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stringlengths 15
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stringlengths 15
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| passages
list | entities
list | events
list | coreferences
list | relations
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|---|---|---|---|---|---|---|
split_0_train_1300 | split_0_train_1300 | [
{
"id": "split_0_train_1300_passage",
"type": "progene_text",
"text": [
"Protein - energy malnutrition was assessed using the creatinine height index ."
],
"offsets": [
[
0,
78
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1301 | split_0_train_1301 | [
{
"id": "split_0_train_1301_passage",
"type": "progene_text",
"text": [
"Peripheral venous blood samples were obtained peri - operatively , and the serum concentrations of interleukin ( IL - ) 6 , IL-1 receptor antagonist ( ra ) , IL-6 soluble receptor ( sR ) C - reactive protein ( CRP ) and the percentage of peripheral neutrophils were determined ."
],
"offsets": [
[
0,
278
]
]
}
]
| [
{
"id": "split_0_train_1915_entity",
"type": "progene_text",
"text": [
"interleukin ( IL - ) 6"
],
"offsets": [
[
99,
121
]
],
"normalized": []
},
{
"id": "split_0_train_1916_entity",
"type": "progene_text",
"text": [
"IL-1 receptor antagonist"
],
"offsets": [
[
124,
148
]
],
"normalized": []
},
{
"id": "split_0_train_1917_entity",
"type": "progene_text",
"text": [
"IL-6 soluble receptor"
],
"offsets": [
[
158,
179
]
],
"normalized": []
},
{
"id": "split_0_train_1918_entity",
"type": "progene_text",
"text": [
"C - reactive protein"
],
"offsets": [
[
187,
207
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],
"normalized": []
},
{
"id": "split_0_train_1919_entity",
"type": "progene_text",
"text": [
"CRP"
],
"offsets": [
[
210,
213
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1302 | split_0_train_1302 | [
{
"id": "split_0_train_1302_passage",
"type": "progene_text",
"text": [
"Excessive operative blood loss was associated with postoperative morbidity ."
],
"offsets": [
[
0,
76
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1303 | split_0_train_1303 | [
{
"id": "split_0_train_1303_passage",
"type": "progene_text",
"text": [
"Pre - operative malnutrition was associated with postoperative mortality when excessive bleeding occurred ."
],
"offsets": [
[
0,
107
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1304 | split_0_train_1304 | [
{
"id": "split_0_train_1304_passage",
"type": "progene_text",
"text": [
"Postoperative IL-6 response was exaggerated and postoperative IL-1ra response was suppressed in nutritionally depleted patients ."
],
"offsets": [
[
0,
129
]
]
}
]
| [
{
"id": "split_0_train_1920_entity",
"type": "progene_text",
"text": [
"IL-6"
],
"offsets": [
[
14,
18
]
],
"normalized": []
},
{
"id": "split_0_train_1921_entity",
"type": "progene_text",
"text": [
"IL-1ra"
],
"offsets": [
[
62,
68
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1305 | split_0_train_1305 | [
{
"id": "split_0_train_1305_passage",
"type": "progene_text",
"text": [
"The postoperative serum concentrations of IL-6sR in malnourished patients remained at the lowest levels when excessive bleeding occurred ."
],
"offsets": [
[
0,
138
]
]
}
]
| [
{
"id": "split_0_train_1922_entity",
"type": "progene_text",
"text": [
"IL-6sR"
],
"offsets": [
[
42,
48
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1306 | split_0_train_1306 | [
{
"id": "split_0_train_1306_passage",
"type": "progene_text",
"text": [
"In these patients , the percentage of peripheral neutrophils remained at high levels even after resolution of the postoperative cytokine storm ."
],
"offsets": [
[
0,
144
]
]
}
]
| [
{
"id": "split_0_train_1923_entity",
"type": "progene_text",
"text": [
"cytokine"
],
"offsets": [
[
128,
136
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1307 | split_0_train_1307 | [
{
"id": "split_0_train_1307_passage",
"type": "progene_text",
"text": [
"A marked activation of the pro - inflammatory cytokine network associated with a decreased antagonistic reaction and an increased consumption of IL-6sR became prominent in malnourished patients when they underwent intense surgical stress ."
],
"offsets": [
[
0,
239
]
]
}
]
| [
{
"id": "split_0_train_1924_entity",
"type": "progene_text",
"text": [
"cytokine"
],
"offsets": [
[
46,
54
]
],
"normalized": []
},
{
"id": "split_0_train_1925_entity",
"type": "progene_text",
"text": [
"IL-6sR"
],
"offsets": [
[
145,
151
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1308 | split_0_train_1308 | [
{
"id": "split_0_train_1308_passage",
"type": "progene_text",
"text": [
"These immunological disturbances may be relevant to neutrophil activation and subsequent clinical outcome ."
],
"offsets": [
[
0,
107
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1309 | split_0_train_1309 | [
{
"id": "split_0_train_1309_passage",
"type": "progene_text",
"text": [
"Enterococcus faecalis conjugative plasmid pAM373 : complete nucleotide sequence and genetic analyses of sex pheromone response ."
],
"offsets": [
[
0,
128
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1310 | split_0_train_1310 | [
{
"id": "split_0_train_1310_passage",
"type": "progene_text",
"text": [
"pAM373 is a 36.7 kb conjugative plasmid in Enterococcus faecalis that encodes a response to a peptide sex pheromone , cAM373 , secreted by plasmid - free ( recipient ) strains of enterococci ."
],
"offsets": [
[
0,
192
]
]
}
]
| [
{
"id": "split_0_train_1926_entity",
"type": "progene_text",
"text": [
"cAM373"
],
"offsets": [
[
118,
124
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1311 | split_0_train_1311 | [
{
"id": "split_0_train_1311_passage",
"type": "progene_text",
"text": [
"It was identified over 15 years ago as one of five plasmids in E. faecalis strain RC73 and was of interest because a related pheromone activity could be detected in culture supernatants of Staphylococcus aureus and Streptococcus gordonii ."
],
"offsets": [
[
0,
239
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1312 | split_0_train_1312 | [
{
"id": "split_0_train_1312_passage",
"type": "progene_text",
"text": [
"Because of increased clinical concern relating to the possibility of mobilizing vancomycin resistance determinants from enterococci , where they are becoming common , into pathogens such as S. aureus , efforts were initiated to characterize pAM373 further ."
],
"offsets": [
[
0,
257
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1313 | split_0_train_1313 | [
{
"id": "split_0_train_1313_passage",
"type": "progene_text",
"text": [
"The results of a complete nucleotide sequence determination of pAM373 , as well as a genetic analysis of key genes related to regulation of the pheromone response , are reported here ."
],
"offsets": [
[
0,
184
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1314 | split_0_train_1314 | [
{
"id": "split_0_train_1314_passage",
"type": "progene_text",
"text": [
"With regard to determinants related to conjugation , the plasmid has a structural organization similar to other known pheromone - responsive plasmids such as pAD1 , pCF10 and pPD1 ; however , there are several unique features ."
],
"offsets": [
[
0,
227
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1315 | split_0_train_1315 | [
{
"id": "split_0_train_1315_passage",
"type": "progene_text",
"text": [
"Although there are significant homologues relating to a pheromone - binding surface protein ( TraC ) and a negatively regulating protein ( TraA ) , there is an absence of a determinant equivalent to traB of pAD1 ( reduces endogenous pheromone ) and a determinant for surface - exclusion protein ."
],
"offsets": [
[
0,
296
]
]
}
]
| [
{
"id": "split_0_train_1927_entity",
"type": "progene_text",
"text": [
"TraC"
],
"offsets": [
[
94,
98
]
],
"normalized": []
},
{
"id": "split_0_train_1928_entity",
"type": "progene_text",
"text": [
"TraA"
],
"offsets": [
[
139,
143
]
],
"normalized": []
},
{
"id": "split_0_train_1929_entity",
"type": "progene_text",
"text": [
"traB"
],
"offsets": [
[
199,
203
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1316 | split_0_train_1316 | [
{
"id": "split_0_train_1316_passage",
"type": "progene_text",
"text": [
"The precursor structure of the inhibitor peptide iAM373 was identified , and its determinant ( iam373 ) was found to be about 500 nt upstream of an apparent transcription terminator t1 ."
],
"offsets": [
[
0,
186
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1317 | split_0_train_1317 | [
{
"id": "split_0_train_1317_passage",
"type": "progene_text",
"text": [
"Tn917 - lac insertion analyses provided interesting insights into aspects of control of the pheromone response and showed that , although the traA product is sensitive to pheromone , it appears to act differently from the traA homologue of pAD1 ."
],
"offsets": [
[
0,
246
]
]
}
]
| [
{
"id": "split_0_train_1930_entity",
"type": "progene_text",
"text": [
"lac"
],
"offsets": [
[
8,
11
]
],
"normalized": []
},
{
"id": "split_0_train_1931_entity",
"type": "progene_text",
"text": [
"traA"
],
"offsets": [
[
142,
146
]
],
"normalized": []
},
{
"id": "split_0_train_1932_entity",
"type": "progene_text",
"text": [
"traA"
],
"offsets": [
[
222,
226
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1318 | split_0_train_1318 | [
{
"id": "split_0_train_1318_passage",
"type": "progene_text",
"text": [
"Collectins and collectin receptors in innate immunity ."
],
"offsets": [
[
0,
55
]
]
}
]
| [
{
"id": "split_0_train_1933_entity",
"type": "progene_text",
"text": [
"Collectins"
],
"offsets": [
[
0,
10
]
],
"normalized": []
},
{
"id": "split_0_train_1934_entity",
"type": "progene_text",
"text": [
"collectin receptors"
],
"offsets": [
[
15,
34
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1319 | split_0_train_1319 | [
{
"id": "split_0_train_1319_passage",
"type": "progene_text",
"text": [
"This thesis is based on nine papers and a review on the collectins and collectin receptors in innate immunity ."
],
"offsets": [
[
0,
111
]
]
}
]
| [
{
"id": "split_0_train_1935_entity",
"type": "progene_text",
"text": [
"collectins"
],
"offsets": [
[
56,
66
]
],
"normalized": []
},
{
"id": "split_0_train_1936_entity",
"type": "progene_text",
"text": [
"collectin receptors"
],
"offsets": [
[
71,
90
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1320 | split_0_train_1320 | [
{
"id": "split_0_train_1320_passage",
"type": "progene_text",
"text": [
"The collectins are a family of proteins in which the individual chains consist of a C - type lectin domain attached to a collagen domain via an alpha-coiled neck region ."
],
"offsets": [
[
0,
170
]
]
}
]
| [
{
"id": "split_0_train_1937_entity",
"type": "progene_text",
"text": [
"collectins"
],
"offsets": [
[
4,
14
]
],
"normalized": []
},
{
"id": "split_0_train_1938_entity",
"type": "progene_text",
"text": [
"C - type lectin"
],
"offsets": [
[
84,
99
]
],
"normalized": []
},
{
"id": "split_0_train_1939_entity",
"type": "progene_text",
"text": [
"collagen"
],
"offsets": [
[
121,
129
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1321 | split_0_train_1321 | [
{
"id": "split_0_train_1321_passage",
"type": "progene_text",
"text": [
"The chains are organized into a triple collagen helix and oligomerized through N-terminally located cysteines ."
],
"offsets": [
[
0,
111
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1322 | split_0_train_1322 | [
{
"id": "split_0_train_1322_passage",
"type": "progene_text",
"text": [
"The collectins have a dual function : one is to bind specifically to carbohydrate structures on the surface of a pathogen ; the other is subsequently to recruit other cells and molecules to destroy the pathogen ."
],
"offsets": [
[
0,
212
]
]
}
]
| [
{
"id": "split_0_train_1940_entity",
"type": "progene_text",
"text": [
"collectins"
],
"offsets": [
[
4,
14
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1323 | split_0_train_1323 | [
{
"id": "split_0_train_1323_passage",
"type": "progene_text",
"text": [
"The C - type lectin domains contain 110 - 130 amino - acid residues arranged in a conserved sequence pattern which allows the domain to fold into a well - defined tertiary structure ."
],
"offsets": [
[
0,
183
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1324 | split_0_train_1324 | [
{
"id": "split_0_train_1324_passage",
"type": "progene_text",
"text": [
"Five collectins have been described ."
],
"offsets": [
[
0,
37
]
]
}
]
| [
{
"id": "split_0_train_1941_entity",
"type": "progene_text",
"text": [
"collectins"
],
"offsets": [
[
5,
15
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1325 | split_0_train_1325 | [
{
"id": "split_0_train_1325_passage",
"type": "progene_text",
"text": [
"Lung surfactant proteins A and D ( SP - A and SP-D ) are mainly found in the surfactant coating the luminal surface of the pulmonary epithelial cells , but are also produced by cells lining the gastrointestinal tract ."
],
"offsets": [
[
0,
218
]
]
}
]
| [
{
"id": "split_0_train_1942_entity",
"type": "progene_text",
"text": [
"Lung surfactant proteins A and D"
],
"offsets": [
[
0,
32
]
],
"normalized": []
},
{
"id": "split_0_train_1943_entity",
"type": "progene_text",
"text": [
"SP - A"
],
"offsets": [
[
35,
41
]
],
"normalized": []
},
{
"id": "split_0_train_1944_entity",
"type": "progene_text",
"text": [
"SP-D"
],
"offsets": [
[
46,
50
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1326 | split_0_train_1326 | [
{
"id": "split_0_train_1326_passage",
"type": "progene_text",
"text": [
"Mannan - binding lectin ( MBL ) , conglutinin and collectin-43 ( CL-43 ) are serum proteins produced by the liver ."
],
"offsets": [
[
0,
115
]
]
}
]
| [
{
"id": "split_0_train_1945_entity",
"type": "progene_text",
"text": [
"Mannan - binding lectin"
],
"offsets": [
[
0,
23
]
],
"normalized": []
},
{
"id": "split_0_train_1946_entity",
"type": "progene_text",
"text": [
"MBL"
],
"offsets": [
[
26,
29
]
],
"normalized": []
},
{
"id": "split_0_train_1947_entity",
"type": "progene_text",
"text": [
"conglutinin"
],
"offsets": [
[
34,
45
]
],
"normalized": []
},
{
"id": "split_0_train_1948_entity",
"type": "progene_text",
"text": [
"collectin-43"
],
"offsets": [
[
50,
62
]
],
"normalized": []
},
{
"id": "split_0_train_1949_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
65,
70
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1327 | split_0_train_1327 | [
{
"id": "split_0_train_1327_passage",
"type": "progene_text",
"text": [
"Conglutinin and CL-43 have so far only been found in Bovidae ."
],
"offsets": [
[
0,
62
]
]
}
]
| [
{
"id": "split_0_train_1950_entity",
"type": "progene_text",
"text": [
"Conglutinin"
],
"offsets": [
[
0,
11
]
],
"normalized": []
},
{
"id": "split_0_train_1951_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
16,
21
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1328 | split_0_train_1328 | [
{
"id": "split_0_train_1328_passage",
"type": "progene_text",
"text": [
"The collectins are involved in innate , nonadaptive immune defense ."
],
"offsets": [
[
0,
68
]
]
}
]
| [
{
"id": "split_0_train_1952_entity",
"type": "progene_text",
"text": [
"collectins"
],
"offsets": [
[
4,
14
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1329 | split_0_train_1329 | [
{
"id": "split_0_train_1329_passage",
"type": "progene_text",
"text": [
"They bind to microbial surface carbohydrates , inducing aggregation and thereby impeding infectivity or mediating phagocytosis through specific receptors on the phagocytes ."
],
"offsets": [
[
0,
173
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1330 | split_0_train_1330 | [
{
"id": "split_0_train_1330_passage",
"type": "progene_text",
"text": [
"After binding microbial carbohydrate , MBL can activate the complement system through a newly discovered pathway which makes use of two serine proteases ( MASP-1 and MASP-2 ) to activate the complement factors C4 and C2 ."
],
"offsets": [
[
0,
221
]
]
}
]
| [
{
"id": "split_0_train_1953_entity",
"type": "progene_text",
"text": [
"MBL"
],
"offsets": [
[
39,
42
]
],
"normalized": []
},
{
"id": "split_0_train_1954_entity",
"type": "progene_text",
"text": [
"serine proteases"
],
"offsets": [
[
136,
152
]
],
"normalized": []
},
{
"id": "split_0_train_1955_entity",
"type": "progene_text",
"text": [
"MASP-1"
],
"offsets": [
[
155,
161
]
],
"normalized": []
},
{
"id": "split_0_train_1956_entity",
"type": "progene_text",
"text": [
"MASP-2"
],
"offsets": [
[
166,
172
]
],
"normalized": []
},
{
"id": "split_0_train_1957_entity",
"type": "progene_text",
"text": [
"complement factors"
],
"offsets": [
[
191,
209
]
],
"normalized": []
},
{
"id": "split_0_train_1958_entity",
"type": "progene_text",
"text": [
"C4"
],
"offsets": [
[
210,
212
]
],
"normalized": []
},
{
"id": "split_0_train_1959_entity",
"type": "progene_text",
"text": [
"C2"
],
"offsets": [
[
217,
219
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1331 | split_0_train_1331 | [
{
"id": "split_0_train_1331_passage",
"type": "progene_text",
"text": [
"In man , low serum MBL concentrations resulting from mutations in the collagen region are associated with a common opsonic defect ."
],
"offsets": [
[
0,
131
]
]
}
]
| [
{
"id": "split_0_train_1960_entity",
"type": "progene_text",
"text": [
"MBL"
],
"offsets": [
[
19,
22
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1332 | split_0_train_1332 | [
{
"id": "split_0_train_1332_passage",
"type": "progene_text",
"text": [
"CL-43 was identified as a new collectin by its calcium - dependent binding to mannan and by its M(r) of 43 kDa in the reduced state on sodium dodecyl sulfate - polyacrylamide gel electrophoresis ( SDS-PAGE ) ."
],
"offsets": [
[
0,
209
]
]
}
]
| [
{
"id": "split_0_train_1961_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
0,
5
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1333 | split_0_train_1333 | [
{
"id": "split_0_train_1333_passage",
"type": "progene_text",
"text": [
"The lectin was isolated by affinity chromatography on mannan - Sepharose , absorption with rabbit anti - bovine Ig coupled to Sepharose-4B and ion - exchange chromatography ."
],
"offsets": [
[
0,
174
]
]
}
]
| [
{
"id": "split_0_train_1962_entity",
"type": "progene_text",
"text": [
"lectin"
],
"offsets": [
[
4,
10
]
],
"normalized": []
},
{
"id": "split_0_train_1963_entity",
"type": "progene_text",
"text": [
"Ig"
],
"offsets": [
[
112,
114
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1334 | split_0_train_1334 | [
{
"id": "split_0_train_1334_passage",
"type": "progene_text",
"text": [
"CL-43 shows an apparent molecular mass of 120 kDa in the unreduced state on SDS - PAGE and elutes with an apparent molecular mass of 750 kDa on gel chromatography under nondissociating conditions ."
],
"offsets": [
[
0,
197
]
]
}
]
| [
{
"id": "split_0_train_1964_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
0,
5
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1335 | split_0_train_1335 | [
{
"id": "split_0_train_1335_passage",
"type": "progene_text",
"text": [
"Amino - acid analysis and susceptibility to collagenase digestion indicated that CL-43 was a collectin ."
],
"offsets": [
[
0,
104
]
]
}
]
| [
{
"id": "split_0_train_1965_entity",
"type": "progene_text",
"text": [
"collagenase"
],
"offsets": [
[
44,
55
]
],
"normalized": []
},
{
"id": "split_0_train_1966_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
81,
86
]
],
"normalized": []
},
{
"id": "split_0_train_1967_entity",
"type": "progene_text",
"text": [
"collectin"
],
"offsets": [
[
93,
102
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1336 | split_0_train_1336 | [
{
"id": "split_0_train_1336_passage",
"type": "progene_text",
"text": [
"Electron microscopy of purified CL-43 revealed only rod - like monomer subunits 37.4 nm long ."
],
"offsets": [
[
0,
94
]
]
}
]
| [
{
"id": "split_0_train_1968_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
32,
37
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1337 | split_0_train_1337 | [
{
"id": "split_0_train_1337_passage",
"type": "progene_text",
"text": [
"Two - dimensional gel electrophoresis showed that CL-43 has two isoforms of pI 4.9 and 5.3 respectively , corresponding to the native form of CL-43 and a truncated form which lacks the first 9 amino - acid residues ."
],
"offsets": [
[
0,
216
]
]
}
]
| [
{
"id": "split_0_train_1969_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
50,
55
]
],
"normalized": []
},
{
"id": "split_0_train_1970_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
142,
147
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1338 | split_0_train_1338 | [
{
"id": "split_0_train_1338_passage",
"type": "progene_text",
"text": [
"The N - terminal amino - acid sequence of CL-43 was used to design primers for PCR with a bovine liver cDNA as template ."
],
"offsets": [
[
0,
121
]
]
}
]
| [
{
"id": "split_0_train_1971_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
42,
47
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1339 | split_0_train_1339 | [
{
"id": "split_0_train_1339_passage",
"type": "progene_text",
"text": [
"The cDNA of CL-43 was cloned and the open reading frame was found to encode a protein of 301 amino - acid residues , including an N - terminal region of 28 residues , a collagen region of 114 residues and a neck - CRD region of 159 residues ."
],
"offsets": [
[
0,
242
]
]
}
]
| [
{
"id": "split_0_train_1972_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
12,
17
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1340 | split_0_train_1340 | [
{
"id": "split_0_train_1340_passage",
"type": "progene_text",
"text": [
"The amino - acid sequence of CL-43 shows 74 % identity with bovine conglutinin and 70 % identity with bovine SP-D , but the collagen region is considerably shorter than those of conglutinin and SP-D ."
],
"offsets": [
[
0,
200
]
]
}
]
| [
{
"id": "split_0_train_1973_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
29,
34
]
],
"normalized": []
},
{
"id": "split_0_train_1974_entity",
"type": "progene_text",
"text": [
"SP-D"
],
"offsets": [
[
109,
113
]
],
"normalized": []
},
{
"id": "split_0_train_1975_entity",
"type": "progene_text",
"text": [
"collagen"
],
"offsets": [
[
124,
132
]
],
"normalized": []
},
{
"id": "split_0_train_1976_entity",
"type": "progene_text",
"text": [
"SP-D"
],
"offsets": [
[
194,
198
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1341 | split_0_train_1341 | [
{
"id": "split_0_train_1341_passage",
"type": "progene_text",
"text": [
"Northern blot analysis showed that CL-43 was only synthesized in bovine liver , no signal being detected in a variety of other bovine tissues , including lung ."
],
"offsets": [
[
0,
160
]
]
}
]
| [
{
"id": "split_0_train_1977_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
35,
40
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1342 | split_0_train_1342 | [
{
"id": "split_0_train_1342_passage",
"type": "progene_text",
"text": [
"No cross - hybridizing signals were detected in mRNA from ovine , human , rat or mouse liver ."
],
"offsets": [
[
0,
94
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1343 | split_0_train_1343 | [
{
"id": "split_0_train_1343_passage",
"type": "progene_text",
"text": [
"Since CL-43 and conglutinin have only been detected in members of the Bovidae , it is probable that an ancestral gene of these two proteins was first derived from a SP-D - like gene and that this ancestral gene underwent duplication during evolution ."
],
"offsets": [
[
0,
251
]
]
}
]
| [
{
"id": "split_0_train_1978_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
6,
11
]
],
"normalized": []
},
{
"id": "split_0_train_1979_entity",
"type": "progene_text",
"text": [
"conglutinin"
],
"offsets": [
[
16,
27
]
],
"normalized": []
},
{
"id": "split_0_train_1980_entity",
"type": "progene_text",
"text": [
"SP-D"
],
"offsets": [
[
165,
169
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1344 | split_0_train_1344 | [
{
"id": "split_0_train_1344_passage",
"type": "progene_text",
"text": [
"The carbohydrate binding profile of CL-43 was analyzed by an inhibition assay with biotinylated CL-43 , using solid - phase mannan as the ligand ."
],
"offsets": [
[
0,
146
]
]
}
]
| [
{
"id": "split_0_train_1981_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
36,
41
]
],
"normalized": []
},
{
"id": "split_0_train_1982_entity",
"type": "progene_text",
"text": [
"CL-43"
],
"offsets": [
[
96,
101
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1345 | split_0_train_1345 | [
{
"id": "split_0_train_1345_passage",
"type": "progene_text",
"text": [
"( ABSTRACT TRUNCATED )"
],
"offsets": [
[
0,
22
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1346 | split_0_train_1346 | [
{
"id": "split_0_train_1346_passage",
"type": "progene_text",
"text": [
"Identification of sat , an autotransporter toxin produced by uropathogenic Escherichia coli ."
],
"offsets": [
[
0,
93
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1347 | split_0_train_1347 | [
{
"id": "split_0_train_1347_passage",
"type": "progene_text",
"text": [
"Urinary tract infection ( UTI ) is a very common extraintestinal infection , and Escherichia coli is by far the most common causative organism ."
],
"offsets": [
[
0,
144
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1348 | split_0_train_1348 | [
{
"id": "split_0_train_1348_passage",
"type": "progene_text",
"text": [
"Uropathogenic E. coli possess traits that distinguish them from commensal strains of E. coli , such as secretion systems that allow virulence factors to be targeted to extracytoplasmic compartments ."
],
"offsets": [
[
0,
199
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1349 | split_0_train_1349 | [
{
"id": "split_0_train_1349_passage",
"type": "progene_text",
"text": [
"One of at least five characterized secretion mechanisms is the autotransporter system , which involves translocation of a protein across the inner membrane , presumably via the sec system , and across the outer membrane through a beta-barrel porin structure formed by the carboxy - terminus autotransporter domain ."
],
"offsets": [
[
0,
315
]
]
}
]
| [
{
"id": "split_0_train_1983_entity",
"type": "progene_text",
"text": [
"sec"
],
"offsets": [
[
177,
180
]
],
"normalized": []
},
{
"id": "split_0_train_1984_entity",
"type": "progene_text",
"text": [
"porin"
],
"offsets": [
[
242,
247
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1350 | split_0_train_1350 | [
{
"id": "split_0_train_1350_passage",
"type": "progene_text",
"text": [
"We identified a 107 kDa protein that was expressed significantly more often by E. coli strains associated with the clinical syndrome of acute pyelonephritis than by faecal strains ( P = 0.029 ) ."
],
"offsets": [
[
0,
195
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1351 | split_0_train_1351 | [
{
"id": "split_0_train_1351_passage",
"type": "progene_text",
"text": [
"We isolated the protein from E. coli CFT073 , a strain cultured from the blood and urine of a patient with acute pyelonephritis ."
],
"offsets": [
[
0,
129
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1352 | split_0_train_1352 | [
{
"id": "split_0_train_1352_passage",
"type": "progene_text",
"text": [
"The N - terminal amino acid sequence showed highest similarity to two known SPATE ( serine protease autotransporters of Enterobacteriaceae ) proteins , Pet and EspC ."
],
"offsets": [
[
0,
166
]
]
}
]
| [
{
"id": "split_0_train_1985_entity",
"type": "progene_text",
"text": [
"serine protease autotransporters"
],
"offsets": [
[
84,
116
]
],
"normalized": []
},
{
"id": "split_0_train_1986_entity",
"type": "progene_text",
"text": [
"Pet"
],
"offsets": [
[
152,
155
]
],
"normalized": []
},
{
"id": "split_0_train_1987_entity",
"type": "progene_text",
"text": [
"EspC"
],
"offsets": [
[
160,
164
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1353 | split_0_train_1353 | [
{
"id": "split_0_train_1353_passage",
"type": "progene_text",
"text": [
"Using a 509 bp probe from the 5' region of pet , 10 cosmid clones of an E. coli CFT073 gene library were positive for hybridization ."
],
"offsets": [
[
0,
133
]
]
}
]
| [
{
"id": "split_0_train_1988_entity",
"type": "progene_text",
"text": [
"pet"
],
"offsets": [
[
43,
46
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1354 | split_0_train_1354 | [
{
"id": "split_0_train_1354_passage",
"type": "progene_text",
"text": [
"From one cosmid clone , a 7.5 kb EcoRI restriction fragment , which reacted strongly with the probe , was shown to include the entire 3885 bp gene ."
],
"offsets": [
[
0,
148
]
]
}
]
| [
{
"id": "split_0_train_1989_entity",
"type": "progene_text",
"text": [
"EcoRI"
],
"offsets": [
[
33,
38
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1355 | split_0_train_1355 | [
{
"id": "split_0_train_1355_passage",
"type": "progene_text",
"text": [
"The predicted 142 kDa protein product possesses the three domains that are typical of SPATE autotransporters : an unusually long signal sequence of 49 amino acids ; a 107 kDa passenger domain containing a consensus serine protease active site ( GDSGSG ) ; and a C - terminal autotransporter domain of 30 kDa ."
],
"offsets": [
[
0,
309
]
]
}
]
| [
{
"id": "split_0_train_1990_entity",
"type": "progene_text",
"text": [
"serine protease"
],
"offsets": [
[
215,
230
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1356 | split_0_train_1356 | [
{
"id": "split_0_train_1356_passage",
"type": "progene_text",
"text": [
"The protein exhibited serine protease activity and displayed cytopathic activity on VERO primary kidney , HK-2 bladder and HEp-2 cell lines ; the name Sat ( secreted autotransporter toxin ) was derived from these properties ."
],
"offsets": [
[
0,
225
]
]
}
]
| [
{
"id": "split_0_train_1991_entity",
"type": "progene_text",
"text": [
"serine protease"
],
"offsets": [
[
22,
37
]
],
"normalized": []
},
{
"id": "split_0_train_1992_entity",
"type": "progene_text",
"text": [
"Sat"
],
"offsets": [
[
151,
154
]
],
"normalized": []
},
{
"id": "split_0_train_1993_entity",
"type": "progene_text",
"text": [
"secreted autotransporter toxin"
],
"offsets": [
[
157,
187
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1357 | split_0_train_1357 | [
{
"id": "split_0_train_1357_passage",
"type": "progene_text",
"text": [
"In addition , Sat antibodies were present in the serum of mice infected with E. coli CFT073 ."
],
"offsets": [
[
0,
93
]
]
}
]
| [
{
"id": "split_0_train_1994_entity",
"type": "progene_text",
"text": [
"Sat"
],
"offsets": [
[
14,
17
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1358 | split_0_train_1358 | [
{
"id": "split_0_train_1358_passage",
"type": "progene_text",
"text": [
"Based upon its association with pathogenic isolates , its cytopathic phenotype and its ability to elicit a strong antibody response after infection , we postulate that Sat represents a novel virulence determinant of uropathogenic E. coli ."
],
"offsets": [
[
0,
239
]
]
}
]
| [
{
"id": "split_0_train_1995_entity",
"type": "progene_text",
"text": [
"Sat"
],
"offsets": [
[
168,
171
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1359 | split_0_train_1359 | [
{
"id": "split_0_train_1359_passage",
"type": "progene_text",
"text": [
"The transmembrane domain of influenza hemagglutinin exhibits a stringent length requirement to support the hemifusion to fusion transition ."
],
"offsets": [
[
0,
140
]
]
}
]
| [
{
"id": "split_0_train_1996_entity",
"type": "progene_text",
"text": [
"hemagglutinin"
],
"offsets": [
[
38,
51
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1360 | split_0_train_1360 | [
{
"id": "split_0_train_1360_passage",
"type": "progene_text",
"text": [
"Glycosylphosphatidylinositol - anchored influenza hemagglutinin ( GPI - HA ) mediates hemifusion , whereas chimeras with foreign transmembrane ( TM ) domains mediate full fusion ."
],
"offsets": [
[
0,
179
]
]
}
]
| [
{
"id": "split_0_train_1997_entity",
"type": "progene_text",
"text": [
"hemagglutinin"
],
"offsets": [
[
50,
63
]
],
"normalized": []
},
{
"id": "split_0_train_1998_entity",
"type": "progene_text",
"text": [
"HA"
],
"offsets": [
[
72,
74
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1361 | split_0_train_1361 | [
{
"id": "split_0_train_1361_passage",
"type": "progene_text",
"text": [
"A possible explanation for these observations is that the TM domain must be a critical length in order for HA to promote full fusion ."
],
"offsets": [
[
0,
134
]
]
}
]
| [
{
"id": "split_0_train_1999_entity",
"type": "progene_text",
"text": [
"HA"
],
"offsets": [
[
107,
109
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1362 | split_0_train_1362 | [
{
"id": "split_0_train_1362_passage",
"type": "progene_text",
"text": [
"To test this hypothesis , we analyzed biochemical properties and fusion phenotypes of HA with alterations in its 27 - amino acid TM domain ."
],
"offsets": [
[
0,
140
]
]
}
]
| [
{
"id": "split_0_train_2000_entity",
"type": "progene_text",
"text": [
"HA"
],
"offsets": [
[
86,
88
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1363 | split_0_train_1363 | [
{
"id": "split_0_train_1363_passage",
"type": "progene_text",
"text": [
"Our mutants included sequential 2-amino acid ( Delta2 - Delta14 ) and an 11 - amino acid deletion from the COOH - terminal end , deletions of 6 or 8 amino acids from the NH ( 2 ) - terminal and middle regions , and a deletion of 12 amino acids from the NH ( 2 ) - terminal end of the TM domain ."
],
"offsets": [
[
0,
295
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1364 | split_0_train_1364 | [
{
"id": "split_0_train_1364_passage",
"type": "progene_text",
"text": [
"We also made several point mutations in the TM domain ."
],
"offsets": [
[
0,
55
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1365 | split_0_train_1365 | [
{
"id": "split_0_train_1365_passage",
"type": "progene_text",
"text": [
"All of the mutants except Delta14 were expressed at the cell surface and displayed biochemical properties virtually identical to wild - type HA ."
],
"offsets": [
[
0,
145
]
]
}
]
| [
{
"id": "split_0_train_2001_entity",
"type": "progene_text",
"text": [
"HA"
],
"offsets": [
[
141,
143
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1366 | split_0_train_1366 | [
{
"id": "split_0_train_1366_passage",
"type": "progene_text",
"text": [
"All the mutants that were expressed at the cell surface promoted full fusion , with the notable exception of deletions of > 10 amino acids ."
],
"offsets": [
[
0,
140
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1367 | split_0_train_1367 | [
{
"id": "split_0_train_1367_passage",
"type": "progene_text",
"text": [
"A mutant in which 11 amino acids were deleted was severely impaired in promoting full fusion ."
],
"offsets": [
[
0,
94
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1368 | split_0_train_1368 | [
{
"id": "split_0_train_1368_passage",
"type": "progene_text",
"text": [
"Mutants in which 12 amino acids were deleted ( from either end ) mediated only hemifusion ."
],
"offsets": [
[
0,
91
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1369 | split_0_train_1369 | [
{
"id": "split_0_train_1369_passage",
"type": "progene_text",
"text": [
"Hence , a TM domain of 17 amino acids is needed to efficiently promote full fusion ."
],
"offsets": [
[
0,
84
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1370 | split_0_train_1370 | [
{
"id": "split_0_train_1370_passage",
"type": "progene_text",
"text": [
"Addition of either the hydrophilic HA cytoplasmic tail sequence or a single arginine to Delta12 HA , the hemifusion mutant that terminates with 15 ( hydrophobic ) amino acids of the HA TM domain , restored full fusion activity ."
],
"offsets": [
[
0,
228
]
]
}
]
| [
{
"id": "split_0_train_2002_entity",
"type": "progene_text",
"text": [
"HA"
],
"offsets": [
[
35,
37
]
],
"normalized": []
},
{
"id": "split_0_train_2003_entity",
"type": "progene_text",
"text": [
"HA"
],
"offsets": [
[
96,
98
]
],
"normalized": []
},
{
"id": "split_0_train_2004_entity",
"type": "progene_text",
"text": [
"HA"
],
"offsets": [
[
182,
184
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1371 | split_0_train_1371 | [
{
"id": "split_0_train_1371_passage",
"type": "progene_text",
"text": [
"Our data support a model in which the TM domain must span the bilayer to promote full fusion ."
],
"offsets": [
[
0,
94
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1372 | split_0_train_1372 | [
{
"id": "split_0_train_1372_passage",
"type": "progene_text",
"text": [
"Endotoxin and cytokine regulation of toll - like receptor ( TLR ) 2 and TLR4 gene expression in murine liver and hepatocytes ."
],
"offsets": [
[
0,
126
]
]
}
]
| [
{
"id": "split_0_train_2005_entity",
"type": "progene_text",
"text": [
"cytokine"
],
"offsets": [
[
14,
22
]
],
"normalized": []
},
{
"id": "split_0_train_2006_entity",
"type": "progene_text",
"text": [
"toll - like receptor ( TLR ) 2"
],
"offsets": [
[
37,
67
]
],
"normalized": []
},
{
"id": "split_0_train_2007_entity",
"type": "progene_text",
"text": [
"TLR4"
],
"offsets": [
[
72,
76
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1373 | split_0_train_1373 | [
{
"id": "split_0_train_1373_passage",
"type": "progene_text",
"text": [
"Toll - like receptor ( TLR ) 2 and TLR4 are members of the interleukin-1 receptor ( IL-1R ) family and transduce similar signals as IL-1R in response to bacteria and bacterial components ."
],
"offsets": [
[
0,
188
]
]
}
]
| [
{
"id": "split_0_train_2008_entity",
"type": "progene_text",
"text": [
"Toll - like receptor ( TLR ) 2"
],
"offsets": [
[
0,
30
]
],
"normalized": []
},
{
"id": "split_0_train_2009_entity",
"type": "progene_text",
"text": [
"TLR4"
],
"offsets": [
[
35,
39
]
],
"normalized": []
},
{
"id": "split_0_train_2010_entity",
"type": "progene_text",
"text": [
"interleukin-1 receptor ( IL-1R ) family"
],
"offsets": [
[
59,
98
]
],
"normalized": []
},
{
"id": "split_0_train_2011_entity",
"type": "progene_text",
"text": [
"IL-1R"
],
"offsets": [
[
132,
137
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1374 | split_0_train_1374 | [
{
"id": "split_0_train_1374_passage",
"type": "progene_text",
"text": [
"In this study , we investigated the regulation of their gene expression in murine tissues , especially in the liver and hepatocytes ."
],
"offsets": [
[
0,
133
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1375 | split_0_train_1375 | [
{
"id": "split_0_train_1375_passage",
"type": "progene_text",
"text": [
"When mice were administered lipopolysaccharide ( LPS ) , TLR2 mRNA was upregulated in the brain , heart , lung , liver , and kidney ."
],
"offsets": [
[
0,
133
]
]
}
]
| [
{
"id": "split_0_train_2012_entity",
"type": "progene_text",
"text": [
"TLR2"
],
"offsets": [
[
57,
61
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1376 | split_0_train_1376 | [
{
"id": "split_0_train_1376_passage",
"type": "progene_text",
"text": [
"In contrast , it was downregulated in the spleen ."
],
"offsets": [
[
0,
50
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1377 | split_0_train_1377 | [
{
"id": "split_0_train_1377_passage",
"type": "progene_text",
"text": [
"TLR4 mRNA was decreased in the brain ."
],
"offsets": [
[
0,
38
]
]
}
]
| [
{
"id": "split_0_train_2013_entity",
"type": "progene_text",
"text": [
"TLR4"
],
"offsets": [
[
0,
4
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1378 | split_0_train_1378 | [
{
"id": "split_0_train_1378_passage",
"type": "progene_text",
"text": [
"In the heart and lung , it increased , and it was not affected in the liver , kidney , and spleen ."
],
"offsets": [
[
0,
99
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1379 | split_0_train_1379 | [
{
"id": "split_0_train_1379_passage",
"type": "progene_text",
"text": [
"TLR mRNA was further analyzed in the liver and hepatocytes ."
],
"offsets": [
[
0,
60
]
]
}
]
| [
{
"id": "split_0_train_2014_entity",
"type": "progene_text",
"text": [
"TLR"
],
"offsets": [
[
0,
3
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1380 | split_0_train_1380 | [
{
"id": "split_0_train_1380_passage",
"type": "progene_text",
"text": [
"Like LPS treatment , administration of IL-1 , IL-6 , or tumor necrosis factor ( TNF ) upregulated TLR2 mRNA ."
],
"offsets": [
[
0,
109
]
]
}
]
| [
{
"id": "split_0_train_2015_entity",
"type": "progene_text",
"text": [
"IL-1"
],
"offsets": [
[
39,
43
]
],
"normalized": []
},
{
"id": "split_0_train_2016_entity",
"type": "progene_text",
"text": [
"IL-6"
],
"offsets": [
[
46,
50
]
],
"normalized": []
},
{
"id": "split_0_train_2017_entity",
"type": "progene_text",
"text": [
"tumor necrosis factor"
],
"offsets": [
[
56,
77
]
],
"normalized": []
},
{
"id": "split_0_train_2018_entity",
"type": "progene_text",
"text": [
"TNF"
],
"offsets": [
[
80,
83
]
],
"normalized": []
},
{
"id": "split_0_train_2019_entity",
"type": "progene_text",
"text": [
"TLR2"
],
"offsets": [
[
98,
102
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1381 | split_0_train_1381 | [
{
"id": "split_0_train_1381_passage",
"type": "progene_text",
"text": [
"However , none of them affected the TLR4 mRNA level ."
],
"offsets": [
[
0,
53
]
]
}
]
| [
{
"id": "split_0_train_2020_entity",
"type": "progene_text",
"text": [
"TLR4"
],
"offsets": [
[
36,
40
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1382 | split_0_train_1382 | [
{
"id": "split_0_train_1382_passage",
"type": "progene_text",
"text": [
"In primary cultured hepatocytes , TLR2 mRNA was upregulated by LPS , IL-1 , or TNF but not by IL-6 or dexamethasone ."
],
"offsets": [
[
0,
117
]
]
}
]
| [
{
"id": "split_0_train_2021_entity",
"type": "progene_text",
"text": [
"TLR2"
],
"offsets": [
[
34,
38
]
],
"normalized": []
},
{
"id": "split_0_train_2022_entity",
"type": "progene_text",
"text": [
"IL-1"
],
"offsets": [
[
69,
73
]
],
"normalized": []
},
{
"id": "split_0_train_2023_entity",
"type": "progene_text",
"text": [
"TNF"
],
"offsets": [
[
79,
82
]
],
"normalized": []
},
{
"id": "split_0_train_2024_entity",
"type": "progene_text",
"text": [
"IL-6"
],
"offsets": [
[
94,
98
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1383 | split_0_train_1383 | [
{
"id": "split_0_train_1383_passage",
"type": "progene_text",
"text": [
"None of them affected TLR4 mRNA expression ."
],
"offsets": [
[
0,
44
]
]
}
]
| [
{
"id": "split_0_train_2025_entity",
"type": "progene_text",
"text": [
"TLR4"
],
"offsets": [
[
22,
26
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1384 | split_0_train_1384 | [
{
"id": "split_0_train_1384_passage",
"type": "progene_text",
"text": [
"Similar responses were observed in the murine hepatoma cell line Hepa 1 - 6 ."
],
"offsets": [
[
0,
77
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1385 | split_0_train_1385 | [
{
"id": "split_0_train_1385_passage",
"type": "progene_text",
"text": [
"These results suggest that in infection with gram - negative bacteria , LPS and proinflammatory cytokines differentially regulate gene expression of TLR2 and TLR4 in murine hepatocytes , which may lead to pathologic and host defense reactions in the liver ."
],
"offsets": [
[
0,
257
]
]
}
]
| [
{
"id": "split_0_train_2026_entity",
"type": "progene_text",
"text": [
"cytokines"
],
"offsets": [
[
96,
105
]
],
"normalized": []
},
{
"id": "split_0_train_2027_entity",
"type": "progene_text",
"text": [
"TLR2"
],
"offsets": [
[
149,
153
]
],
"normalized": []
},
{
"id": "split_0_train_2028_entity",
"type": "progene_text",
"text": [
"TLR4"
],
"offsets": [
[
158,
162
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1386 | split_0_train_1386 | [
{
"id": "split_0_train_1386_passage",
"type": "progene_text",
"text": [
"Interdependence of activation at rhaSR by cyclic AMP receptor protein , the RNA polymerase alpha subunit C - terminal domain , and rhaR ."
],
"offsets": [
[
0,
137
]
]
}
]
| [
{
"id": "split_0_train_2029_entity",
"type": "progene_text",
"text": [
"rhaSR"
],
"offsets": [
[
33,
38
]
],
"normalized": []
},
{
"id": "split_0_train_2030_entity",
"type": "progene_text",
"text": [
"cyclic AMP receptor protein"
],
"offsets": [
[
42,
69
]
],
"normalized": []
},
{
"id": "split_0_train_2031_entity",
"type": "progene_text",
"text": [
"RNA polymerase alpha"
],
"offsets": [
[
76,
96
]
],
"normalized": []
},
{
"id": "split_0_train_2032_entity",
"type": "progene_text",
"text": [
"rhaR"
],
"offsets": [
[
131,
135
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1387 | split_0_train_1387 | [
{
"id": "split_0_train_1387_passage",
"type": "progene_text",
"text": [
"The Escherichia coli rhaSR operon encodes two AraC family transcription activators , RhaS and RhaR , and is activated by RhaR in the presence of L-rhamnose ."
],
"offsets": [
[
0,
157
]
]
}
]
| [
{
"id": "split_0_train_2033_entity",
"type": "progene_text",
"text": [
"rhaSR operon"
],
"offsets": [
[
21,
33
]
],
"normalized": []
},
{
"id": "split_0_train_2034_entity",
"type": "progene_text",
"text": [
"AraC family"
],
"offsets": [
[
46,
57
]
],
"normalized": []
},
{
"id": "split_0_train_2035_entity",
"type": "progene_text",
"text": [
"RhaS"
],
"offsets": [
[
85,
89
]
],
"normalized": []
},
{
"id": "split_0_train_2036_entity",
"type": "progene_text",
"text": [
"RhaR"
],
"offsets": [
[
94,
98
]
],
"normalized": []
},
{
"id": "split_0_train_2037_entity",
"type": "progene_text",
"text": [
"RhaR"
],
"offsets": [
[
121,
125
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1388 | split_0_train_1388 | [
{
"id": "split_0_train_1388_passage",
"type": "progene_text",
"text": [
"beta-Galactosidase assays of various rhaS - lacZ promoter fusions combined with mobility shift assays indicated that a cyclic AMP receptor protein ( CRP ) site located at - 111.5 is also required for full activation of rhaSR expression ."
],
"offsets": [
[
0,
237
]
]
}
]
| [
{
"id": "split_0_train_2038_entity",
"type": "progene_text",
"text": [
"beta-Galactosidase"
],
"offsets": [
[
0,
18
]
],
"normalized": []
},
{
"id": "split_0_train_2039_entity",
"type": "progene_text",
"text": [
"rhaS"
],
"offsets": [
[
37,
41
]
],
"normalized": []
},
{
"id": "split_0_train_2040_entity",
"type": "progene_text",
"text": [
"lacZ"
],
"offsets": [
[
44,
48
]
],
"normalized": []
},
{
"id": "split_0_train_2041_entity",
"type": "progene_text",
"text": [
"cyclic AMP receptor protein"
],
"offsets": [
[
119,
146
]
],
"normalized": []
},
{
"id": "split_0_train_2042_entity",
"type": "progene_text",
"text": [
"CRP"
],
"offsets": [
[
149,
152
]
],
"normalized": []
},
{
"id": "split_0_train_2043_entity",
"type": "progene_text",
"text": [
"rhaSR"
],
"offsets": [
[
219,
224
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1389 | split_0_train_1389 | [
{
"id": "split_0_train_1389_passage",
"type": "progene_text",
"text": [
"To address the mechanisms of activation by CRP and the RNA polymerase alpha - subunit C - terminal domain ( alpha-CTD ) at rhaSR , we tested the effects of alanine substitutions in CRP activating regions 1 and 2 , overexpression of a truncated version of alpha ( alpha-Delta235 ) , and alanine substitutions throughout alpha-CTD ."
],
"offsets": [
[
0,
330
]
]
}
]
| [
{
"id": "split_0_train_2044_entity",
"type": "progene_text",
"text": [
"CRP"
],
"offsets": [
[
43,
46
]
],
"normalized": []
},
{
"id": "split_0_train_2045_entity",
"type": "progene_text",
"text": [
"RNA polymerase alpha"
],
"offsets": [
[
55,
75
]
],
"normalized": []
},
{
"id": "split_0_train_2046_entity",
"type": "progene_text",
"text": [
"rhaSR"
],
"offsets": [
[
123,
128
]
],
"normalized": []
},
{
"id": "split_0_train_2047_entity",
"type": "progene_text",
"text": [
"CRP"
],
"offsets": [
[
181,
184
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1390 | split_0_train_1390 | [
{
"id": "split_0_train_1390_passage",
"type": "progene_text",
"text": [
"We found that DNA - contacting residues in alpha-CTD are required for full activation , and for simplicity , we discuss alpha-CTD as a third activator of rhaSR ."
],
"offsets": [
[
0,
161
]
]
}
]
| [
{
"id": "split_0_train_2048_entity",
"type": "progene_text",
"text": [
"rhaSR"
],
"offsets": [
[
154,
159
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1391 | split_0_train_1391 | [
{
"id": "split_0_train_1391_passage",
"type": "progene_text",
"text": [
"CRP and RhaR could each partially activate transcription in the absence of the other two activators , and alpha-CTD was not capable of activation alone ."
],
"offsets": [
[
0,
153
]
]
}
]
| [
{
"id": "split_0_train_2049_entity",
"type": "progene_text",
"text": [
"CRP"
],
"offsets": [
[
0,
3
]
],
"normalized": []
},
{
"id": "split_0_train_2050_entity",
"type": "progene_text",
"text": [
"RhaR"
],
"offsets": [
[
8,
12
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1392 | split_0_train_1392 | [
{
"id": "split_0_train_1392_passage",
"type": "progene_text",
"text": [
"In the case of CRP , this suggests that this activation involves neither an alpha-CTD interaction nor cooperative binding with RhaR , while in the case of RhaR , this suggests the likelihood of direct interactions with core RNA polymerase ."
],
"offsets": [
[
0,
240
]
]
}
]
| [
{
"id": "split_0_train_2051_entity",
"type": "progene_text",
"text": [
"CRP"
],
"offsets": [
[
15,
18
]
],
"normalized": []
},
{
"id": "split_0_train_2052_entity",
"type": "progene_text",
"text": [
"RhaR"
],
"offsets": [
[
127,
131
]
],
"normalized": []
},
{
"id": "split_0_train_2053_entity",
"type": "progene_text",
"text": [
"RhaR"
],
"offsets": [
[
155,
159
]
],
"normalized": []
},
{
"id": "split_0_train_2054_entity",
"type": "progene_text",
"text": [
"RNA polymerase"
],
"offsets": [
[
224,
238
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1393 | split_0_train_1393 | [
{
"id": "split_0_train_1393_passage",
"type": "progene_text",
"text": [
"We also found that CRP , RhaR , and alpha-CTD each have synergistic effects on activation by the others , suggesting direct or indirect interactions among all three ."
],
"offsets": [
[
0,
166
]
]
}
]
| [
{
"id": "split_0_train_2055_entity",
"type": "progene_text",
"text": [
"CRP"
],
"offsets": [
[
19,
22
]
],
"normalized": []
},
{
"id": "split_0_train_2056_entity",
"type": "progene_text",
"text": [
"RhaR"
],
"offsets": [
[
25,
29
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1394 | split_0_train_1394 | [
{
"id": "split_0_train_1394_passage",
"type": "progene_text",
"text": [
"We have some evidence that the alpha-CTD - CRP and alpha-CTD - RhaR interactions might be direct ."
],
"offsets": [
[
0,
98
]
]
}
]
| [
{
"id": "split_0_train_2057_entity",
"type": "progene_text",
"text": [
"CRP"
],
"offsets": [
[
43,
46
]
],
"normalized": []
},
{
"id": "split_0_train_2058_entity",
"type": "progene_text",
"text": [
"RhaR"
],
"offsets": [
[
63,
67
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1395 | split_0_train_1395 | [
{
"id": "split_0_train_1395_passage",
"type": "progene_text",
"text": [
"The magnitude of the synergistic effects was usually greater with just two activators than with all three , suggesting possible redundancies in the mechanisms of activation by CRP , alpha-CTD , and RhaR ."
],
"offsets": [
[
0,
204
]
]
}
]
| [
{
"id": "split_0_train_2059_entity",
"type": "progene_text",
"text": [
"CRP"
],
"offsets": [
[
176,
179
]
],
"normalized": []
},
{
"id": "split_0_train_2060_entity",
"type": "progene_text",
"text": [
"RhaR"
],
"offsets": [
[
198,
202
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1396 | split_0_train_1396 | [
{
"id": "split_0_train_1396_passage",
"type": "progene_text",
"text": [
"Functional interaction of phytochrome B and cryptochrome 2 ."
],
"offsets": [
[
0,
60
]
]
}
]
| [
{
"id": "split_0_train_2061_entity",
"type": "progene_text",
"text": [
"phytochrome B"
],
"offsets": [
[
26,
39
]
],
"normalized": []
},
{
"id": "split_0_train_2062_entity",
"type": "progene_text",
"text": [
"cryptochrome 2"
],
"offsets": [
[
44,
58
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1397 | split_0_train_1397 | [
{
"id": "split_0_train_1397_passage",
"type": "progene_text",
"text": [
"Light is a crucial environmental signal that controls many photomorphogenic and circadian responses in plants ."
],
"offsets": [
[
0,
111
]
]
}
]
| []
| []
| []
| []
|
split_0_train_1398 | split_0_train_1398 | [
{
"id": "split_0_train_1398_passage",
"type": "progene_text",
"text": [
"Perception and transduction of light is achieved by at least two principal groups of photoreceptors , phytochromes and cryptochromes ."
],
"offsets": [
[
0,
134
]
]
}
]
| [
{
"id": "split_0_train_2063_entity",
"type": "progene_text",
"text": [
"photoreceptors"
],
"offsets": [
[
85,
99
]
],
"normalized": []
},
{
"id": "split_0_train_2064_entity",
"type": "progene_text",
"text": [
"phytochromes"
],
"offsets": [
[
102,
114
]
],
"normalized": []
},
{
"id": "split_0_train_2065_entity",
"type": "progene_text",
"text": [
"cryptochromes"
],
"offsets": [
[
119,
132
]
],
"normalized": []
}
]
| []
| []
| []
|
split_0_train_1399 | split_0_train_1399 | [
{
"id": "split_0_train_1399_passage",
"type": "progene_text",
"text": [
"Phytochromes are red / far - red light - absorbing receptors encoded by a gene family of five members ( phyA to phyE ) in Arabidopsis ."
],
"offsets": [
[
0,
135
]
]
}
]
| [
{
"id": "split_0_train_2066_entity",
"type": "progene_text",
"text": [
"Phytochromes"
],
"offsets": [
[
0,
12
]
],
"normalized": []
},
{
"id": "split_0_train_2067_entity",
"type": "progene_text",
"text": [
"phyA to phyE"
],
"offsets": [
[
104,
116
]
],
"normalized": []
}
]
| []
| []
| []
|
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