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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: The von Hippel - Lindau tumor suppressor gene product interacts with Sp1 to repress vascular endothelial growth factor promoter activity . ### Output Text:

The <span class="disease">von Hippel - Lindau tumor</span> suppressor gene product interacts with Sp1 to repress vascular endothelial growth factor promoter activity .

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 von Hippel - Lindau tumor suppressor gene ( VHL ) has a critical role in the pathogenesis of clear - cell renal cell carcinoma ( RCC ) , as VHL mutations have been found in both von Hippel - Lindau disease - associated and sporadic RCCs . ### Output Text:

The <span class="disease">von Hippel - Lindau tumor</span> suppressor gene ( VHL ) has a critical role in the pathogenesis of <span class="disease">clear - cell renal cell carcinoma</span> ( <span class="disease">RCC</span> ) , as VHL mutations have been found in both <span class="disease">von Hippel - Lindau disease - associated and sporadic RCCs</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: Recent studies suggest that vascular endothelial growth factor ( VEGF ) mRNA is upregulated in RCC - and von Hippel - Lindau disease - associated tumors . ### Output Text:

Recent studies suggest that vascular endothelial growth factor ( VEGF ) mRNA is upregulated in <span class="disease">RCC - and von Hippel - Lindau disease - associated tumors</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 have therefore assessed the effect of the VHL gene product on VEGF expression . ### Output Text:

We have therefore assessed the effect of the VHL gene product on VEGF expression .

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: VEGF promoter - luciferase constructs were transiently cotransfected with a wild - type VHL ( wt - VHL ) vector in several cell lines , including 293 embryonic kidney and RCC cell lines . ### Output Text:

VEGF promoter - luciferase constructs were transiently cotransfected with a wild - type VHL ( wt - VHL ) vector in several cell lines , including 293 embryonic kidney and <span class="disease">RCC</span> cell lines .

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: wt - VHL protein inhibited VEGF promoter activity in a dose - dependent manner up to 5 - to 10 - fold . ### Output Text:

wt - VHL protein inhibited VEGF promoter activity in a dose - dependent manner up to 5 - to 10 - fold .

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: Deletion analysis defined a 144 - bp region of the VEGF promoter necessary for VHL repression . ### Output Text:

Deletion analysis defined a 144 - bp region of the VEGF promoter necessary for VHL repression .

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 VHL - responsive element is GC rich and specifically binds the transcription factor Sp1 in crude nuclear extracts . ### Output Text:

This VHL - responsive element is GC rich and specifically binds the transcription factor Sp1 in crude nuclear extracts .

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 Drosophila cells , cotransfected VHL represses Sp1 - mediated activation but not basal activity of the VEGF promoter . ### Output Text:

In Drosophila cells , cotransfected VHL represses Sp1 - mediated activation but not basal activity of the VEGF promoter .

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 next demonstrated in coimmunoprecipitates that VHL and Sp1 were part of the same complex and , by using a glutathione - S - transferase - VHL fusion protein and purified Sp1 , that VHL and Sp1 directly interact . ### Output Text:

We next demonstrated in coimmunoprecipitates that VHL and Sp1 were part of the same complex and , by using a glutathione - S - transferase - VHL fusion protein and purified Sp1 , that VHL and Sp1 directly interact .

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 , endogenous VEGF mRNA levels were suppressed in permanent RCC cell lines expressing wt - VHL , and nuclear run - on studies indicated that VHL regulation of VEGF occurs at least partly at the transcriptional level . ### Output Text:

Furthermore , endogenous VEGF mRNA levels were suppressed in permanent <span class="disease">RCC</span> cell lines expressing wt - VHL , and nuclear run - on studies indicated that VHL regulation of VEGF occurs at least partly at the transcriptional level .

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 observations support a new mechanism for VHL - mediated transcriptional repression via a direct inhibitory action on Sp1 and suggest that loss of Sp1 inhibition may be important in the pathogenesis of von Hippel - Lindau disease and RCC . . ### Output Text:

These observations support a new mechanism for VHL - mediated transcriptional repression via a direct inhibitory action on Sp1 and suggest that loss of Sp1 inhibition may be important in the pathogenesis of <span class="disease">von Hippel - Lindau disease</span> and <span class="disease">RCC</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: Adult onset globoid cell leukodystrophy ( Krabbe disease ) : analysis of galactosylceramidase cDNA from four Japanese patients . ### Output Text:

<span class="disease">Adult onset globoid cell leukodystrophy</span> ( <span class="disease">Krabbe disease</span> ) : analysis of galactosylceramidase cDNA from four Japanese 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: We examined galactosylceramidase ( GALC ) cDNA in four Japanese patients with adult onset globoid cell leukodystrophy ( Krabbe disease ; AO - GLD ) by polymerase chain reaction / single - strand conformation polymorphism ( PCR - SSCP ) analysis , subsequent sequence determination , and restriction enzyme digestion of PCR products , initial symptoms were the onset of slowly progressive spastic paraplegia from the middle of the second decade , and all patients had diminished GALC activity in their leukocytes . ### Output Text:

We examined galactosylceramidase ( GALC ) cDNA in four Japanese patients with <span class="disease">adult onset globoid cell leukodystrophy</span> ( <span class="disease">Krabbe disease</span> ; <span class="disease">AO - GLD</span> ) by polymerase chain reaction / single - strand conformation polymorphism ( PCR - SSCP ) analysis , subsequent sequence determination , and restriction enzyme digestion of PCR products , initial symptoms were the onset of slowly progressive <span class="disease">spastic paraplegia</span> from the middle of the second decade , and all patients had <span class="disease">diminished GALC activity</span> in their leukocytes .

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 identified three missense mutations ( I66M , G270D , L618S ) and one exon - 6 skipping ( 535 - 573del ) . ### Output Text:

We identified three missense mutations ( I66M , G270D , L618S ) and one exon - 6 skipping ( 535 - 573del ) .

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: Two of the patients had only the I66M mutant mRNA , and one only the G27OD mutant mRNA . ### Output Text:

Two of the patients had only the I66M mutant mRNA , and one only the G27OD mutant mRNA .

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 fourth patient carried a compound heterozygous mutation of 535 - 573del and L618S . ### Output Text:

The fourth patient carried a compound heterozygous mutation of 535 - 573del and L618S .

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 determine the enzymatic activities produced by these mutations , we constructed mutated GALC cDNAs and expressed them in COS - 1 cells . ### Output Text:

To determine the enzymatic activities produced by these mutations , we constructed mutated GALC cDNAs and expressed them in COS - 1 cells .

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: Three mutations , viz . , G270D , L618S , and exon - 6 skipping ( 535 - 573del ) , produced diminished GALC activity as expected . ### Output Text:

Three mutations , viz . , G270D , L618S , and exon - 6 skipping ( 535 - 573del ) , produced <span class="disease">diminished GALC activity</span> as expected .

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 I66M mutation in the wild - type GALC cDNA ( I289 ) had normal activity , but when this mutation and the V289 polymorphism were introduced into the same allele , it had decreased activity . ### Output Text:

The I66M mutation in the wild - type GALC cDNA ( I289 ) had normal activity , but when this mutation and the V289 polymorphism were introduced into the same allele , it had decreased activity .

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: Thus , the combination of a unique mutation and polymorphism causes conformational change in the GALC enzyme , resulting in low enzymatic activity . ### Output Text:

Thus , the combination of a unique mutation and polymorphism causes conformational change in the GALC enzyme , resulting in low enzymatic activity .

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: AO - GLD mutations , including those found here , are located in the N - terminus ( I66M , G270D , 535 - 573del ) or C - terminus ( L618S ) of the GALC enzyme , whereas the reported mutations in the infantile form ( IF - GLD ) are in the central domain . ### Output Text:

<span class="disease">AO - GLD</span> mutations , including those found here , are located in the N - terminus ( I66M , G270D , 535 - 573del ) or C - terminus ( L618S ) of the GALC enzyme , whereas the reported mutations in the infantile form ( <span class="disease">IF - GLD</span> ) are in the central domain .

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 difference in mutation sites may affect the clinical features of GLD . ### Output Text:

This difference in mutation sites may affect the clinical features of <span class="disease">GLD</span> .