> gene was analysed in 190 unrelated <span class="disease">FAP</span> and 15 non - FAP <span class="disease">colorectal cancer</span> patients using denaturing gradient gel electrophoresis , the protein truncation test , and direct sequencing .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: RESULTS Chain terminating signals were only identified in patients belonging to the FAP group ( 105 patients ) . ### Output Text:

RESULTS Chain terminating signals were only identified in patients belonging to the <span class="disease">FAP</span> group ( 105 patients ) .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Amino acid changes were identified in four patients , three of whom belonged to the non - FAP group of colorectal cancer patients . ### Output Text:

Amino acid changes were identified in four patients , three of whom belonged to the non - FAP group of <span class="disease">colorectal cancer</span> patients .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Genotype - phenotype correlations identified significant differences in the nature of certain extracolonic manifestations in FAP patients belonging to three mutation subgroups . ### Output Text:

Genotype - phenotype correlations identified significant differences in the nature of certain extracolonic manifestations in <span class="disease">FAP</span> patients belonging to three mutation subgroups .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: CONCLUSIONS Extended genotype - phenotype correlations made in this study may have the potential to determine the most appropriate surveillance and prophylactic treatment regimens for those patients with mutations associated with life threatening conditions . ### Output Text:

CONCLUSIONS Extended genotype - phenotype correlations made in this study may have the potential to determine the most appropriate surveillance and prophylactic treatment regimens for those patients with mutations associated with life threatening conditions .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: This study also provided evidence for the pathological nature of amino acid changes in APC associated with both FAP and non - FAP colorectal cancer patients . . ### Output Text:

This study also provided evidence for the pathological nature of amino acid changes in APC associated with both <span class="disease">FAP</span> and non - FAP <span class="disease">colorectal cancer</span> patients . .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Inherited colorectal polyposis and cancer risk of the APC I1307K polymorphism . ### Output Text:

<span class="disease">Inherited colorectal polyposis</span> and <span class="disease">cancer</span> risk of the APC I1307K polymorphism .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Germ - line and somatic truncating mutations of the APC gene are thought to initiate colorectal tumor formation in familial adenomatous polyposis syndrome and sporadic colorectal carcinogenesis , respectively . ### Output Text:

Germ - line and somatic truncating mutations of the <span class="disease">APC</span> gene are thought to initiate <span class="disease">colorectal tumor</span> formation in <span class="disease">familial adenomatous polyposis syndrome</span> and sporadic colorectal carcinogenesis , respectively .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Recently , an isoleucine - - > lysine polymorphism at codon 1307 ( I1307K ) of the APC gene has been identified in 6 % - 7 % of the Ashkenazi Jewish population . ### Output Text:

Recently , an isoleucine - - > lysine polymorphism at codon 1307 ( I1307K ) of the <span class="disease">APC</span> gene has been identified in 6 % - 7 % of the Ashkenazi Jewish population .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: To assess the risk of this common APC allelic variant in colorectal carcinogenesis , we have analyzed a large cohort of unselected Ashkenazi Jewish subjects with adenomatous polyps and . or colorectal cancer , for the APC I1307K polymorphism . ### Output Text:

To assess the risk of this common <span class="disease">APC</span> allelic variant in colorectal carcinogenesis , we have analyzed a large cohort of unselected Ashkenazi Jewish subjects with <span class="disease">adenomatous polyps</span> and . or <span class="disease">colorectal cancer ,</span> for the APC I1307K polymorphism .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: The APC I1307K allele was identified in 48 ( 10 . 1 % ) of 476 patients . ### Output Text:

The APC I1307K allele was identified in 48 ( 10 . 1 % ) of 476 patients .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Compared with the frequency in two separate population control groups , the APC I1307K allele is associated with an estimated relative risk of 1 . ### Output Text:

Compared with the frequency in two separate population control groups , the APC I1307K allele is associated with an estimated relative risk of 1 .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: 5 - 1 . ### Output Text:

5 - 1 .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: 7 for colorectal neoplasia ( both P = . 01 ) . ### Output Text:

7 for <span class="disease">colorectal neoplasia</span> ( both P = . 01 ) .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Furthermore , compared with noncarriers , APC I1307K carriers had increased numbers of adenomas and colorectal cancers per patient ( P = . 03 ) , as well as a younger age at diagnosis . ### Output Text:

Furthermore , compared with noncarriers , APC I1307K carriers had increased numbers of <span class="disease">adenomas</span> and <span class="disease">colorectal cancers</span> per patient ( P = . 03 ) , as well as a younger age at diagnosis .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: We conclude that the APC I1307K variant leads to increased adenoma formation and directly contributes to 3 % - 4 % of all Ashkenazi Jewish colorectal cancer . ### Output Text:

We conclude that the APC I1307K variant leads to increased <span class="disease">adenoma</span> formation and directly contributes to 3 % - 4 % of all Ashkenazi Jewish <span class="disease">colorectal cancer</span> .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: The estimated relative risk for carriers may justify specific clinical screening for the 360 , 000 Americans expected to harbor this allele , and genetic testing in the setting of long - term - outcome studies may impact significantly on colorectal cancer prevention in this population . ### Output Text:

The estimated relative risk for carriers may justify specific clinical screening for the 360 , 000 Americans expected to harbor this allele , and genetic testing in the setting of long - term - outcome studies may impact significantly on <span class="disease">colorectal cancer</span> prevention in this population .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Localization of human BRCA1 and its loss in high - grade , non - inherited breast carcinomas . ### Output Text:

Localization of human BRCA1 and its loss in high - grade , <span class="disease">non - inherited breast carcinomas</span> .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Although the link between the BRCA1 tumour - suppressor gene and hereditary breast and ovarian cancer is established , the role , if any , of BRCA1 in non - familial cancers is unclear . ### Output Text:

Although the link between the BRCA1 <span class="disease">tumour</span> - suppressor gene and <span class="disease">hereditary breast and ovarian cancer</span> is established , the role , if any , of BRCA1 in <span class="disease">non - familial cancers</span> is unclear .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: BRCA1 mutations are rare in sporadic cancers , but loss of BRCA1 resulting from reduced expression or incorrect subcellular localization is postulated to be important in non - familial breast and ovarian cancers . ### Output Text:

BRCA1 mutations are rare in <span class="disease">sporadic cancers</span> , but loss of BRCA1 resulting from reduced expression or incorrect subcellular localization is postulated to be important in <span class="disease">non - familial breast and ovarian cancers</span> .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Epigenetic loss , however , has not received general acceptance due to controversy regarding the subcellular localization of BRCA1 proteins , reports of which have ranged from exclusively nuclear , to conditionally nuclear , to the ER / golgi , to cytoplasmic invaginations into the nucleus . ### Output Text:

Epigenetic loss , however , has not received general acceptance due to controversy regarding the subcellular localization of BRCA1 proteins , reports of which have ranged from exclusively nuclear , to conditionally nuclear , to the ER / golgi , to cytoplasmic invaginations into the nucleus .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: In an attempt to resolve this issue , we have comprehensively characterized 19 anti - BRCA1 antibodies . ### Output Text:

In an attempt to resolve this issue , we have comprehensively characterized 19 anti - BRCA1 antibodies .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: These reagents detect a 220 - kD protein localized in discrete nuclear foci in all epithelial cell lines , including those derived from breast malignancies . ### Output Text:

These reagents detect a 220 - kD protein localized in discrete nuclear foci in all epithelial cell lines , including those derived from <span class="disease">breast malignancies</span> .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Immunohistochemical staining of human breast specimens also revealed BRCA1 nuclear foci in benign breast , invasive lobular cancers and low - grade ductal carcinomas . ### Output Text:

Immunohistochemical staining of human breast specimens also revealed BRCA1 nuclear foci in benign breast , <span class="disease">invasive lobular cancers</span> and <span class="disease">low - grade ductal carcinomas</span> .

In the sentence extracted from biomedical literature, identify all the disease entities. The required answer format is the same sentence with HTML <span> tags to mark up specific entities. ### Entity Markup Guides: Use <span class="disease"> to denote a disease. ### Input Text: Conversely , BRCA1 expression was reduced or undetectable in the majority of high - grade , ductal carcinomas , suggesting that absence of BRCA1 may contribute to the pathogenesis of a significant percentage of sporadic breast cancers . . ### Output Text:

Conversely , BRCA1 expression was reduced or undetectable in the majority of high - grade , <span class="disease">ductal carcinomas</span> , suggesting that absence of BRCA1 may contribute to the pathogenesis of a significant percentage of <span class="disease">sporadic breast cancers</span> . .